Index (Gemma 2.0.0-alpha API)

A B C D E F G H I J K L M N O P Q R S T U V W X Z _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

abandonClient(URL, FTPClient) - Method in interface ubic.gemma.core.loader.util.ftp.FTPClientFactory: Abandon an FTP client.
abandonClient(URL, FTPClient) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
abbreviateInBytes(String, String, int, boolean, Charset) - Static method in class ubic.gemma.core.util.StringUtils: Abbreviate the value of a field stored with the given charset if it exceeds a certain length in bytes.
abbreviateInBytes(String, String, int, Charset) - Static method in class ubic.gemma.core.util.StringUtils: Abbreviate the value of a field stored with the given charset if it exceeds a certain length in bytes.
abbreviateWithSuffix(String, String, String, int, boolean, Charset) - Static method in class ubic.gemma.core.util.StringUtils: Abbreviate a string with a suffix as per StringUtils.abbreviateInBytes(String, String, int, boolean, Charset).
abort(String) - Method in class ubic.gemma.cli.util.AbstractCLI: Abort the execution of the CLI with the given message.
ABORTED - Static variable in class ubic.gemma.cli.util.AbstractCLI: Exit code used when a AbstractCLI.doWork() is aborted.
ABSOLUTE - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementType
AbstractAnnDataSingleCellDataLoaderConfigurer - Class in ubic.gemma.core.loader.expression.singleCell: Base class for AnnDataSingleCellDataLoader configurers.
AbstractAnnDataSingleCellDataLoaderConfigurer(Path, SingleCellDataTransformationFactory) - Constructor for class ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer
AbstractArg<T> - Class in ubic.gemma.rest.util.args: Base class for non Object-specific functionality argument types, that can be malformed on input (E.g an argument representing a number was a non-numeric string in the request).
AbstractArg(T) - Constructor for class ubic.gemma.rest.util.args.AbstractArg: Constructor for well-formed value.
AbstractArrayArg<T> - Class in ubic.gemma.rest.util.args: Represents a comma-delimited array API argument.
AbstractArrayArg(List) - Constructor for class ubic.gemma.rest.util.args.AbstractArrayArg
AbstractAsyncFactoryBean<T> - Class in ubic.gemma.core.context: Base implementation of AsyncFactoryBean.
AbstractAsyncFactoryBean() - Constructor for class ubic.gemma.core.context.AbstractAsyncFactoryBean
AbstractAsyncFactoryBean(ExecutorService) - Constructor for class ubic.gemma.core.context.AbstractAsyncFactoryBean
AbstractAuditable - Class in ubic.gemma.model.common.auditAndSecurity: An entity which can have an audit trail attached to it.
AbstractAuditable() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AbstractAuditable
AbstractAuthenticatedCLI - Class in ubic.gemma.cli.util: Subclass this to create command line interface (CLI) tools that need authentication.
AbstractAuthenticatedCLI() - Constructor for class ubic.gemma.cli.util.AbstractAuthenticatedCLI
AbstractAutoSeekingCLI<T> - Class in ubic.gemma.cli.util: Provide auto-seeking capabilities to a CLI.
AbstractAutoSeekingCLI(Class) - Constructor for class ubic.gemma.cli.util.AbstractAutoSeekingCLI
AbstractBaseCodeOntologyService - Class in ubic.gemma.core.ontology.providers: Base class for all ontologies built-in to the baseCode project.
AbstractBaseCodeOntologyService(String, String) - Constructor for class ubic.gemma.core.ontology.providers.AbstractBaseCodeOntologyService: Intentionally package-private constructor.
AbstractBaseCodeOntologyService(String, String, boolean, String) - Constructor for class ubic.gemma.core.ontology.providers.AbstractBaseCodeOntologyService
AbstractBioAssayMapper - Class in ubic.gemma.core.loader.util.mapper
AbstractBioAssayMapper() - Constructor for class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
AbstractBulkExpressionDataMatrix<T> - Class in ubic.gemma.core.datastructure.matrix: Base class for bulk expression data matrices.
AbstractBulkExpressionDataMatrix(List) - Constructor for class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
AbstractBulkExpressionDataMatrix(ExpressionExperiment, BioAssayDimension, QuantitationType, List) - Constructor for class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
AbstractBulkExpressionDataVectorService<T> - Class in ubic.gemma.persistence.service.expression.bioAssayData
AbstractBulkExpressionDataVectorService(DesignElementDataVectorDao) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService
AbstractCellRangerBasedTransformation - Class in ubic.gemma.core.loader.expression.singleCell.transform
AbstractCellRangerBasedTransformation(String) - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation
AbstractCLI - Class in ubic.gemma.cli.util: Basic implementation of the CLI interface.
AbstractCLI() - Constructor for class ubic.gemma.cli.util.AbstractCLI
AbstractCriteriaFilteringVoEnabledDao<O,VO> - Class in ubic.gemma.persistence.service: Partial implementation of FilteringVoEnabledDao based on the JPA Criteria API.
AbstractCriteriaFilteringVoEnabledDao(Class, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
AbstractCriteriaFilteringVoEnabledDao.CriteriaContext<T,R> - Class in ubic.gemma.persistence.service: Holder for the JPA Criteria primitives needed to assemble a filtering query.
AbstractCuratableDao<C,VO> - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Created by tesarst on 07/03/17.
AbstractCuratableDao(String, Class, SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
AbstractCuratableValueObject<C> - Class in ubic.gemma.model.common.auditAndSecurity.curation: Created by tesarst on 07/03/17.
AbstractCuratableValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject: Required when using the implementing classes as a spring beans.
AbstractCuratableValueObject(C) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
AbstractCuratableValueObject(C, boolean) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject: Variant of AbstractCuratableValueObject(Curatable) that skips reading the three last*Event associations off CurationDetails.
AbstractCuratableValueObject(Long) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
AbstractCuratableValueObject(AbstractCuratableValueObject) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject: Copy constructor.
AbstractCuratableValueObject.LastEventTriple - Record Class in ubic.gemma.model.common.auditAndSecurity.curation: Pre-fetched triple of "last X event" associations off a CurationDetails, batch-loaded per page of curatable entities to avoid the N×3-SELECT proxy-init cost of letting each VO constructor touch the three lazy proxies on its own.
AbstractDao<T> - Class in ubic.gemma.persistence.service: AbstractDao finds the generic type at runtime and provides default BaseDao implementations on top of SessionFactory.
AbstractDao(Class, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractDao
AbstractDelegatingDataLoader - Class in ubic.gemma.core.loader.expression
AbstractDelegatingDataLoader(DataLoader) - Constructor for class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
AbstractDelegatingExecutor - Class in ubic.gemma.core.util.concurrent
AbstractDelegatingExecutor(Executor) - Constructor for class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutor
AbstractDelegatingExecutorService - Class in ubic.gemma.core.util.concurrent: A delegating executor service inspired by DelegatingSecurityContextExecutorService.
AbstractDelegatingExecutorService(ExecutorService) - Constructor for class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
AbstractDelegatingOntologyService - Class in ubic.gemma.core.ontology.providers
AbstractDelegatingOntologyService(OntologyService) - Constructor for class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
AbstractDelegatingSequencingDataLoader - Class in ubic.gemma.core.loader.expression.sequencing
AbstractDelegatingSequencingDataLoader(SequencingDataLoader) - Constructor for class ubic.gemma.core.loader.expression.sequencing.AbstractDelegatingSequencingDataLoader
AbstractDelegatingSingleCellDataLoader - Class in ubic.gemma.core.loader.expression.singleCell
AbstractDelegatingSingleCellDataLoader(SingleCellDataLoader) - Constructor for class ubic.gemma.core.loader.expression.singleCell.AbstractDelegatingSingleCellDataLoader
AbstractDescribable - Class in ubic.gemma.model.common
AbstractDescribable() - Constructor for class ubic.gemma.model.common.AbstractDescribable
AbstractDesignElementDataVectorDao<T> - Class in ubic.gemma.persistence.service.expression.bioAssayData
AbstractDesignElementDataVectorDao(Class, SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
AbstractEntityArg<T,O,S> - Class in ubic.gemma.rest.util.args: Interface representing and API call argument that can represent various identifiers of different types.
AbstractEntityArg(String, Class, T) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArg
AbstractEntityArgService<T,S> - Class in ubic.gemma.rest.util.args
AbstractEntityArgService(S) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArgService
AbstractEntityArrayArg<O,S> - Class in ubic.gemma.rest.util.args
AbstractEntityArrayArg(Class, List) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArrayArg
AbstractExceptionMapper<E> - Class in ubic.gemma.rest.providers
AbstractExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.AbstractExceptionMapper
AbstractExpressionDataMatrix<T> - Class in ubic.gemma.core.datastructure.matrix
AbstractExpressionDataMatrix() - Constructor for class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix
AbstractFactorValueValueObject - Class in ubic.gemma.model.expression.experiment: The bare minimum to represent a factor value.
AbstractFactorValueValueObject() - Constructor for class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject
AbstractFactorValueValueObject(Long) - Constructor for class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject
AbstractFactorValueValueObject(FactorValue, boolean) - Constructor for class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject
AbstractFactorValueValueObjectSerializer<T> - Class in ubic.gemma.rest.serializers: Base serializer for FactorValue VOs.
AbstractFactorValueValueObjectSerializer(Class) - Constructor for class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer
AbstractFetcher - Class in ubic.gemma.core.loader.util.fetcher
AbstractFetcher - Class in ubic.gemma.core.loader.util.fetcher2: Base class for fetchers that provide data downloading, file locking, progress reporting, logging and parallel task execution capabilities.
AbstractFetcher() - Constructor for class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
AbstractFetcher(SimpleDownloader) - Constructor for class ubic.gemma.core.loader.util.fetcher2.AbstractFetcher
AbstractFilter<M,R,C,V> - Class in ubic.gemma.core.util.matrix.datafilter: Base implementation of the filter interface.
AbstractFilter() - Constructor for class ubic.gemma.core.util.matrix.datafilter.AbstractFilter
AbstractFilteringVoEnabledDao<O,VO> - Class in ubic.gemma.persistence.service: Base implementation for FilteringVoEnabledDao.
AbstractFilteringVoEnabledDao(String, Class, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer - Class in ubic.gemma.persistence.service: Configurer for filterable properties and their aliases.
AbstractFilteringVoEnabledDao.FilterablePropertyMeta - Class in ubic.gemma.persistence.service: Meta-information for a filterable property.
AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder - Class in ubic.gemma.persistence.service
AbstractFilteringVoEnabledService<O,VO> - Class in ubic.gemma.persistence.service: Base implementation for FilteringVoEnabledService.
AbstractFilteringVoEnabledService(FilteringVoEnabledDao) - Constructor for class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
AbstractFTPClientAuthenticator - Class in ubic.gemma.core.loader.util.ftp
AbstractFTPClientAuthenticator() - Constructor for class ubic.gemma.core.loader.util.ftp.AbstractFTPClientAuthenticator
AbstractGeneIdentifierBasedDesignElementMapper<K> - Class in ubic.gemma.core.loader.util.mapper: Base class for design element mapper that use gene identifiers.
AbstractGeneIdentifierBasedDesignElementMapper(Map) - Constructor for class ubic.gemma.core.loader.util.mapper.AbstractGeneIdentifierBasedDesignElementMapper
AbstractGzipHeaderDecorator - Class in ubic.gemma.rest.providers: Base class for decorators that handle the GZIP annotation.
AbstractGzipHeaderDecorator() - Constructor for class ubic.gemma.rest.providers.AbstractGzipHeaderDecorator
AbstractIdentifiable - Class in ubic.gemma.model.common: Base class for identifiable entities.
AbstractIdentifiable() - Constructor for class ubic.gemma.model.common.AbstractIdentifiable
AbstractLexicalOntologyService - Class in ubic.gemma.core.ontology.lexical: Base class for flat lexical vocabularies served as an OntologyService.
AbstractLexicalOntologyService(String, String, String, boolean) - Constructor for class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
AbstractMatrix<R,C,V> - Class in ubic.gemma.core.util.matrix
AbstractMatrix() - Constructor for class ubic.gemma.core.util.matrix.AbstractMatrix
AbstractMatrixReader<M,V> - Class in ubic.gemma.core.util.matrix: Abstract class representing an object that can read in a Matrix2D from a file.
AbstractMatrixReader() - Constructor for class ubic.gemma.core.util.matrix.AbstractMatrixReader
AbstractMeterRegistryConfigurer - Class in ubic.gemma.core.metrics
AbstractMeterRegistryConfigurer(MeterRegistry) - Constructor for class ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer
AbstractMexSingleCellDataLoaderConfigurer - Class in ubic.gemma.core.loader.expression.singleCell
AbstractMexSingleCellDataLoaderConfigurer(SingleCellDataTransformationFactory) - Constructor for class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer
AbstractMultiAssayExpressionDataMatrix<T> - Class in ubic.gemma.core.datastructure.matrix: Base class for ExpressionDataMatrix implementations that can deal with multiple BioAssays per BioMaterial.
AbstractMultiAssayExpressionDataMatrix(AbstractMultiAssayExpressionDataMatrix) - Constructor for class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix: Copy constructor.
AbstractMultiAssayExpressionDataMatrix(ExpressionExperiment) - Constructor for class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix: Create a simple multi-assay matrix.
AbstractMultiAssayExpressionDataMatrix(ExpressionExperiment, Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
AbstractNoopFilteringVoEnabledDao<O,VO> - Class in ubic.gemma.persistence.service: Base class to use to pretend to offer filtering, but actually supporting no filterable properties.
AbstractNoopFilteringVoEnabledDao(Class, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
AbstractOntologyResourceSimple - Class in ubic.gemma.core.ontology.simple
AbstractOntologyResourceSimple(String, String, String) - Constructor for class ubic.gemma.core.ontology.simple.AbstractOntologyResourceSimple
AbstractOntologyService - Class in ubic.gemma.core.ontology.jena
AbstractOntologyService(String, String, boolean, String) - Constructor for class ubic.gemma.core.ontology.jena.AbstractOntologyService
AbstractProgressReporter - Class in ubic.gemma.core.util
AbstractProgressReporter() - Constructor for class ubic.gemma.core.util.AbstractProgressReporter
AbstractPythonScriptBasedAnnDataTransformation - Class in ubic.gemma.core.loader.expression.singleCell.transform
AbstractPythonScriptBasedAnnDataTransformation(String) - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedAnnDataTransformation
AbstractPythonScriptBasedTransformation - Class in ubic.gemma.core.loader.expression.singleCell.transform
AbstractPythonScriptBasedTransformation(String) - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedTransformation
AbstractQueryFilteringVoEnabledDao<O,VO> - Class in ubic.gemma.persistence.service: Partial implementation of FilteringVoEnabledDao based on Hibernate Query.
AbstractQueryFilteringVoEnabledDao(String, Class, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
AbstractScriptBasedTransformation - Class in ubic.gemma.core.loader.expression.singleCell.transform
AbstractScriptBasedTransformation(String) - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.AbstractScriptBasedTransformation
AbstractService<O> - Class in ubic.gemma.persistence.service: Base for all services handling DAO access.
AbstractService(BaseDao) - Constructor for class ubic.gemma.persistence.service.AbstractService
AbstractSingleCellDetector - Class in ubic.gemma.core.loader.expression.geo.singleCell
AbstractSingleCellDetector() - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector
AbstractSingleCellExpressionDataMatrix<T> - Class in ubic.gemma.core.datastructure.matrix
AbstractSingleCellExpressionDataMatrix() - Constructor for class ubic.gemma.core.datastructure.matrix.AbstractSingleCellExpressionDataMatrix
AbstractSingleFileInSeriesSingleCellDetector - Class in ubic.gemma.core.loader.expression.geo.singleCell: Handle detection and download of single-cell data from a single file in the supplementary materials of a GEO series.
AbstractSingleFileInSeriesSingleCellDetector(String, String) - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector
AbstractSingleH5FileInSeriesSingleCellDetector - Class in ubic.gemma.core.loader.expression.geo.singleCell
AbstractSingleH5FileInSeriesSingleCellDetector(String, String) - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleH5FileInSeriesSingleCellDetector
AbstractTask<C> - Class in ubic.gemma.core.job
AbstractTask() - Constructor for class ubic.gemma.core.job.AbstractTask
AbstractTask(C) - Constructor for class ubic.gemma.core.job.AbstractTask
AbstractVoEnabledDao<O,VO> - Class in ubic.gemma.persistence.service: Created by tesarst on 01/06/17.
AbstractVoEnabledDao(Class, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractVoEnabledDao
AbstractVoEnabledService<O,VO> - Class in ubic.gemma.persistence.service: Created by tesarst on 01/06/17.
AbstractVoEnabledService(BaseVoEnabledDao) - Constructor for class ubic.gemma.persistence.service.AbstractVoEnabledService
accept(StatementValueObject, U) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyUtils.StatementVisitor
ACCEPTED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.FindingDisposition: The curator agrees; the finding should be acted on.
ACCEPTED - Enum constant in enum class ubic.gemma.model.common.description.PublicationAssociationStatus: This publication belongs to this experiment.
acceptedNames - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject: Every spelling the refresh / rebuild-slim endpoints accept for this ontology.
accepts(String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector: Indicate if the given supplementary file is accepted.
accepts(String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AnnDataDetector
accepts(String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.SeuratDiskDetector
accepts(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource: Indicate if this source accepts the given search settings.
accepts(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
accepts(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
accepts(SearchSettings) - Method in class ubic.gemma.core.search.source.GeneOntologySearchSource
accepts(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
accepts(SearchSettings) - Method in class ubic.gemma.core.search.source.OntologySearchSource
accessDecisionManager() - Method in class ubic.gemma.core.security.MethodSecurityConfig: Return the existing accessDecisionManager bean (UnanimousBased with all the securable read/edit + collection + map voters wired in gsec XML).
AccessDeniedExceptionMapper - Class in ubic.gemma.rest.providers: Map Spring Security's AccessDeniedException to a 403 Forbidden response.
AccessDeniedExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.AccessDeniedExceptionMapper
accession - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
accession - Variable in class ubic.gemma.rest.AdminWebService.BlacklistRequest: GEO accession (GPL* for platform; GSE* for experiment).
accession - Variable in class ubic.gemma.rest.PreboardedWebService.CreatePreboardedRequest
accession - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
accession - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowQueueEntryResponse
AccessionAlreadyExistsException(String, Long, String) - Constructor for exception class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.AccessionAlreadyExistsException
accessions - Variable in class ubic.gemma.rest.AdminWebService.GeoGrabRequest: GEO series accessions (e.g.
accessions - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest: GEO (or ArrayExpress) accessions to import.
AccessionSourceStat() - Constructor for class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat
AccessionSourceStat(String, long) - Constructor for class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat
ACCURATE - Enum constant in enum class ubic.gemma.model.common.search.SearchSettings.SearchMode: Prefer correctness to speed.
AclAdvice - Class in ubic.gemma.core.security.authorization.acl: Gemma-specific extension points for BaseAclAdvice: identifies User / UserGroup, supplies their granted authority, marks the entity types that should keep private ACLs on admin-driven creation, and runs the DEA → ExpressionAnalysisResultSet parent-ACL special case.
AclAdvice(AclService, SessionFactory, ObjectIdentityRetrievalStrategy) - Constructor for class ubic.gemma.core.security.authorization.acl.AclAdvice
aclAuditLogger() - Method in class ubic.gemma.core.security.acl.GemmaAclConfiguration
aclAuthorizationStrategy(RoleHierarchy) - Method in class ubic.gemma.core.security.acl.GemmaAclConfiguration
AclAuthorizationStrategyImpl - Class in ubic.gemma.core.security.acl: This is only needed because we use a custom Sid implementation.
AclAuthorizationStrategyImpl(GrantedAuthority[], SidRetrievalStrategy) - Constructor for class ubic.gemma.core.security.acl.AclAuthorizationStrategyImpl: Constructor.
aclCache(CacheManager, PermissionGrantingStrategy, AclAuthorizationStrategy) - Method in class ubic.gemma.core.security.acl.GemmaAclConfiguration
AclClassIdInitializer - Class in ubic.gemma.persistence.util: Stash the SessionFactoryImplementor onto AclQueryUtils.sessionFactory at Spring init.
AclClassIdInitializer(SessionFactory) - Constructor for class ubic.gemma.persistence.util.AclClassIdInitializer
AclClassMetadata - Class in ubic.gemma.core.security.authorization.acl: Provide ACL-related metadata.
AclClassMetadata(SessionFactory) - Constructor for class ubic.gemma.core.security.authorization.acl.AclClassMetadata
AclDao - Interface in ubic.gemma.core.security.acl.domain
AclDaoImpl - Class in ubic.gemma.core.security.acl.domain: We have our own implementation of the AclDao in part because of deadlock problems caused by the default JDBC-based spring security DAO.
AclDaoImpl(SessionFactory, AclAuthorizationStrategy, AclCache) - Constructor for class ubic.gemma.core.security.acl.domain.AclDaoImpl
AclEntry - Class in ubic.gemma.core.security.acl.domain: Hibernate-mapped acl_entry row.
AclEntry() - Constructor for class ubic.gemma.core.security.acl.domain.AclEntry
AclEntry(Acl, AclSid, Permission, boolean) - Constructor for class ubic.gemma.core.security.acl.domain.AclEntry
AclEntryAfterInvocationByAssociationCollectionFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Subclass this when you want to filter collections based not on the security of the object itself, but by an associated object.
AclEntryAfterInvocationByAssociationCollectionFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: Subclass this when filtering a collection based not on the security of the element itself but on the security of an associated parent domain object.
AclEntryAfterInvocationByAssociationCollectionFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProvider
AclEntryAfterInvocationByAssociationCollectionFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationByAssociationCollectionFilteringProvider
AclEntryAfterInvocationByAssociationFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation
AclEntryAfterInvocationByAssociationFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: Single-object after-invocation provider that evaluates ACLs on an associated (parent) domain object rather than on the returned object itself.
AclEntryAfterInvocationByAssociationFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProvider
AclEntryAfterInvocationByAssociationFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationByAssociationFilteringProvider
AclEntryAfterInvocationCollectionFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Overrides the functionality of the spring-provided AclEntryAfterInvocationCollectionFilteringProvider to be more efficient with large collections.
AclEntryAfterInvocationCollectionFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: Overrides the functionality of the spring-provided AclEntryAfterInvocationCollectionFilteringProvider to be more efficient with large collections by using AclService.readAclsById(List, List) to bulk-fetch ACLs for every element of the returned collection in a single query.
AclEntryAfterInvocationCollectionFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
AclEntryAfterInvocationCollectionFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCollectionFilteringProvider
AclEntryAfterInvocationCollectionFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
AclEntryAfterInvocationCollectionFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCollectionFilteringProvider
AclEntryAfterInvocationCompositeSequenceByArrayDesignFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: Filter CompositeSequence based on the permissions of the associated ArrayDesign.
AclEntryAfterInvocationCompositeSequenceByArrayDesignFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCompositeSequenceByArrayDesignFilteringProvider
AclEntryAfterInvocationCompositeSequenceCollectionByArrayDesignFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: Filter collections of CompositeSequence based on the permissions of the associated ArrayDesign(s).
AclEntryAfterInvocationCompositeSequenceCollectionByArrayDesignFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCompositeSequenceCollectionByArrayDesignFilteringProvider
AclEntryAfterInvocationDataVectorCollectionByExpressionExperimentFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: Filter collections of DataVector and DataVectorValueObjects based on the permissions of the associated ExpressionExperiment(s).
AclEntryAfterInvocationDataVectorCollectionByExpressionExperimentFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationDataVectorCollectionByExpressionExperimentFilteringProvider
AclEntryAfterInvocationDifferentialExpressionAnalysisResultCollectionByResultSetFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: Filter collections of DifferentialExpressionAnalysisResult by the ExpressionAnalysisResultSet they belong to.
AclEntryAfterInvocationDifferentialExpressionAnalysisResultCollectionByResultSetFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationDifferentialExpressionAnalysisResultCollectionByResultSetFilteringProvider
AclEntryAfterInvocationMapFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Like the AclEntryAfterInvocationCollectionFilteringProvider, but filters on the keys AND values of a Map, where the keys are Securable and the values MAY be Securable.
AclEntryAfterInvocationMapFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProvider
AclEntryAfterInvocationMapValueFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Filter a one-to-one map where the keys are NON-SECURABLE and the values ARE securable (or at least, can be).
AclEntryAfterInvocationMapValueFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProvider
AclEntryAfterInvocationOwnedCollectionFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Filter out public Securables, leaving only ones that the user owns and can edit.
AclEntryAfterInvocationOwnedCollectionFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: Filter a collection of Securable so that only the entries the current user owns (or is an admin on) and can edit remain.
AclEntryAfterInvocationOwnedCollectionFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProvider
AclEntryAfterInvocationOwnedCollectionFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationOwnedCollectionFilteringProvider
AclEntryAfterInvocationPrivateCollectionFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Filter out public Securables, leaving only ones that the user specifically can view but aren't public.
AclEntryAfterInvocationPrivateCollectionFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: Filter a collection of Securable to keep only entries that are not public AND that the current user can read (this includes data sets that are read-only-shared by another user).
AclEntryAfterInvocationPrivateCollectionFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProvider
AclEntryAfterInvocationPrivateCollectionFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationPrivateCollectionFilteringProvider
AclEntryAfterInvocationProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Overrides default behaviour by returning null, rather than throwing an access denied exception
AclEntryAfterInvocationProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProvider
AclEntryAfterInvocationQuietReadProvider - Class in ubic.gemma.core.security.authorization.acl: After-invocation provider for the AFTER_ACL_READ_QUIET config attribute: same ACL check as the stock AclEntryAfterInvocationProvider (READ or ADMINISTRATION on the returned single domain object), but denial is converted to a null return value rather than propagated.
AclEntryAfterInvocationQuietReadProvider(AclService) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationQuietReadProvider
AclEntryAfterInvocationQuietReadProvider(AclService, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationQuietReadProvider
AclEntryAfterInvocationStreamFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Filter domain objects from a Stream.
AclEntryAfterInvocationStreamFilteringProvider - Class in ubic.gemma.core.security.authorization.acl: After-invocation provider that filters a Stream of domain objects, retaining only those for which the authenticated user holds one of the requirePermission grants.
AclEntryAfterInvocationStreamFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProvider
AclEntryAfterInvocationStreamFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationStreamFilteringProvider
AclEntryAfterInvocationValueObjectCollectionFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Security check for reading collections of SecureValueObjects, or maps that have SecureValueObjects as keys - map values are NOT checked.
AclEntryAfterInvocationValueObjectCollectionFilteringProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProvider
AclEntryAfterInvocationValueObjectCollectionFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProvider
AclEntryAfterInvocationValueObjectCollectionReadProvider - Class in ubic.gemma.core.security.authorization.acl: Gemma-owned after-invocation provider for the AFTER_ACL_VALUE_OBJECT_COLLECTION_READ config attribute: bulk ACL check + per-row SecureValueObject security-metadata population over a returned collection.
AclEntryAfterInvocationValueObjectCollectionReadProvider(AclService, String, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectCollectionReadProvider: Subclass constructor used by Map-shaped variants that delegate to this collection provider with a different config attribute (e.g.
AclEntryAfterInvocationValueObjectCollectionReadProvider(AclService, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectCollectionReadProvider
AclEntryAfterInvocationValueObjectMapFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation
AclEntryAfterInvocationValueObjectMapFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProvider
AclEntryAfterInvocationValueObjectMapReadProvider - Class in ubic.gemma.core.security.authorization.acl: Gemma-owned after-invocation provider for the AFTER_ACL_VALUE_OBJECT_MAP_READ config attribute: bulk ACL check + per-key SecureValueObject security-metadata population over a returned Map whose keys are SecureValueObjects.
AclEntryAfterInvocationValueObjectMapReadProvider(AclService, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectMapReadProvider
AclEntryAfterInvocationValueObjectMapValueFilteringProvider - Class in ubic.gemma.core.security.acl.afterinvocation
AclEntryAfterInvocationValueObjectMapValueFilteringProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProvider
AclEntryAfterInvocationValueObjectProvider - Class in ubic.gemma.core.security.acl.afterinvocation: Security check for reading value objects.
AclEntryAfterInvocationValueObjectProvider(AclService, List) - Constructor for class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProvider
AclEntryAfterInvocationValueObjectReadProvider - Class in ubic.gemma.core.security.authorization.acl: Gemma-owned after-invocation provider for the AFTER_ACL_VALUE_OBJECT_READ config attribute: single-object ACL check on a SecureValueObject return value.
AclEntryAfterInvocationValueObjectReadProvider(AclService, List) - Constructor for class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectReadProvider
AclEntryCollectionVoter - Class in ubic.gemma.core.security.acl.voter: Customized voter that looks at collections to see if permissions are present for objects contained in the collection; the processDomainObjectClass set refers to the types of objects in the collection.
AclEntryCollectionVoter(AclService, String, Permission[]) - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter
AclEntryMapValueVoter - Class in ubic.gemma.core.security.acl.voter: A voter for the value of a map.
AclEntryMapValueVoter(AclService, String, Permission[]) - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryMapValueVoter
AclEntryMapVoter - Class in ubic.gemma.core.security.acl.voter: A voter over the keys of a map.
AclEntryMapVoter(AclService, String, Permission[]) - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryMapVoter
AclEntryVoter - Class in ubic.gemma.core.security.acl.voter: An extension of AclEntryVoter.
AclEntryVoter(AclService, String, Permission[]) - Constructor for class ubic.gemma.core.security.acl.voter.AclEntryVoter
AclEventListener - Class in ubic.gemma.core.security.acl: Renovations Phase 3: drive ACL maintenance directly off Hibernate's per-entity insert and delete events instead of @AfterReturning AOP advice on DAO methods.
AclEventListener(BaseAclAdvice, SessionFactory) - Constructor for class ubic.gemma.core.security.acl.AclEventListener
AclEventListenerConfig - Class in ubic.gemma.core.security.acl: Renovations Phase 3: register AclEventListener with Hibernate's EventListenerRegistry so PostInsert and PostDelete events drive ACL maintenance directly, replacing the @AfterReturning AOP advice that walked DAO arguments via reflection.
AclEventListenerConfig() - Constructor for class ubic.gemma.core.security.acl.AclEventListenerConfig
AclGrantedAuthoritySid - Class in ubic.gemma.core.security.acl.domain: Hibernate-mapped row for a granted-authority entry in acl_sid (discriminator principal=0).
AclGrantedAuthoritySid() - Constructor for class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
AclGrantedAuthoritySid(String) - Constructor for class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
AclGrantedAuthoritySid(GrantedAuthority) - Constructor for class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
AclImpl - Class in ubic.gemma.core.security.acl.domain: Represents an access control list (ACL) for a domain object.
AclImpl(AclObjectIdentity, AclAuthorizationStrategy, Acl) - Constructor for class ubic.gemma.core.security.acl.domain.AclImpl: Full constructor
AclLinterCli - Class in ubic.gemma.apps
AclLinterCli() - Constructor for class ubic.gemma.apps.AclLinterCli
AclLinterConfig - Class in ubic.gemma.core.security.authorization.acl: Configuration for the ACL linter.
AclLinterConfig.AclLinterConfigBuilder - Class in ubic.gemma.core.security.authorization.acl
AclLinterHelperService - Interface in ubic.gemma.core.security.authorization.acl: Transaction boundary for the ACL linter's parent-linking repair.
AclLinterHelperServiceImpl - Class in ubic.gemma.core.security.authorization.acl
AclLinterHelperServiceImpl() - Constructor for class ubic.gemma.core.security.authorization.acl.AclLinterHelperServiceImpl
AclLinterService - Interface in ubic.gemma.core.security.authorization.acl: Lint and possibly fix ACL issues.
AclLinterService.LintResult - Class in ubic.gemma.core.security.authorization.acl
AclLinterServiceImpl - Class in ubic.gemma.core.security.authorization.acl
AclLinterServiceImpl() - Constructor for class ubic.gemma.core.security.authorization.acl.AclLinterServiceImpl
AclObjectIdentity - Class in ubic.gemma.core.security.acl.domain: Implementation of ObjectIdentity.
AclObjectIdentity() - Constructor for class ubic.gemma.core.security.acl.domain.AclObjectIdentity
AclObjectIdentity(Class, Long) - Constructor for class ubic.gemma.core.security.acl.domain.AclObjectIdentity
AclObjectIdentity(String, Long) - Constructor for class ubic.gemma.core.security.acl.domain.AclObjectIdentity
AclObjectIdentity(Securable) - Constructor for class ubic.gemma.core.security.acl.domain.AclObjectIdentity: If the object is a proxy, its superclass must be the correct one to give the OBJECT_CLASS (type) in the ACL tables.
AclPrincipalSid - Class in ubic.gemma.core.security.acl.domain: Hibernate-mapped row for a principal entry in acl_sid (discriminator principal=1).
AclPrincipalSid() - Constructor for class ubic.gemma.core.security.acl.domain.AclPrincipalSid
AclPrincipalSid(String) - Constructor for class ubic.gemma.core.security.acl.domain.AclPrincipalSid
AclPrincipalSid(Authentication) - Constructor for class ubic.gemma.core.security.acl.domain.AclPrincipalSid
AclQueryUtils - Class in ubic.gemma.persistence.util: Utilities for integrating ACL into Query.
AclQueryUtils() - Constructor for class ubic.gemma.persistence.util.AclQueryUtils
aclSecurableCollectionEditAuthorizationManager(AccessDecisionVoter) - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerConfig
aclSecurableCollectionEditIgnoreTransientAuthorizationManager(AccessDecisionVoter) - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerConfig
aclSecurableCollectionReadAuthorizationManager(AccessDecisionVoter) - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerConfig
aclSecurableEditAuthorizationManager(AccessDecisionVoter) - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerConfig
aclSecurableEditIgnoreTransientAuthorizationManager(AccessDecisionVoter) - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerConfig
aclSecurableReadAuthorizationManager(AccessDecisionVoter) - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerConfig
aclService(DataSource, LookupStrategy, AclCache) - Method in class ubic.gemma.core.security.acl.GemmaAclConfiguration: The primary ACL bean Gemma consumes (under id aclService).
AclService - Interface in ubic.gemma.core.security.acl.domain
AclServiceImpl - Class in ubic.gemma.core.security.acl.domain
AclServiceImpl(AclDao) - Constructor for class ubic.gemma.core.security.acl.domain.AclServiceImpl
AclSid - Class in ubic.gemma.core.security.acl.domain: Hibernate-mapped abstract base for acl_sid rows.
AclSid() - Constructor for class ubic.gemma.core.security.acl.domain.AclSid
AclSidRetrievalStrategyImpl - Class in ubic.gemma.core.security.acl: Sid retrieval strategy that mirrors Spring Security's stock SidRetrievalStrategyImpl but threads through an injected RoleHierarchy (Spring's stock impl uses a NullRoleHierarchy by default).
AclSidRetrievalStrategyImpl(RoleHierarchy) - Constructor for class ubic.gemma.core.security.acl.AclSidRetrievalStrategyImpl
AclVoterAuthorizationManager - Class in ubic.gemma.core.security.authorization.acl: Spring Security 6 AuthorizationManager adapter that delegates to a legacy AccessDecisionVoter bound to a single ConfigAttribute string.
AclVoterAuthorizationManager(AccessDecisionVoter, String) - Constructor for class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManager
AclVoterAuthorizationManagerConfig - Class in ubic.gemma.core.security.authorization.acl: Wires AclVoterAuthorizationManager beans, one per active ACL_SECURABLE_* config attribute, on top of the existing gsec voter beans.
AclVoterAuthorizationManagerConfig() - Constructor for class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerConfig
acquire(Investigation, String, boolean, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService: Take or refresh the lock.
acquire(Investigation, String, boolean, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl
acquire(Investigation, String, boolean, int, String, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService: As CurationLockService.acquire(Investigation, String, boolean, int), recording WHAT is taking the lock as well as who it is for.
acquire(Investigation, String, boolean, int, String, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl
acquireCurationLock(DatasetArg, Boolean, Integer, String, String, String) - Method in class ubic.gemma.rest.DatasetsWebService
acquireCurationLocks(Boolean, Integer, String, String, String, DatasetsWebService.CurationLockBulkRequest) - Method in class ubic.gemma.rest.DatasetsWebService
acquirePathLock(Path, boolean) - Method in interface ubic.gemma.core.util.locking.FileLockManager: Lock a given path.
acquirePathLock(Path, boolean) - Method in class ubic.gemma.core.util.locking.FileLockManagerImpl
acquireReadLock(Cache, Object) - Static method in class ubic.gemma.persistence.cache.CacheUtils
acquireWriteLock(Cache, Object) - Static method in class ubic.gemma.persistence.cache.CacheUtils
ActingIdentity - Class in ubic.gemma.core.security.util: The curator an action is being taken FOR, for the duration of one call.
ActingIdentity.Scope - Interface in ubic.gemma.core.security.util: Closeable that does not throw, so it can sit in a try-with-resources without a catch.
activeConnections - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
activeIngredientIn - Static variable in class ubic.gemma.core.ontology.jena.RO
activeSessionCount - Variable in class ubic.gemma.rest.AdminWebService.SessionsResponse: Sum of non-expired sessions across all principals.
actor - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowHistoryEntry
A curator's ruling on ONE finding inside an audit. - Section in enum class ubic.gemma.model.common.auditAndSecurity.curation.FindingDisposition
A curator's standing ruling that a change must NOT be made — or may be. - Section in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
add(int, T) - Method in class ubic.gemma.model.util.UninitializedList
add(O) - Method in class ubic.gemma.persistence.util.Slice: Deprecated.
add(T) - Method in class ubic.gemma.model.util.UninitializedCollection
add(ObjectMatrix) - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix: Append additional factors/covariates to this
add(SearchResult) - Method in class ubic.gemma.model.common.search.SearchResultSet
add(ArrayDesign) - Method in class ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
add(ArrayDesign, Map) - Method in class ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
add(ArrayDesign, Set) - Method in class ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
addAccession(NCBIGene2Accession) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
addAclParameters(Query, Class) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Bind Query parameters to a join clause generated with AclQueryUtils.formAclRestrictionClause(String) and add ACL restriction parameters defined in AclQueryUtils.formAclRestrictionClause(String).
addAclParameters(Query, Class) - Static method in class ubic.gemma.persistence.util.EE2CAclQueryUtils
addAffyDataFromAPTOutput(ExpressionExperiment, String) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
addAffyDataFromAPTOutput(ExpressionExperiment, String) - Method in class ubic.gemma.core.loader.expression.DataUpdaterImpl: Affymetrix: Use to bypass the automated running of apt-probeset-summarize.
addAll(int, Collection) - Method in class ubic.gemma.model.util.UninitializedList
addAll(Collection) - Method in class ubic.gemma.model.util.UninitializedCollection
addAllByName(Collection, Collection) - Static method in class ubic.gemma.model.common.DescribableUtils: Add all the describables to a given collection.
addAllByName(Collection, Collection, boolean, boolean) - Static method in class ubic.gemma.model.common.DescribableUtils: Add all the describables to a given collection.
addAllByName(Collection, Collection, BiFunction, BiFunction, boolean, boolean) - Static method in class ubic.gemma.model.common.DescribableUtils: Add all the describables to a given collection.
addAnnotation(ExpressionExperiment, Characteristic) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Add a single experiment-level tag to ee as part of the per-tag REST write flow.
addAnnotation(ExpressionExperiment, Characteristic) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Per-tag REST-write counterpart to ExpressionExperimentServiceImpl.addCharacteristic(ExpressionExperiment, Characteristic).
addAnnotation(ExpressionExperiment, Characteristic, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: As ExpressionExperimentService.addAnnotation(ExpressionExperiment, Characteristic), with a caller-supplied reason appended to the audit note after the server's own description.
addAnnotation(ExpressionExperiment, Characteristic, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Reason-carrying overload.
addAnnotation(ExpressionExperiment, BioMaterial, Characteristic) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Per-tag add of a characteristic to a biomaterial, the sample-level counterpart of ExpressionExperimentService.addAnnotation(ExpressionExperiment, Characteristic).
addAnnotation(ExpressionExperiment, BioMaterial, Characteristic) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
addAnnotation(ExpressionExperiment, BioMaterial, Characteristic, String) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: As BioMaterialService.addAnnotation(ExpressionExperiment, BioMaterial, Characteristic), with a caller-supplied reason appended to the audit note after the server's own description.
addAnnotation(ExpressionExperiment, BioMaterial, Characteristic, String) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl: Reason-carrying overload.
addAnyNewAccessions(GeneProduct, GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneWriteService: Add accessions from geneProduct into existing if not already present (matched by accession string).
addAnyNewAccessions(GeneProduct, GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl
addAutoOption(Options) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Add the -auto option.
addAutoOption(Options, Class) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Add the -auto option for a specific AuditEventType.
addAutoOption(Options, String, String, String, String, String, String) - Static method in class ubic.gemma.cli.util.OptionsUtils
addAutoOption(Options, String, String, String, String, String, String, String) - Static method in class ubic.gemma.cli.util.OptionsUtils: Add an option with three possible values: true, false, or null.
addBatchOption(Options) - Method in class ubic.gemma.cli.util.AbstractCLI: Add the -batchFormat and -batchOutputFile options.
addBeanPostProcessor(ConfigurableBeanFactory, int, BeanPostProcessor) - Static method in class ubic.gemma.core.context.BeanFactoryUtils: Add a BeanPostProcessor at a specific index of a bean factory.
addBinToQuery(String, Long, Long) - Static method in class ubic.gemma.core.analysis.sequence.SequenceBinUtils: Directly ported from jksrc binRange.c and hdb.c From the binRange.c comments: There's a bin for each 128k segment, for each 1M segment, for each 8M segment, for each 64M segment, and for each chromosome (which is assumed to be less than 512M.) A range goes into the smallest bin it will fit in.
addBioAssays(List) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
addBioMaterialAssociation(BioAssay, BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService: Associates a bioMaterial with a specified bioAssay.
addBioMaterialAssociation(BioAssay, BioMaterial) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
addBlackCell(Long, String, double, double, int, int) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
addBlacklistEntry(AdminWebService.BlacklistRequest) - Method in class ubic.gemma.rest.AdminWebService: Adds a single blacklist entry.
addByName(Collection, S) - Static method in class ubic.gemma.model.common.DescribableUtils: Add a Describable to a collection.
addCell(Long, String, Double, Double, Integer, Integer, Double) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
addCellLevelCharacteristics(ExpressionExperiment, SingleCellDimension, CellLevelCharacteristics) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Add new cell-level characteristics.
addCellLevelCharacteristics(ExpressionExperiment, SingleCellDimension, CellLevelCharacteristics) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
addCellMetadataFileOptions(Options, String, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
addCellMetadataFileOptions(Options, String, boolean, BiConsumer) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
addCellTypeAssignment(ExpressionExperiment, QuantitationType, SingleCellDimension, CellTypeAssignment, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
addCellTypeAssignment(ExpressionExperiment, QuantitationType, SingleCellDimension, CellTypeAssignment, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
addChangelogEntry(ExpressionExperiment, String) - Method in interface ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileService
addChangelogEntry(ExpressionExperiment, String) - Method in class ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileServiceImpl
addChangelogEntry(ExpressionExperiment, String, LocalDate) - Method in interface ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileService: Add a changelog entry to the changelog file of the given experiment.
addChangelogEntry(ExpressionExperiment, String, LocalDate) - Method in class ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileServiceImpl
addChannel() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addCharacteristic(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
addCharacteristic(BioMaterial, Characteristic) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Will persist the give vocab characteristic to the given biomaterial
addCharacteristic(BioMaterial, Characteristic) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
addCharacteristic(ExpressionExperiment, Characteristic) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Will add the vocab characteristic to the expression experiment and persist the changes.
addCharacteristic(ExpressionExperiment, Characteristic) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
addCharacteristic(ExpressionExperiment, Characteristic) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService
addCharacteristic(ExpressionExperiment, Characteristic) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl: Will add the characteristic to the expression experiment and persist the changes.
addColumnName(C) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix: Add a column name when we don't care what the index will be.
addColumnName(C) - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Add a column name, to the end of the current column names.
addColumnName(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
addCommaDelimitedPlatformOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils: Add an option for supplying a comma-delimited list of platforms.
addComment(Ticket, Contact, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Append a comment event (free-form payload).
addComment(Ticket, Contact, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
addCondition(DifferentialExpressionGenesConditionsValueObject.Condition) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject: Initialize the column of cells for the given Condition, treating them as missing values.
addContrastsFactorValue(long, String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
addContributor(GeoContact) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addCorrespondence(String, String) - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
addCountData(ExpressionExperiment, ArrayDesign, DoubleMatrix, DoubleMatrix, Map, boolean) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
addCountData(ExpressionExperiment, ArrayDesign, DoubleMatrix, DoubleMatrix, Map, boolean) - Method in class ubic.gemma.core.loader.expression.DataUpdaterImpl: RNA-seq: Replaces data.
addData(ExpressionExperiment, ArrayDesign, ExpressionDataDoubleMatrix) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
addData(ExpressionExperiment, ArrayDesign, ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.loader.expression.DataUpdaterImpl: Generic but in practice used for RNA-seq.
addDataFileOptions(Options, String, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
addDataFileOptions(Options, String, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
addDataFileOptions(Options, String, boolean, boolean, boolean, boolean, boolean, BiConsumer) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils: Add options for writing data files, such as raw or processed data files.
addDataFileOptions(Options, String, boolean, BiConsumer) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
addDataSet(GeoDataset) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addDatasetAnnotation(DatasetArg, AnnotationsWebService.AnnotationDto, Long) - Method in class ubic.gemma.rest.AnnotationsWebService
addDatasetAnnotationTag(DatasetArg, AnnotationsWebService.AnnotationDto, Long) - Method in class ubic.gemma.rest.DatasetsWebService
addDatasetGroupOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils: Add an option for supplying an EE set.
addDatasetOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils: Add an option for supplying a dataset.
addDateOption(String, String, String, Options) - Static method in class ubic.gemma.cli.util.OptionsUtils: Add a date option with support for fuzzy dates (i.e.
addDesignFileOptions(Options, String, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
addDesignFileOptions(Options, String, boolean, BiConsumer) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
AddedInWindow() - Constructor for class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow
AddedInWindow(int, Date, long) - Constructor for class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow
addElements(ArrayDesign) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService: For the rare cases (Exon arrays) where we load the platform in two stages.
addElements(ArrayDesign) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
addEmailAlert() - Method in interface ubic.gemma.core.job.SubmittedTask: Add email notification of task completion.
addEmailNotification(CompletableFuture, EmailNotificationContext, Executor) - Method in interface ubic.gemma.core.job.notification.TaskPostProcessing
addEmailNotification(CompletableFuture, EmailNotificationContext, Executor) - Method in class ubic.gemma.core.job.notification.TaskPostProcessingImpl
addEnumOption(Options, String, String, String, Class) - Static method in class ubic.gemma.cli.util.OptionsUtils: Add an enumerated option with localized descriptions.
addEnumOption(Options, String, String, String, Class, EnumMap) - Static method in class ubic.gemma.cli.util.OptionsUtils: Add an enumerated option with descriptions.
addEnumSetOption(Options, String, String, String, Class) - Static method in class ubic.gemma.cli.util.OptionsUtils
addErrorObject(Serializable, Exception) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter: Add an error object based on an exception.
addErrorObject(Serializable, Exception) - Method in class ubic.gemma.cli.util.AbstractCLI: Add an error object based on an exception.
addErrorObject(Serializable, String) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter: Add an error object without a cause stacktrace.
addErrorObject(Serializable, String) - Method in class ubic.gemma.cli.util.AbstractCLI: Add an error object without a cause stacktrace.
addErrorObject(Serializable, String, Throwable) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter: Add an error object with a stacktrace to indicate failure in a batch processing.
addErrorObject(Serializable, String, Throwable) - Method in class ubic.gemma.cli.util.AbstractCLI: Add an error object with a stacktrace to indicate failure in a batch processing.
addErrorObject(T, Exception) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addErrorObject(T, String) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addErrorObject(T, String, Throwable) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addErrorObject(ExpressionExperiment, QuantitationType, Exception) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
addErrorObject(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
addErrorObject(ExpressionExperiment, QuantitationType, String, Throwable) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
addEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail: Append a new AuditEvent to this trail AND repoint AuditTrail.lastEvent when the new event is more recent than the current pointer under (date desc, id desc) ordering.
addEventsToMap(Map, Long, AuditEvent) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
addExpressedCells(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int, boolean[], boolean[]) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics: Populate a boolean vector that indicates if a cell has at least one expressed gene.
addExpressionDataFileOptions(Options, String, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
addExpressionDataFileOptions(Options, String, boolean, BiConsumer) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
addFactor(ExpressionExperiment, ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
addFactor(ExpressionExperiment, ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
addFactor(ExpressionExperiment, ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService
addFactor(ExpressionExperiment, ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl
addFactorsToInclude(Collection) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Add a collection of factors to include in the analysis.
addFactorValue(ExpressionExperiment, FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
addFactorValue(ExpressionExperiment, FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
addFactorValue(ExpressionExperiment, FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService
addFactorValue(ExpressionExperiment, FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl
addFactorValues(ExpressionExperiment, Map) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Intended with the case of a continuous factor being added.
addFactorValues(ExpressionExperiment, Map) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
addFactorValues(ExpressionExperiment, Map) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService
addFactorValues(ExpressionExperiment, Map) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl
addForceOption(Options) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addForceOption(Options, String) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addGene(DifferentialExpressionGenesConditionsValueObject.DiffExGene) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
addGene(GeneProductValueObject, GeneValueObject) - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
addGenericPlatformOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils: Add an option for supplying a generic platform.
addGroupAuthority(String, GrantedAuthority) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
addGroupAuthority(UserGroup, String) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
addGroupAuthority(UserGroup, String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
Adding ACLs to entities at creation time - Section in package ubic.gemma.core.security
addInteraction() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix: Add interaction term; only works if there exactly two factors so this can figure out which interaction to add.
addInteraction(String...) - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix: This will not add the interaction unless all of the terms are already part of the design, and interactions that obviously can't be estimated will be dropped if possible, but otherwise this is fairly brain dead.
addInteractionsToInclude(Collection) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
addInteractionToInclude(Collection) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Add an interaction of two factors to include in the analysis.
ADDITIONAL_PIPELINE_CONFIGURATIONS - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
additionalAuthenticationChecks(UserDetails, UsernamePasswordAuthenticationToken) - Method in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider
addLimitingDateOption(Options) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Add the -mdate option.
addMatrices(ExpressionDataDoubleMatrix, ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder: Add two matrices.
addMember(Long, GroupsWebService.MemberAddRequest) - Method in class ubic.gemma.rest.GroupsWebService: Add a member to a group.
addNewObjects(Collection) - Method in class ubic.gemma.core.analysis.report.WhatsNew: adds a collection of auditables to the new object list
addNewObjects(Auditable) - Method in class ubic.gemma.core.analysis.report.WhatsNew: adds a single auditable to the new object list
addNonTroubledFilter(Filters, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: Restrict results to non-troubled curatable entities for callers who do not curate.
addOrUpdateAcl(MutableAcl, Securable, Acl) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice: Renovations Phase 3: visibility relaxed so AclEventListener (in the same package) can drive ACL maintenance directly off Hibernate insert events without going through the AOP advice's entity-graph walk.
addOtherIssues(String) - Method in class ubic.gemma.model.expression.experiment.Geeq
addPlatform(GeoPlatform) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addPlatformOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils: Add an option for supplying a platform.
addProbes(ArrayDesign, Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
addProbes(ArrayDesign, Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
addProbes(ArrayDesign, Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
addProbes(ArrayDesign, Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
addPropertyDirect(String, Object) - Method in class ubic.gemma.core.config.PropertySourcesConfiguration: Deprecated.
addQuantitationType(GeoPlatform, String, Integer) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Add raw data vectors with the given quantitation type.
addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService: Add raw data vectors for a quantitation type.
addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Used when we want to add data for a quantitation type.
addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
addRelation(String, String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
addReplication(GeoReplication) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addRestrictionParameters(Query, Filters) - Static method in class ubic.gemma.persistence.util.FilterQueryUtils: Adds all parameters contained in the filters argument to the query by calling Query.setParameter(String, Object) or Query.setParameterList(String, Collection) as needed.
addResult(Object) - Method in class ubic.gemma.core.loader.genome.FastaParser
addResult(Object) - Method in class ubic.gemma.core.loader.genome.gene.SwissProtParser
addResult(Object) - Method in class ubic.gemma.core.loader.util.parser.RecordParser: Add an object to the results collection.
addResult(T) - Method in class ubic.gemma.core.loader.util.parser.BasicLineParser
addResult(NCBIGene2Accession) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
addResult(Gene2GOAssociation) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
addResult(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
addResult(BlatResult) - Method in class ubic.gemma.core.loader.genome.BlatResultParser
addRowName(R) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix: Add a row name when we don't care what the index will be.
addSample(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addSample(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
addSample(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: Only call this to add a sample for which there are no data.
addSampleCharacteristic(DatasetArg, Long, DatasetsWebService.AnnotationTagInput) - Method in class ubic.gemma.rest.DatasetsWebService
addSamples(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries: Add a group of samples to this series.
addSeries(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
addSeriesAppearsIn(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addSingleCellDataVectors(ExpressionExperiment, QuantitationType, Collection, String, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Add single-cell data vectors.
addSingleCellDataVectors(ExpressionExperiment, QuantitationType, Collection, String, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
addSingleCellDataVectors(ExpressionExperiment, QuantitationType, SingleCellDimension, Stream, String, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Streaming variant of SingleCellExpressionExperimentService.addSingleCellDataVectors(ExpressionExperiment, QuantitationType, Collection, String, boolean, boolean) that avoids materializing all vectors in memory.
addSingleCellDataVectors(ExpressionExperiment, QuantitationType, SingleCellDimension, Stream, String, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
addSingleCellExpressionDataFileOptions(Options, String, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
addSingleCellExpressionDataFileOptions(Options, String, boolean, BiConsumer) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
addSingleExperimentAutoOption(Options, String, String, String, String, String, String) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Add an auto option that is only available in single-experiment mode.
addSingleExperimentEnumOption(Options, String, String, String, Class, EnumMap) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Add an enumerated option that is only available in single-experiment mode.
addSingleExperimentOption(Options, String, String, boolean, String) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Add an option that is only available in single-experiment mode.
addSingleExperimentOption(Options, Option) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Add an option that is only available in single-experiment mode.
addSubSeries(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addSubset(GeoSubset) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
addSuccessObject(Serializable) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter
addSuccessObject(Serializable) - Method in class ubic.gemma.cli.util.AbstractCLI
addSuccessObject(Serializable, String) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter: Add a success object to indicate success in a batch processing.
addSuccessObject(Serializable, String) - Method in class ubic.gemma.cli.util.AbstractCLI: Add a success object to indicate success in a batch processing.
addSuccessObject(T) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addSuccessObject(T, String) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addSuccessObject(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
addTarget(Ticket, TicketTargetType, Long, Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Add a target to a ticket that was already opened.
addTarget(Ticket, TicketTargetType, Long, Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
AddTargetRequest() - Constructor for class ubic.gemma.rest.TicketsWebService.AddTargetRequest
AddTargetsResult(List, List, TicketValueObject) - Constructor for class ubic.gemma.rest.TicketsWebService.AddTargetsResult
addTaxonOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils: Add an option for supplying a taxon.
addThreadsOption(Options) - Method in class ubic.gemma.cli.util.AbstractCLI: Add the -threads option.
addTicketTarget(Long, TicketsWebService.AddTargetRequest) - Method in class ubic.gemma.rest.TicketsWebService: Add a target to a ticket that is open to additions.
addToCache(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
addToCache(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
addToCache(DiffExprGeneSearchResult) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
addToCache(DiffExprGeneSearchResult) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
addToCache(CompositeSequence) - Method in class ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
addToColumnData(String, String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform: Add a value to a column.
addToDataProcessing(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addToDbXRefs(String, String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
addToExtractProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
addToGrowthProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
addToHybProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addToKeyWords(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addToOrganisms(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
addToPubmedIds(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addToRepeatsSampleList(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
addToResultSetCountsCache(Long, ResultSetCountsValueObject) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache: Populate the per-result-set hit-list counts cache.
addToResultSetCountsCache(Long, ResultSetCountsValueObject) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
addToRowMaps(BulkExpressionDataVector) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
addToRowMaps(CompositeSequence, QuantitationType, BioAssayDimension) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix: Add a design element to the row maps.
addToScanProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addToSeriesTypes(GeoSeriesType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addToSummaries(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries: Add a summary to the series.
addToSupplementaryFiles(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addToSupplementaryFiles(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addToSynonyms(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
addToTopHitsCache(ExpressionAnalysisResultSet, List) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
addToTopHitsCache(ExpressionAnalysisResultSet, List) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
addToTreatmentProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
addToVariables(Integer, GeoVariable) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addToVariableSampleList(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
addUpdatedObjects(Collection) - Method in class ubic.gemma.core.analysis.report.WhatsNew: adds a collection of auditables to the updated object list
addUpdatedObjects(Auditable) - Method in class ubic.gemma.core.analysis.report.WhatsNew: adds a single auditable to the updated object list
addUpdateEvent(Auditable, Class, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
addUpdateEvent(Auditable, Class, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
addUpdateEvent(Auditable, Class, String, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
addUpdateEvent(Auditable, Class, String, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
addUpdateEvent(Auditable, Class, String, String, Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService: Add an update audit event of a specific type to the passed auditable entity.
addUpdateEvent(Auditable, Class, String, String, Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
addUpdateEvent(Auditable, Class, String, Throwable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService: Add an update audit event with an exception.
addUpdateEvent(Auditable, Class, String, Throwable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl: This is using the Propagation.REQUIRES_NEW so that if the throwable is raised, it will not roll back the audit trail event.
addUpdateEvent(Auditable, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService: Add an update event defined by the given parameters, to the given auditable.
addUpdateEvent(Auditable, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
addUpdateEventWithPayload(Auditable, Class, String, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService: Add an update audit event of a specific type, attaching a JSON payload string.
addUpdateEventWithPayload(Auditable, Class, String, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
addUserToGroup(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
addUserToGroup(String, String) - Method in interface ubic.gemma.core.security.SecurityService: Add a given user to a group by name.
addUserToGroup(String, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
addUserToGroup(UserGroup, User) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
addUserToGroup(UserGroup, User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
addValue(GeoSample, Integer, String, String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: Store a value.
addVariable(GeoVariable) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addWarningObject(Serializable, String) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter
addWarningObject(Serializable, String) - Method in class ubic.gemma.cli.util.AbstractCLI
addWarningObject(Serializable, String, Throwable) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter
addWarningObject(Serializable, String, Throwable) - Method in class ubic.gemma.cli.util.AbstractCLI: Add a warning object with a stacktrace to indicate a recoverable failure in a batch processing.
addWarningObject(T, String) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addWarningObject(T, String, Throwable) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addWarnings(Iterable, String, LocationType) - Method in class ubic.gemma.rest.util.ResponseDataObject: Add a bunch of warnings to ResponseDataObject.getWarnings().
adjustLibrarySizes(boolean) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder: Perform adjustment of library sizes to better reflect the number of reads in the source sample.
ADMIN_GROUP_AUTHORITY - Static variable in class ubic.gemma.core.security.AuthorityConstants: The name of the administrator group authority.
ADMIN_GROUP_NAME - Static variable in class ubic.gemma.core.security.AuthorityConstants: The name of the administrator group.
adminChangePassword(String, String) - Method in interface ubic.gemma.core.security.authentication.UserManager: Administrative password reset: set a new password for the named user without requiring their current password.
adminChangePassword(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
AdminEditableBaseImmutableService<O> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity: Interface for services of immutable entities that can only be edited by admins.
AdminEditableBaseService<O> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity: Interface for services of entities that can only be edited by admins.
AdminPipelineWebService - Class in ubic.gemma.rest: Admin REST surface for curator-driven pipeline batch submissions.
AdminPipelineWebService() - Constructor for class ubic.gemma.rest.AdminPipelineWebService
AdminPipelineWebService.SubmitBatchRequest - Class in ubic.gemma.rest
AdminWebService - Class in ubic.gemma.rest: Admin-only system monitoring surface for the gemma-curation-ui admin panel.
AdminWebService(CacheManager, SessionFactory, TaskRunningService, SessionRegistry, List, OntologyService, DataSource, UserManager, AnnotationSetService, TicketService, TaxonArgService, BlacklistedEntityService, ExternalDatabaseReadService, GeoScrapeService, IndexerService, PlatformArgService, ArrayDesignReportService) - Constructor for class ubic.gemma.rest.AdminWebService
AdminWebService.AgentRunsBlock - Class in ubic.gemma.rest
AdminWebService.BlacklistListResponse - Class in ubic.gemma.rest
AdminWebService.BlacklistRequest - Class in ubic.gemma.rest
AdminWebService.CacheListResponse - Class in ubic.gemma.rest
AdminWebService.CacheStatRow - Class in ubic.gemma.rest
AdminWebService.CreateUserRequest - Class in ubic.gemma.rest
AdminWebService.CreateUserResponse - Class in ubic.gemma.rest
AdminWebService.CurationAgentHealthResponse - Class in ubic.gemma.rest
AdminWebService.CurationStatusResponse - Class in ubic.gemma.rest: Response shape for AdminWebService.getCurationStatus().
AdminWebService.DbPoolResponse - Class in ubic.gemma.rest
AdminWebService.GeoGrabRequest - Class in ubic.gemma.rest
AdminWebService.GeoGrabResponse - Class in ubic.gemma.rest
AdminWebService.GeoRecordValueObject - Class in ubic.gemma.rest
AdminWebService.GeoScrapeDryRunResponse - Class in ubic.gemma.rest: Dry-run response.
AdminWebService.GeoScrapeRequest - Class in ubic.gemma.rest
AdminWebService.GeoScrapeSubmitResponse - Class in ubic.gemma.rest
AdminWebService.GeoScrapeWatermarkValueObject - Class in ubic.gemma.rest
AdminWebService.HibernateStatsResponse - Class in ubic.gemma.rest
AdminWebService.ImportGeoBatchRequest - Class in ubic.gemma.rest
AdminWebService.ImportGeoBatchResponse - Class in ubic.gemma.rest
AdminWebService.IndexStatusValueObject - Class in ubic.gemma.rest
AdminWebService.JobsListResponse - Class in ubic.gemma.rest
AdminWebService.MemoryBlock - Class in ubic.gemma.rest
AdminWebService.MultifunctionalityRecomputeResponse - Class in ubic.gemma.rest
AdminWebService.ObsoleteTermCorrectionSubmission - Class in ubic.gemma.rest
AdminWebService.OntologiesResponse - Class in ubic.gemma.rest
AdminWebService.OntologyRefreshResponse - Class in ubic.gemma.rest: Body shape for AdminWebService.refreshOntology(String, boolean) returns.
AdminWebService.OntologyStatusValueObject - Class in ubic.gemma.rest
AdminWebService.ProposalsBlock - Class in ubic.gemma.rest
AdminWebService.ReindexAcceptedResponse - Class in ubic.gemma.rest: Wire shape for AdminWebService.reindexSearchIndices(String): list of entity classes whose reindex was queued.
AdminWebService.ResetPasswordResponse - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectBlacklistedValueObject - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectCreateUserResponse - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectDbPoolResponse - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectGeoScrapeSubmitResponse - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectImportGeoBatchResponse - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectMultifunctionalityRecomputeResponse - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectObsoleteTermCorrectionSubmission - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectOntologyRefreshResponse - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectReindexAcceptedResponse - Class in ubic.gemma.rest
AdminWebService.ResponseDataObjectSubmittedJobResponse - Class in ubic.gemma.rest
AdminWebService.SearchIndicesResponse - Class in ubic.gemma.rest
AdminWebService.SessionPrincipalValueObject - Class in ubic.gemma.rest
AdminWebService.SessionsResponse - Class in ubic.gemma.rest
AdminWebService.SubmittedJobResponse - Class in ubic.gemma.rest: Payload of POST /admin/tasks/platform-reports: the id of the task that was queued.
AdminWebService.SystemSnapshotResponse - Class in ubic.gemma.rest
AdminWebService.ThreadBlock - Class in ubic.gemma.rest
AdminWebService.TicketsBlock - Class in ubic.gemma.rest
AdminWebService.UpdateUserRequest - Class in ubic.gemma.rest
AdminWebService.UsersListResponse - Class in ubic.gemma.rest
AdminWebService.UserValueObject - Class in ubic.gemma.rest
advance(Investigation, WorkflowState, String, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.WorkflowService: Advance the given dataset to targetState.
advance(Investigation, WorkflowState, String, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceImpl
advanceDatasetWorkflow(Long, WorkflowWebService.AdvanceWorkflowRequest) - Method in class ubic.gemma.rest.WorkflowWebService: Advance a dataset to a new workflow state.
AdvanceWorkflowRequest() - Constructor for class ubic.gemma.rest.WorkflowWebService.AdvanceWorkflowRequest
AFFX - Enum constant in enum class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
AFFY_COLLAPSED - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType: Represents Affymetrix probe sequences that have been "collapsed" or combined into a single sequence.
AFFY_PROBE - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType: Represents a single probe sequence for Affymetrix reporters
AFFY_TARGET - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType: Represents the target sequence provided by the manufacturer.
AffyChipTypeExtractor - Class in ubic.gemma.core.loader.expression.arrayDesign: Extract the chip type from Affymetrix CEL files.
AffyChipTypeExtractor() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractor
AffyDataFromCelCli - Class in ubic.gemma.apps: Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.
AffyDataFromCelCli() - Constructor for class ubic.gemma.apps.AffyDataFromCelCli
AffyPowerToolsProbesetSummarize - Class in ubic.gemma.core.loader.expression
AffyProbeCollapseCli - Class in ubic.gemma.apps: Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
AffyProbeCollapseCli() - Constructor for class ubic.gemma.apps.AffyProbeCollapseCli
AffyProbeNameFilter - Class in ubic.gemma.core.analysis.preprocess.filter
AffyProbeNameFilter(AffyProbeNameFilter.Pattern[]) - Constructor for class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter
AffyProbeNameFilter.Pattern - Enum Class in ubic.gemma.core.analysis.preprocess.filter
AffyProbeReader - Class in ubic.gemma.core.loader.expression.arrayDesign: Reads Affymetrix Probe files, including exon arrays.
AffyProbeReader() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
AffyScanDateExtractor - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Extract the scan date from Affymetrix CEL files.
AffyScanDateExtractor() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractor
AFTER_REBUILD_REGIONS - Static variable in class ubic.gemma.cli.util.RestCacheEviction: The regions a table rebuild leaves stale.
afterAclCompositeSequenceCollectionRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig
afterAclCompositeSequenceRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig
afterAclDataVectorCollectionRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig
afterAclDifferentialExpressionAnalysisResultCollectionRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig
afterAuditedConditionalMethod(JoinPoint, AuditedConditional, Object) - Method in class ubic.gemma.core.security.audit.AuditedAspect: Phase C: AuditedConditional fires only when its SpEL AuditedConditional.when() predicate evaluates to true against the post-invocation context.
afterAuditedMethod(JoinPoint, Audited, Object) - Method in class ubic.gemma.core.security.audit.AuditedAspect
afterAuditedOnErrorMethod(JoinPoint, AuditedOnError, Throwable) - Method in class ubic.gemma.core.security.audit.AuditedAspect: Phase C: AuditedOnError fires when the annotated method exits by throwing.
afterAuditedOnErrorsMethod(JoinPoint, AuditedOnErrors, Throwable) - Method in class ubic.gemma.core.security.audit.AuditedAspect: Phase C: repeated AuditedOnError declarations (wrapped by the compiler in AuditedOnErrors) — multi-catch shape.
afterCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.BashCompletionGenerator
afterCompletion(PrintWriter) - Method in interface ubic.gemma.cli.completion.CompletionGenerator: Executed after all completions have been generated.
afterCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.FishCompletionGenerator
afterCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.WikiCompletionGenerator
afterInvocationManager() - Method in class ubic.gemma.core.security.MethodSecurityConfig: Aggregate the after-invocation providers from MethodSecurityConfig.AFTER_INVOCATION_PROVIDER_BEAN_NAMES into an AfterInvocationProviderManager.
afterPropertiesSet() - Method in class ubic.gemma.apps.ExperimentalDesignImportCli
afterPropertiesSet() - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli
afterPropertiesSet() - Method in class ubic.gemma.apps.GeoGrabberCli
afterPropertiesSet() - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCli
afterPropertiesSet() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI
afterPropertiesSet() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.core.analysis.report.HomeStatsServiceImpl: Load any persisted snapshot on bean startup so that HomeStatsServiceImpl.getCached() doesn't have to hit disk on the first REST request.
afterPropertiesSet() - Method in class ubic.gemma.core.config.SentinelPropertyValidator
afterPropertiesSet() - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl
afterPropertiesSet() - Method in interface ubic.gemma.core.logging.log4j.ThreadContextPopulator
afterPropertiesSet() - Method in class ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer
afterPropertiesSet() - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.core.search.SearchServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.core.security.acl.AclEventListenerConfig
afterPropertiesSet() - Method in class ubic.gemma.core.util.BuildInfo
afterPropertiesSet() - Method in class ubic.gemma.core.util.DummyMailSender
afterPropertiesSet() - Method in class ubic.gemma.persistence.audit.AuditTrailEventListenerConfig
afterPropertiesSet() - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.persistence.util.AclClassIdInitializer
afterPropertiesSet() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
age - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
agent - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
AGENT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSource
AGENT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageJudgeKind: An automated run: triage pass, QC gate, audit pipeline.
AGENT - Enum constant in enum class ubic.gemma.model.common.description.PublicationAssociationSource: A machine assertion from a curation agent (pub_finder and friends).
AGENT_GROUP_AUTHORITY - Static variable in class ubic.gemma.core.security.AuthorityConstants
AGENT_GROUP_NAME - Static variable in class ubic.gemma.core.security.AuthorityConstants
AgentCurationKind - Enum Class in ubic.gemma.model.expression.experiment: Discriminator on AgentProposal rows: which kind of agent activity a row records — a forward-looking proposal (pre-curation suggestion), an audit (a post-hoc review of an existing dataset, reporting findings to act on), or an evaluation (a scored assessment of curation that already exists).
agentName - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest: Which specialist produced it (cell_type, disease, …); "the agent" is a fleet.
agentName - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
agentName - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
agentName - Variable in class ubic.gemma.rest.AnnotationSetsWebService.ProvenanceRequest
agentName - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockResponse
agentRuns - Variable in class ubic.gemma.rest.AdminWebService.CurationStatusResponse
AgentRunsBlock() - Constructor for class ubic.gemma.rest.AdminWebService.AgentRunsBlock
agentVersion - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
agentVersion - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
agentVersion - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
agentVersion - Variable in class ubic.gemma.rest.AnnotationSetsWebService.ProvenanceRequest
agentVersion - Variable in class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
agentVersion - Variable in class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest
aggregate(Collection, SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod, CellLevelCharacteristics, boolean) - Static method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils: Aggregate a collection of vectors.
aggregate(SingleCellExpressionDataMatrix, SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod, Class) - Static method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils: Aggregate a single-cell data matrix.
AggregatedAssay(String, Integer, Integer, Integer, Integer, Integer, Double, Double) - Constructor for record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Creates an instance of a AggregatedAssay record class.
aggregatedAssays() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload: Returns the value of the aggregatedAssays record component.
AggregatedSingleDataAddedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Special case of DataAddedEvent for aggregated single-cell data.
AggregatedSingleDataAddedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AggregatedSingleDataAddedEvent
aggregateVectors(ExpressionExperiment, QuantitationType, List, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellAggregationConfig) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateService: Aggregate preferred single-cell data vectors by the given cell-level characteristics.
aggregateVectors(ExpressionExperiment, QuantitationType, List, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellAggregationConfig) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl
aggregateVectorsByCellType(ExpressionExperiment, List, SingleCellAggregationConfig) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateService: Aggregate preferred single-cell data vectors by the preferred cell type assignment and the only cell type factor of the experiment.
aggregateVectorsByCellType(ExpressionExperiment, List, SingleCellAggregationConfig) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl
aggressiveQtRemoval - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest
AGILENT_DATE_PATTERN - Static variable in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractor
AgilentScanDateExtractor - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Because agilent makes slides that work with any scanner, the formats are not that predictable.
AgilentScanDateExtractor() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractor
agreement - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.PriorCurationUsage: This term's share of every annotation made from this string, in [0, 1].
AjaxAuthenticationFailureHandler - Class in ubic.gemma.core.security.authentication: Strategy used to handle a failed user authentication if it is a ajax style login (ajaxLoginTrue parameter = true) then no redirect happens and a some JSON is sent to the client if the request is not ajax style then the default redirection takes place
AjaxAuthenticationFailureHandler() - Constructor for class ubic.gemma.core.security.authentication.AjaxAuthenticationFailureHandler
AjaxAuthenticationSuccessHandler - Class in ubic.gemma.core.security.authentication: Strategy used to handle a successful user authentication if it is a ajax style login (ajaxLoginTrue parameter = true) then no redirect happens and a some JSON is sent to the client if the request is not ajax-style then the default redirection takes place
AjaxAuthenticationSuccessHandler() - Constructor for class ubic.gemma.core.security.authentication.AjaxAuthenticationSuccessHandler
Alias(String, String, String) - Constructor for class ubic.gemma.persistence.util.Subquery.Alias
ALIAS - Enum constant in enum class ubic.gemma.model.common.search.SearchMatchType: Exact match on a registered gene alias/synonym.
ALIGNMENT_METADATA - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
AlignmentBasedGeneMappingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Signifies a mapping based on sequence alignment performed by the system.
AlignmentBasedGeneMappingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AlignmentBasedGeneMappingEvent
all - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode
all(Class) - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrlChooser
all(List, String, Filters, String[], Sort) - Static method in class ubic.gemma.rest.util.Responders
all(List, Filters, String[], Sort) - Static method in class ubic.gemma.rest.util.Responders: Produce all results.
ALL - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField: This is the default if omitted.
ALL - Enum constant in enum class ubic.gemma.persistence.util.SubqueryMode: Produce a clause of the form id not in {not(subquery)}.
ALL - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
ALL - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
ALL() - Method in class ubic.gemma.rest.util.args.FilterArgParser.QuantifierContext
ALL() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
AllAnalysesFailedException - Exception Class in ubic.gemma.core.analysis.expression.diff: Exception raised when all analyses fail.
AllAnalysesFailedException(String, Collection, DifferentialExpressionAnalysisConfig) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.AllAnalysesFailedException
allOf(Predicate...) - Static method in class ubic.gemma.cli.util.OptionsUtils: Make sure that all the given predicates are true.
allowArrayExpressDesign - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest
ALLOWED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionType: This change is agreed to.
allowedNextStates() - Method in enum class ubic.gemma.model.expression.experiment.WorkflowState
allowedValues(List) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder: A short list of allowed values if that can be determined, or null.
allowMappingDesignElementsToGeneSymbols(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder
allowPositionalArguments() - Method in class ubic.gemma.cli.util.AbstractCLI
allowPositionalArguments() - Method in interface ubic.gemma.cli.util.CLI: Indicate if this CLI allows positional arguments.
AllowsUnknownQueryParameters - Annotation Interface in ubic.gemma.rest.annotations: Exempts a resource method (or every method of a resource class) from the unknown-query-parameter rejection performed by UnknownQueryParameterFilter.
allowSuperSeriesLoad - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest
allowUseExisting - Variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher: Whether we are allowed to use an existing file rather than downloading again, in the case where we can't connect to the remote host to check the size of the file.
AllSubSetAnalysesFailedException - Exception Class in ubic.gemma.core.analysis.expression.diff: Exception raised when all subset analyses failed with an AnalysisException.
AllSubSetAnalysesFailedException(String, Collection, DifferentialExpressionAnalysisConfig) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.AllSubSetAnalysesFailedException
alreadyCompressed() - Element in annotation interface ubic.gemma.rest.annotations.GZIP: Indicate that the payload is already compressed.
AlreadyExistsInSystemException - Exception Class in ubic.gemma.core.loader.util: Can be thrown when an attempt is made to load data into the system that already exists.
AlreadyExistsInSystemException(String) - Constructor for exception class ubic.gemma.core.loader.util.AlreadyExistsInSystemException
AlreadyExistsInSystemException(String, Object) - Constructor for exception class ubic.gemma.core.loader.util.AlreadyExistsInSystemException
ALT_LABEL - Enum constant in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia
AlternateName - Class in ubic.gemma.model.expression.arrayDesign: Hibernate Search 7 mapping: contributes its AlternateName.getName() as a tokenized field to ArrayDesign's document via @IndexedEmbedded.
AlternateName() - Constructor for class ubic.gemma.model.expression.arrayDesign.AlternateName
AlternateName.Factory - Class in ubic.gemma.model.expression.arrayDesign
alternativeLabel - Static variable in class ubic.gemma.core.ontology.jena.IAO
alternativeToProperAffyPlatform(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
AMOUNT - Enum constant in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Referring to a measured or derived "amount", indicating the relative or absolute level of something.
AMPLICON - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
Analysis - Class in ubic.gemma.model.analysis: An analysis of one or more Investigations.
Analysis() - Constructor for class ubic.gemma.model.analysis.Analysis: No-arg constructor added to satisfy javabean contract
ANALYSIS - Enum constant in enum class ubic.gemma.cli.util.CLI.CommandGroup
AnalysisDao<T> - Interface in ubic.gemma.persistence.service.analysis
analysisDescription() - Method in record class ubic.gemma.core.security.audit.payload.DifferentialExpressionAnalysisPayload: Returns the value of the analysisDescription record component.
AnalysisException - Exception Class in ubic.gemma.core.analysis.expression.diff: Base exception for all differential analysis-related exceptions.
AnalysisException(String, DifferentialExpressionAnalysisConfig) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.AnalysisException
AnalysisException(DifferentialExpressionAnalysisConfig, Throwable) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.AnalysisException
AnalysisRef(Long, String, Long) - Constructor for class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef
AnalysisResult - Class in ubic.gemma.model.analysis: Abstract class representing a single result from an Analysis and a typical part of an AnalysisResultSet.
AnalysisResult() - Constructor for class ubic.gemma.model.analysis.AnalysisResult
AnalysisResultSet<R> - Class in ubic.gemma.model.analysis: An abstract class representing a related set of generic analysis results, part of an analysis.
AnalysisResultSet() - Constructor for class ubic.gemma.model.analysis.AnalysisResultSet: No-arg constructor added to satisfy javabean contract
AnalysisResultSetDao<K,O> - Interface in ubic.gemma.persistence.service.analysis: Generic DAO for manipulating AnalysisResultSet.
AnalysisResultSetService<K,O> - Interface in ubic.gemma.persistence.service.analysis: Interface for services providing AnalysisResultSet.
AnalysisResultSetsWebService - Class in ubic.gemma.rest: Endpoint for AnalysisResultSet
AnalysisResultSetsWebService() - Constructor for class ubic.gemma.rest.AnalysisResultSetsWebService
AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject - Class in ubic.gemma.rest: Similar to PaginatedResponseDataObject, but the data.results is paginated instead of data
AnalysisResultSetsWebService.PvalueDistributionResponseDataObject - Class in ubic.gemma.rest: Concrete ResponseDataObject type for the pvalueDistribution endpoint so Swagger has a non-generic schema to reference.
AnalysisResultSetValueObject<K,R> - Class in ubic.gemma.model.analysis: Exposes an AnalysisResultSet to the public API.
AnalysisResultSetValueObject() - Constructor for class ubic.gemma.model.analysis.AnalysisResultSetValueObject
AnalysisResultSetValueObject(Long) - Constructor for class ubic.gemma.model.analysis.AnalysisResultSetValueObject
AnalysisResultSetValueObject(R) - Constructor for class ubic.gemma.model.analysis.AnalysisResultSetValueObject
AnalysisResultValueObject<A> - Class in ubic.gemma.model.analysis: Wraps an AnalysisResult to expose it on the public API.
AnalysisResultValueObject() - Constructor for class ubic.gemma.model.analysis.AnalysisResultValueObject
AnalysisResultValueObject(A) - Constructor for class ubic.gemma.model.analysis.AnalysisResultValueObject
AnalysisService<T> - Interface in ubic.gemma.persistence.service.analysis: Provides basic services for dealing with analyses
AnalysisSuitabilityEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Used for indication of the suitability, or unsuitability, of an entity for a particular type of analysis.
AnalysisSuitabilityEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AnalysisSuitabilityEvent
AnalysisType - Enum Class in ubic.gemma.core.analysis.expression.diff: Defines the different types of analyses our linear modeling framework supports: GENERICLM - generic linear regression (interactions are omitted, but this could change) OSTTEST - one sample t-test OWA - one-way ANOVA TTEST - two sample t-test TWO_WAY_ANOVA_WITH_INTERACTION TWO_WAY_ANOVA_NO_INTERACTION
AnalysisUtilService - Interface in ubic.gemma.core.analysis.expression
AnalysisUtilServiceImpl - Class in ubic.gemma.core.analysis.expression: Utility methods for dealing with analyses.
AnalysisUtilServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.AnalysisUtilServiceImpl
AnalysisValueObject<T> - Class in ubic.gemma.model.analysis
AnalysisValueObject() - Constructor for class ubic.gemma.model.analysis.AnalysisValueObject
AnalysisValueObject(T) - Constructor for class ubic.gemma.model.analysis.AnalysisValueObject
AnalyticsApplicationEventListener - Class in ubic.gemma.rest.providers: Register AnalyticsRequestEventListener
AnalyticsApplicationEventListener() - Constructor for class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
AnalyticsConfig - Class in ubic.gemma.rest.analytics.ga4: Java replacement for applicationContext-analytics.xml, wiring the Google Analytics 4 provider used by the gemma-rest module's request/event listeners.
AnalyticsConfig() - Constructor for class ubic.gemma.rest.analytics.ga4.AnalyticsConfig
AnalyticsProvider - Interface in ubic.gemma.rest.analytics: Interface for analytics providers.
AnalyticsRequestEventListener - Class in ubic.gemma.rest.providers: Request event listener that publishes an event when a request is finished.
AnalyticsRequestEventListener(String, Date, AnalyticsProvider) - Constructor for class ubic.gemma.rest.providers.AnalyticsRequestEventListener
analyze(Collection) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService
analyze(Collection) - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceImpl
and() - Method in class ubic.gemma.persistence.util.Filters: Start a new clause.
and() - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder: Shortcut for build and starting a new clause.
and(String, String, Class, Filter.Operator, Collection) - Method in class ubic.gemma.persistence.util.Filters: Add a new clause of one explicit clause with a collection right hand side to to the conjunction.
and(String, String, Class, Filter.Operator, Collection, String) - Method in class ubic.gemma.persistence.util.Filters
and(String, String, Class, Filter.Operator, T) - Method in class ubic.gemma.persistence.util.Filters: Add a clause of one explicit clause to the conjunction.
and(String, String, Class, Filter.Operator, T, String) - Method in class ubic.gemma.persistence.util.Filters
and(String, String, Class, Filter.Operator, Subquery) - Method in class ubic.gemma.persistence.util.Filters
and(String, String, Class, Filter.Operator, Subquery, String) - Method in class ubic.gemma.persistence.util.Filters
and(Filter...) - Method in class ubic.gemma.persistence.util.Filters: Add a clause of one or more Filter sub-clauses to the conjunction.
and(Filters) - Method in class ubic.gemma.persistence.util.Filters: Add all the clauses of another filter to this.
andThen(Sort) - Method in class ubic.gemma.persistence.util.Sort: Add a next sort.
AnnData - Class in ubic.gemma.core.loader.util.anndata
ANNDATA - Enum constant in enum class ubic.gemma.core.loader.expression.singleCell.SingleCellDataType: AnnData
AnnDataDetector - Class in ubic.gemma.core.loader.expression.geo.singleCell: Detects AnnData in GEO series.
AnnDataDetector() - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.AnnDataDetector
AnnDataException - Exception Class in ubic.gemma.core.loader.util.anndata
AnnDataException(String) - Constructor for exception class ubic.gemma.core.loader.util.anndata.AnnDataException
AnnDataSingleCellDataLoader - Class in ubic.gemma.core.loader.expression.singleCell: Reads single-cell vectors from the AnnData on-disk HDF5 format.
AnnDataSingleCellDataLoader(Path) - Constructor for class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
AnnDataSingleCellDataLoaderConfig - Class in ubic.gemma.core.loader.expression.singleCell: A configuration for loading single-cell data form AnnData format.
AnnDataSingleCellDataLoaderConfig(AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder) - Constructor for class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C,B> - Class in ubic.gemma.core.loader.expression.singleCell
AnnDataSingleCellDataLoaderConfigBuilder() - Constructor for class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
AnnDataSingleCellDataLoaderConfigurer - Class in ubic.gemma.core.loader.expression.singleCell
AnnDataSingleCellDataLoaderConfigurer(Path, Collection, BioAssayMapper, SingleCellDataTransformationFactory) - Constructor for class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfigurer
Annotation(String, String) - Constructor for class ubic.gemma.core.ontology.FactorValueOntologyUtils.Annotation
ANNOTATION_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
AnnotationAssociation - Class in ubic.gemma.model.genome.sequenceAnalysis: An association between BioSequence and GeneProduct that is provided through an external annotation source, rather than our own sequence analysis.
AnnotationAssociation() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
AnnotationAssociation.Factory - Class in ubic.gemma.model.genome.sequenceAnalysis
AnnotationAssociationDao - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
AnnotationAssociationDaoImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis
AnnotationAssociationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
AnnotationAssociationReadService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis: Read-only retrieval service for AnnotationAssociation.
AnnotationAssociationReadServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis: Implementation of AnnotationAssociationReadService.
AnnotationAssociationReadServiceImpl(AnnotationAssociationDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationReadServiceImpl
AnnotationAssociationService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
AnnotationAssociationServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis
AnnotationAssociationServiceImpl(AnnotationAssociationDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationServiceImpl
AnnotationBasedGeneMappingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: To signify the array design was mapped from an external source, not by our own sequence analysis.
AnnotationBasedGeneMappingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationBasedGeneMappingEvent
AnnotationCategoryValueObject(String, String, List, List) - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationCategoryValueObject
AnnotationDrivenSchedulingConfig - Class in ubic.gemma.core.config: Turns on annotation-driven scheduling (@Scheduled) for real deployments.
AnnotationDrivenSchedulingConfig() - Constructor for class ubic.gemma.core.config.AnnotationDrivenSchedulingConfig
AnnotationDto() - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
AnnotationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
AnnotationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationEvent
AnnotationIds(String, String, String) - Constructor for class ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
annotationOf - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Inverse of TGFVO.hasAnnotation.
AnnotationProperty - Interface in ubic.gemma.core.ontology.model
AnnotationRelation - Class in ubic.gemma.model.common.description: One term stands in some relation to another term: subject — predicate → object, plus where that came from.
AnnotationRelation() - Constructor for class ubic.gemma.model.common.description.AnnotationRelation
AnnotationRelationBasis - Enum Class in ubic.gemma.model.common.description: How an AnnotationRelation came to be known, ranked best first.
AnnotationRelationDao - Interface in ubic.gemma.persistence.service.common.description: Reads over AnnotationRelation.
AnnotationRelationDao.Direction - Enum Class in ubic.gemma.persistence.service.common.description: Which end of the relation a caller is seeding from.
AnnotationRelationDao.RelationQuery - Class in ubic.gemma.persistence.service.common.description: What to look for.
AnnotationRelationDao.RelationSummary - Class in ubic.gemma.persistence.service.common.description: A relation aggregated over its attesting experiments, for one basis.
AnnotationRelationDao.RelationSummary.RelationSummaryBuilder - Class in ubic.gemma.persistence.service.common.description
AnnotationRelationDaoImpl - Class in ubic.gemma.persistence.service.common.description: Hibernate implementation of AnnotationRelationDao.
AnnotationRelationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoImpl
AnnotationRelationService - Interface in ubic.gemma.persistence.service.common.description: Read access to the relations Gemma knows between annotation terms.
AnnotationRelationServiceImpl - Class in ubic.gemma.persistence.service.common.description: Read-only service over AnnotationRelationDao.
AnnotationRelationServiceImpl(AnnotationRelationDao) - Constructor for class ubic.gemma.persistence.service.common.description.AnnotationRelationServiceImpl
AnnotationRelationStatus - Enum Class in ubic.gemma.model.common.description: Whether a source is stating that a relation holds, or stating that it does not.
AnnotationReplaceReport(Long, int, int, List, List, int, List, List) - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport: Creates a new AnnotationReplaceReport instance.
AnnotationSearchBatchRequest() - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
AnnotationSearchBatchResultValueObject(String, String, List, String) - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchResultValueObject
AnnotationSearchBatchResultValueObject(String, String, List, String, AnnotationsWebService.NegativeEvidenceValueObject) - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchResultValueObject
AnnotationSearchRankingStrategy - Interface in ubic.gemma.rest.ranking: Strategy hook for re-ordering a flat list of annotation-search hits before they are wrapped in the response value-object and returned to the client.
AnnotationSearchResponseDataObject(List, AnnotationsWebService.NegativeEvidenceValueObject) - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResponseDataObject
AnnotationSearchResponseDataObject(List, AnnotationsWebService.NegativeEvidenceValueObject, List) - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResponseDataObject
AnnotationSearchResultValueObject(String, String, String, String, Integer, String, List, String, String, Long, Map, Long, String, String, AnnotationsWebService.ExampleUsageValueObject, Long, AnnotationsWebService.LexicalTermMetadataValueObject, AnnotationsWebService.TaxonConstraintValueObject, Boolean) - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Creates a new AnnotationSearchResultValueObject instance.
AnnotationSet - Class in ubic.gemma.model.common.auditAndSecurity.curation: A "curation hypothesis" attached to an Investigation: a JSON description of one annotation set in one of three lifecycle shapes (see AnnotationSetRole).
AnnotationSet() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
AnnotationSetDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: DAO for AnnotationSet rows.
AnnotationSetDao.SummarySort - Enum Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Field a cross-experiment listing is ordered by.
AnnotationSetDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Hibernate implementation of AnnotationSetDao.
AnnotationSetDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
AnnotationSetDisposition - Class in ubic.gemma.model.common.auditAndSecurity.curation: One ruling on one finding inside an AnnotationSet.
AnnotationSetDisposition() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
AnnotationSetDispositionDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: DAO for AnnotationSetDisposition rows — a curator's rulings on the individual findings inside an audit set.
AnnotationSetDispositionDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Hibernate implementation of AnnotationSetDispositionDao.
AnnotationSetDispositionDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDaoImpl
AnnotationSetDispositionService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: A curator's rulings on the individual findings inside an audit AnnotationSet.
AnnotationSetDispositionServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Default AnnotationSetDispositionService.
AnnotationSetDispositionServiceImpl(AnnotationSetDispositionDao) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionServiceImpl
AnnotationSetEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted when an AnnotationSet row is appended to a PreboardedExperiment (or, for the private curation API, to a loaded ExpressionExperiment).
AnnotationSetEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationSetEvent
annotationSetId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.ClearDispositionsResponse
annotationSetId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse
annotationSetId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageResponse
annotationSetId - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionRequest: The proposal answered.
annotationSetId - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
annotationSetId - Variable in class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
AnnotationSetPayloadCounts - Class in ubic.gemma.model.common.auditAndSecurity.curation: How many factors and tags an annotation-set payload proposes.
AnnotationSetRequest() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
AnnotationSetResponse() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
AnnotationSetRole - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Role discriminator on AnnotationSet rows.
AnnotationSetService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Service surface for AnnotationSet rows.
AnnotationSetService.AttachedAnnotationSet - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Return value of AnnotationSetService.attach(Investigation, AnnotationSetRole, AnnotationSetSource, AgentCurationKind, String, String, String, String, Date, String, AnnotationSet).
AnnotationSetService.RunProvenance - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Who produced an annotation set, and from which build.
AnnotationSetServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Default AnnotationSetService implementation.
AnnotationSetServiceImpl(AnnotationSetDao) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
AnnotationSetSnapshotResponse() - Constructor for class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
AnnotationSetSource - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Source discriminator on AnnotationSet rows.
annotationSetsRebound - Variable in class ubic.gemma.rest.PreboardedWebService.PromoteResponse
AnnotationSetSummaryResponse() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
AnnotationSetSummaryValueObject - Class in ubic.gemma.model.common.auditAndSecurity.curation: Thin metadata projection of an AnnotationSet row, served by the REST surface when ?shape=meta is requested.
AnnotationSetSummaryValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
AnnotationSetSummaryValueObject(Long, AnnotationSetRole, AnnotationSetSource, AgentCurationKind, String, String, Date, Date, Date, String, String, String, String, String, Date, Long, Long, Long, String, Integer, Integer, String) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: Projection constructor used by the HQL SELECT NEW ... query in AnnotationSetDaoImpl.
AnnotationSetsWebService - Class in ubic.gemma.rest: REST surface for the unified AnnotationSet entity.
AnnotationSetsWebService() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService
AnnotationSetsWebService.AnnotationSetRequest - Class in ubic.gemma.rest: Body for AnnotationSetsWebService.submitAnnotationSet(DatasetArg, AnnotationSetsWebService.AnnotationSetRequest).
AnnotationSetsWebService.AnnotationSetResponse - Class in ubic.gemma.rest: Full-payload response shape.
AnnotationSetsWebService.AnnotationSetSummaryResponse - Class in ubic.gemma.rest: Thin metadata response shape (no payloadJson).
AnnotationSetsWebService.ClearDispositionsResponse - Class in ubic.gemma.rest: Body of AnnotationSetsWebService.clearDispositions(Long).
AnnotationSetsWebService.DispositionRequest - Class in ubic.gemma.rest: Body for AnnotationSetsWebService.ruleOnFinding(Long, String, AnnotationSetsWebService.DispositionRequest).
AnnotationSetsWebService.DispositionResponse - Class in ubic.gemma.rest: Wire shape of one per-finding ruling.
AnnotationSetsWebService.FinalizeRequest - Class in ubic.gemma.rest: Body for AnnotationSetsWebService.finalizeAnnotationSet(Long, String, AnnotationSetsWebService.FinalizeRequest); optional, and one field.
AnnotationSetsWebService.ProvenanceRequest - Class in ubic.gemma.rest: Body for AnnotationSetsWebService.updateAnnotationSetProvenance(Long, AnnotationSetsWebService.ProvenanceRequest).
AnnotationSetsWebService.StatusRequest - Class in ubic.gemma.rest: Body for AnnotationSetsWebService.setAnnotationSetStatus(Long, AnnotationSetsWebService.StatusRequest).
AnnotationSetsWebService.TriageRequest - Class in ubic.gemma.rest: Body for AnnotationSetsWebService.triageAnnotationSet(Long, String, AnnotationSetsWebService.TriageRequest).
AnnotationSetsWebService.TriageResponse - Class in ubic.gemma.rest: Wire shape of one triage ruling.
AnnotationSetsWebService.UpsertDraftRequest - Class in ubic.gemma.rest: Body for AnnotationSetsWebService.upsertDraftForDataset(DatasetArg, String, AnnotationSetsWebService.UpsertDraftRequest).
AnnotationSetTriage - Class in ubic.gemma.model.common.auditAndSecurity.curation: One judge's standing ruling on how much an AnnotationSet matters.
AnnotationSetTriage() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
AnnotationSetTriageDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: DAO for AnnotationSetTriage rows — one standing ruling per (annotation set, judge).
AnnotationSetTriageDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Hibernate implementation of AnnotationSetTriageDao.
AnnotationSetTriageDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDaoImpl
AnnotationSetTriageService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Triage rulings on AnnotationSets: how much a set matters, one standing judgement per judge.
AnnotationSetTriageServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Default AnnotationSetTriageService.
AnnotationSetTriageServiceImpl(AnnotationSetTriageDao) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
AnnotationsReplaceRequest() - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationsReplaceRequest
AnnotationsUpdateRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.AnnotationsUpdateRequest
AnnotationsWebService - Class in ubic.gemma.rest: RESTful interface for annotations.
AnnotationsWebService() - Constructor for class ubic.gemma.rest.AnnotationsWebService: Required by spring
AnnotationsWebService(OntologyService, SearchService, CharacteristicService, ExpressionExperimentService, DatasetArgService, TaxonArgService) - Constructor for class ubic.gemma.rest.AnnotationsWebService: Back-compat constructor for tests that wire only the core collaborators.
AnnotationsWebService(OntologyService, SearchService, CharacteristicService, ExpressionExperimentService, DatasetArgService, TaxonArgService, GeneService, Map) - Constructor for class ubic.gemma.rest.AnnotationsWebService: Constructor for service autowiring
AnnotationsWebService.AnnotationCategoryValueObject - Class in ubic.gemma.rest: Wire shape for GET /annotations/categories — carries the ontology term info plus a preferred-prefix list per category (config-driven via annotation.category.prefixes).
AnnotationsWebService.AnnotationDto - Class in ubic.gemma.rest
AnnotationsWebService.AnnotationRelationValueObject - Class in ubic.gemma.rest: A relation on the wire.
AnnotationsWebService.AnnotationReplaceReport - Class in ubic.gemma.rest: Diff-and-apply summary returned by the bulk PUT.
AnnotationsWebService.AnnotationSearchBatchRequest - Class in ubic.gemma.rest: Request body for AnnotationsWebService.searchAnnotationsBatch(AnnotationsWebService.AnnotationSearchBatchRequest).
AnnotationsWebService.AnnotationSearchBatchRequest.Item - Class in ubic.gemma.rest: One batch item: a literal label plus its optional per-item category hint.
AnnotationsWebService.AnnotationSearchBatchResultValueObject - Class in ubic.gemma.rest
AnnotationsWebService.AnnotationSearchResponseDataObject - Class in ubic.gemma.rest: GET /annotations/search envelope: the standard data array plus, when identity matching ran, the AnnotationsWebService.NegativeEvidenceValueObject beside it.
AnnotationsWebService.AnnotationSearchResultValueObject - Class in ubic.gemma.rest
AnnotationsWebService.AnnotationsReplaceRequest - Class in ubic.gemma.rest: Request body for AnnotationsWebService.replaceDatasetAnnotations(DatasetArg, AnnotationsWebService.AnnotationsReplaceRequest): the full desired tag set plus an optional annotationSetId to attach to emitted audit events (linkage is parked until the source-AnnotationSet → emitted-event audit link lands — see STATUS_PUT_DATASETS_DESIGN.md).
AnnotationsWebService.CanonicalUriValueObject - Class in ubic.gemma.rest: One row of the canonicalization table: the URI as stored, and the URI Gemma reports instead.
AnnotationsWebService.ExampleUsageValueObject - Class in ubic.gemma.rest: A single representative usage of a searched term, for showing a hit in context.
AnnotationsWebService.ExternalIdentificationValueObject - Class in ubic.gemma.rest: What an external naming authority says a query string is, when nothing Gemma has loaded names it — plus enough provenance to check the claim.
AnnotationsWebService.LexicalTermMetadataValueObject - Class in ubic.gemma.rest: Wire shape for LexicalTermMetadata.
AnnotationsWebService.MatchedVia - Enum Class in ubic.gemma.rest: JSON-friendly enumeration of which Lucene field produced a hit.
AnnotationsWebService.NegativeEvidenceValueObject - Class in ubic.gemma.rest
AnnotationsWebService.OntologyTermSimpleValueObject - Class in ubic.gemma.rest
AnnotationsWebService.OntologyTermSynonymValueObject - Class in ubic.gemma.rest: A single synonym of an ontology term plus its scope.
AnnotationsWebService.OntologyTermValueObject - Class in ubic.gemma.rest
AnnotationsWebService.PriorCurationValueObject - Class in ubic.gemma.rest: A term prior curators chose for the query string, with the number of distinct experiments they chose it on.
AnnotationsWebService.RuledOutTermValueObject - Class in ubic.gemma.rest: One term that was retrieved for the query and rejected as not naming it.
AnnotationsWebService.TaxonConstraintValueObject - Class in ubic.gemma.rest: What the ontology says about this term's species applicability.
AnnotationsWebService.TaxonValueObject - Class in ubic.gemma.rest: An organism an entry derives from.
AnnotationTagInput() - Constructor for class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
AnnotationValueObject - Class in ubic.gemma.model.common.description
AnnotationValueObject() - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationValueObject(Long) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationValueObject(String, String, String, String, Class) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationValueObject(Characteristic) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationValueObject(Characteristic, Class) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationWithUsageStatisticsValueObject(Characteristic, Long, Set) - Constructor for class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject
ANONYMOUS_USER - Static variable in class ubic.gemma.rest.servlet.RequestIdMdcFilter
AnonymousFTPCLientAuthenticator - Class in ubic.gemma.core.loader.util.ftp
AnonymousFTPCLientAuthenticator() - Constructor for class ubic.gemma.core.loader.util.ftp.AnonymousFTPCLientAuthenticator
anova() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: Compute ANOVA based on the model fit (Type I SSQ, sequential)
AnovaEffect - Class in ubic.gemma.core.util.math.linearmodels: Represents one row of an ANOVA table
AnovaEffect(String, double, double, double, double, boolean, boolean) - Constructor for class ubic.gemma.core.util.math.linearmodels.AnovaEffect
AnovaResult - Interface in ubic.gemma.core.util.math.linearmodels
AnsiEscapeCodes - Class in ubic.gemma.cli.util: Generate various ANSI escape codes.
AnsiEscapeCodes() - Constructor for class ubic.gemma.cli.util.AnsiEscapeCodes
antibody - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
ANY - Enum constant in enum class ubic.gemma.persistence.util.SubqueryMode: Produce a clause of the form id in {subquery}.
ANY - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
ANY - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
ANY() - Method in class ubic.gemma.rest.util.args.FilterArgParser.QuantifierContext
ANY() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
anyOf(Predicate...) - Static method in class ubic.gemma.cli.util.OptionsUtils: Make sure that at least one of the given predicate is true.
anyPublicMethod() - Method in class ubic.gemma.persistence.util.Pointcuts: A public method.
AOI_ALIAS - Static variable in class ubic.gemma.persistence.util.AclQueryUtils: Alias used for the object identity AclObjectIdentity and the owner identity AclSid inside the EXISTS body.
ApiInfoValueObject(String, OpenAPI, URI, URI, List, BuildInfo) - Constructor for class ubic.gemma.rest.RootWebService.ApiInfoValueObject
apiVersion(String) - Method in class ubic.gemma.rest.util.ResponseErrorObject.ResponseErrorObjectBuilder: API version.
appearsInMultipleSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
append(String, String, String) - Static method in class ubic.gemma.core.util.StringUtil
append(LogEvent) - Method in class ubic.gemma.core.logging.log4j.ProgressUpdateAppender
append(LogEvent) - Method in class ubic.gemma.core.logging.log4j.SlackAppender
appendBaseHeader(String, BuildInfo, Date, Writer) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils
appendBaseHeader(String, BuildInfo, Date, Writer) - Static method in class ubic.gemma.core.util.TsvUtils: Append a base header to a file.
appendBaseHeader(ExpressionExperiment, String, String, BuildInfo, Date, Writer) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils: Appends base header information (about the experiment) to a file.
appendBaseHeader(ExpressionExperiment, QuantitationType, Class, String, String, BuildInfo, Date, Writer) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils: Append base header information (about the experiment) to a file with some information about the quantitation type.
appendToDescription(QuantitationType, String) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils: Append a suffix to a QuantitationType description.
appendWithDelimiter(String, String) - Static method in class ubic.gemma.core.util.StringUtils
appendWithDelimiter(String, String, String) - Static method in class ubic.gemma.core.util.StringUtils: Append a suffix to a string, with a delimiter if the string is not empty.
APPLICATION_10X_MEX - Static variable in class ubic.gemma.rest.DatasetsWebService: Cell Ranger Feature Barcode Matrices (MEX Format)
APPLICATION_10X_MEX_TYPE - Static variable in class ubic.gemma.rest.DatasetsWebService
applied() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage: Returns the value of the applied record component.
appliedProposalId - Variable in class ubic.gemma.rest.PreboardedWebService.PromoteResponse
appliesTo(T) - Method in interface ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter: Check if the filter is applicable to the given data matrix.
appliesTo(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.LowVarianceFilter
appliesTo(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter
appliesTo(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter
appliesTo(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilter
apply() - Method in class ubic.gemma.cli.logging.log4j.Log4jConfigurer
apply() - Method in interface ubic.gemma.cli.logging.LoggingConfigurer: Apply pending changes to the configuration.
apply(String) - Method in class ubic.gemma.cli.util.EnumConverter
apply(String) - Method in class ubic.gemma.cli.util.EnumeratedByCommandStringConverter
apply(String) - Method in class ubic.gemma.cli.util.EnumeratedStringConverter
apply(Collection, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.ObsoleteTermCorrectionService: Apply the corrections.
apply(Collection, boolean, long, TimeUnit) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceImpl
apply10xFilter(Boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder: Filter 10x MEX data to remove low-quality cells.
applyDesignChange(ExpressionExperiment, ExperimentalDesignValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Apply proposed as the experiment's new ExperimentalDesign.
applyDesignChange(ExpressionExperiment, ExperimentalDesignValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
applyDesignChange(DatasetArg, ExperimentalDesignValueObject, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Validate and apply a proposed design replacement.
applyFixes(boolean) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder: If true, attempt to fix any issues are found.
applyLastEventTriple(AbstractCuratableValueObject.LastEventTriple) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject: Apply a batched AbstractCuratableValueObject.LastEventTriple onto this VO.
applyLatestProposal - Variable in class ubic.gemma.rest.PreboardedWebService.PromoteRequest
applyObsoleteTermCorrections(Boolean, List, Integer) - Method in class ubic.gemma.rest.AdminWebService: Rewrite annotations that use an obsolete ontology term to the successor its ontology asserts.
applyTo(List) - Method in interface ubic.gemma.persistence.hibernate.TypedResultTransformer: Apply this transformer to a list of rows that were fetched without the transformer wired into the query.
applyToIndicesMatchingCriteria(DoubleMatrix1D, DoubleFunction, DoubleFunction) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
ArchiveBasedSingleCellDetector - Interface in ubic.gemma.core.loader.expression.geo.singleCell: Interface implemented by SingleCellDetector have the capabilities of looking-up archives.
ArchiveFetcher - Interface in ubic.gemma.core.loader.util.fetcher: Interface defining a class that downloads archives and unpacks them.
areAllElementsAssignable(Class, Collection) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter
arePrivate(Collection) - Method in interface ubic.gemma.core.security.SecurityService: Check if the given securables are private.
arePrivate(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
arePublic(Collection) - Method in interface ubic.gemma.core.security.SecurityService: Check if the given securables are public.
arePublic(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
areShared(Collection) - Method in interface ubic.gemma.core.security.SecurityService: Check if the given securable are shared.
areShared(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
Arg<T> - Interface in ubic.gemma.rest.util.args
ArgUtils - Class in ubic.gemma.rest.util: Utilities for working with Arg.
ArgUtils() - Constructor for class ubic.gemma.rest.util.ArgUtils
aroundWriteTo(WriterInterceptorContext) - Method in class ubic.gemma.rest.providers.AbstractGzipHeaderDecorator
aroundWriteTo(WriterInterceptorContext) - Method in class ubic.gemma.rest.providers.CacheControlHeaderDecorator
Array<T> - Interface in ubic.gemma.core.loader.util.anndata
ARRAY - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
ARRAY_DESIGN - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetType
ARRAY_EXPRESS - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
ARRAY_SCHEMA_COMPRESSION_DESCRIPTION - Static variable in class ubic.gemma.rest.util.args.AbstractArrayArg: A description of the base64-gzip encoding to use in array schema descriptions in subclasses.
ARRAY_SCHEMA_DESCRIPTION - Static variable in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg
ARRAY_SCHEMA_DESCRIPTION - Static variable in class ubic.gemma.rest.util.args.DatabaseEntryArrayArg
ARRAY_SCHEMA_DESCRIPTION - Static variable in class ubic.gemma.rest.util.args.DatasetArrayArg
ARRAY_SCHEMA_DESCRIPTION - Static variable in class ubic.gemma.rest.util.args.GeneArrayArg
ARRAY_SCHEMA_DESCRIPTION - Static variable in class ubic.gemma.rest.util.args.PlatformArrayArg
ARRAY_SCHEMA_DESCRIPTION - Static variable in class ubic.gemma.rest.util.args.StringArrayArg
ARRAY_SCHEMA_DESCRIPTION - Static variable in class ubic.gemma.rest.util.args.TaxonArrayArg
ARRAY_SCHEMA_DESCRIPTION_PREFIX - Static variable in class ubic.gemma.rest.util.args.AbstractArrayArg: Prefix to use to describe the array schema in subclasses.
arrayCGH - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
ArrayDesign - Class in ubic.gemma.model.expression.arrayDesign: Represents an assembly of design elements that are assayed all at once.
ArrayDesign() - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesign: No-arg constructor added to satisfy javabean contract
ArrayDesign.Factory - Class in ubic.gemma.model.expression.arrayDesign
ArrayDesignAlternativePopulateCli - Class in ubic.gemma.apps: This only needs to be re-run when the mappings change.
ArrayDesignAlternativePopulateCli() - Constructor for class ubic.gemma.apps.ArrayDesignAlternativePopulateCli
ArrayDesignAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: An event involving the analysis of an ArrayDesign
ArrayDesignAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent
ArrayDesignAnnotationFileCli - Class in ubic.gemma.apps: Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or merged into another AD.
ArrayDesignAnnotationFileCli() - Constructor for class ubic.gemma.apps.ArrayDesignAnnotationFileCli
ArrayDesignAnnotationService - Interface in ubic.gemma.core.analysis.service: Methods to generate annotations for array designs, based on information already in the database.
ArrayDesignAnnotationService.OutputType - Enum Class in ubic.gemma.core.analysis.service
ArrayDesignAnnotationServiceImpl - Class in ubic.gemma.core.analysis.service
ArrayDesignAnnotationServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
ArrayDesignAuditTrailCleanupCli - Class in ubic.gemma.apps: work in progress
ArrayDesignAuditTrailCleanupCli() - Constructor for class ubic.gemma.apps.ArrayDesignAuditTrailCleanupCli
ArrayDesignBioSequenceDetachCli - Class in ubic.gemma.apps: Remove all associations that this array design has with BioSequences.
ArrayDesignBioSequenceDetachCli() - Constructor for class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli
ArrayDesignBlatCli - Class in ubic.gemma.apps: Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
ArrayDesignBlatCli() - Constructor for class ubic.gemma.apps.ArrayDesignBlatCli
ArrayDesignDao - Interface in ubic.gemma.persistence.service.expression.arrayDesign: Created by tesarst on 13/03/17.
ArrayDesignDaoImpl - Class in ubic.gemma.persistence.service.expression.arrayDesign
ArrayDesignDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
ArrayDesignGeneMappingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: The mapping of probes to genes for an ArrayDesign
ArrayDesignGeneMappingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignGeneMappingEvent
ArrayDesignMapResultService - Interface in ubic.gemma.core.analysis.sequence
ArrayDesignMapResultServiceImpl - Class in ubic.gemma.core.analysis.sequence: Supports obtaining detailed information about the sequence analysis of probes on microarrays.
ArrayDesignMapResultServiceImpl(BlatResultReadService, BlatAssociationReadService, ArrayDesignService, CompositeSequenceService) - Constructor for class ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl
ArrayDesignMapSummaryCli - Class in ubic.gemma.apps: CLI for ArrayDesignMapSummaryService
ArrayDesignMapSummaryCli() - Constructor for class ubic.gemma.apps.ArrayDesignMapSummaryCli
ArrayDesignMergeAuditService - Interface in ubic.gemma.core.loader.expression.arrayDesign: Co-bean carrying the ArrayDesignMergeEvent emission that ArrayDesignMergeHelperServiceImpl.persistMerging(ArrayDesign, ArrayDesign, Collection, boolean, Collection) records against each participating platform.
ArrayDesignMergeAuditServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign: Implementation of ArrayDesignMergeAuditService: a thin co-bean that exists so each ArrayDesignMergeAuditServiceImpl.recordMerge(ArrayDesign, String) call is invoked through a Spring proxy and the Audited aspect can intercept it and emit the ArrayDesignMergeEvent.
ArrayDesignMergeAuditServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeAuditServiceImpl
ArrayDesignMergeCli - Class in ubic.gemma.apps: make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees Separate operations: For an EE, Remap DesignElement references to old array designs to new one, and old BioAssay AD refs to new one.
ArrayDesignMergeCli() - Constructor for class ubic.gemma.apps.ArrayDesignMergeCli
ArrayDesignMergeEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
ArrayDesignMergeEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignMergeEvent
ArrayDesignMergeHelperService - Interface in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignMergeHelperServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignMergeHelperServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperServiceImpl
ArrayDesignMergeService - Interface in ubic.gemma.core.loader.expression.arrayDesign: Make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees
ArrayDesignMergeServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignMergeServiceImpl(ArrayDesignService, ArrayDesignReportService, ArrayDesignMergeHelperService) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceImpl
arrayDesignName - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest
ArrayDesignPersister - Class in ubic.gemma.persistence.persister: Handles persisting array designs.
ArrayDesignPersister() - Constructor for class ubic.gemma.persistence.persister.ArrayDesignPersister
ArrayDesignProbeCleanupCLI - Class in ubic.gemma.apps: Delete design elements (probes) that are invalid for one reason or another.
ArrayDesignProbeCleanupCLI() - Constructor for class ubic.gemma.apps.ArrayDesignProbeCleanupCLI
ArrayDesignProbeMapperCli - Class in ubic.gemma.apps: Process the blat results for an array design to map them onto genes.
ArrayDesignProbeMapperCli() - Constructor for class ubic.gemma.apps.ArrayDesignProbeMapperCli
ArrayDesignProbeMapperService - Interface in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignProbeMapperServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign: For an array design, generate gene product mappings for the sequences.
ArrayDesignProbeMapperServiceImpl(AnnotationAssociationService, ArrayDesignAnnotationService, ArrayDesignReportService, ArrayDesignService, ProbeMapper, BioSequenceService, BlatResultReadService, CompositeSequenceService, ExpressionDataFileService, GeneProductService, GeneService, GenomePersister, GoldenPathSequenceAnalysisFactory, TaskExecutor) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
ArrayDesignProbeMapperTask - Interface in ubic.gemma.core.tasks.analysis.sequence
ArrayDesignProbeMapperTaskImpl - Class in ubic.gemma.core.tasks.analysis.sequence: A probe mapper spaces task .
ArrayDesignProbeMapperTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapperTaskImpl
ArrayDesignProbeMapTaskCommand - Class in ubic.gemma.core.tasks.analysis.sequence: A command object to be used by spaces.
ArrayDesignProbeMapTaskCommand() - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
ArrayDesignProbeMapTaskCommand(String, boolean, ArrayDesign) - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
ArrayDesignProbeRenamingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Signifies that the probes were renamed from their original values.
ArrayDesignProbeRenamingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignProbeRenamingEvent
ArrayDesignReadService - Interface in ubic.gemma.persistence.service.expression.arrayDesign: Thin read-only retrieval service for ArrayDesign.
ArrayDesignReadServiceImpl - Class in ubic.gemma.persistence.service.expression.arrayDesign: Implementation of ArrayDesignReadService.
ArrayDesignReadServiceImpl(ArrayDesignDao, AuditEventDao) - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
ArrayDesignReferenceValueObject - Class in ubic.gemma.model.expression.arrayDesign: Compact platform identity — enough to name a platform and link to it.
ArrayDesignReferenceValueObject() - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject
ArrayDesignReferenceValueObject(Long, String) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: The identity-only form, for the callers that select two columns.
ArrayDesignReferenceValueObject(Long, String, String) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: Identity plus name, for the callers that have no technology type in hand.
ArrayDesignReferenceValueObject(Long, String, String, String) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: Creates a new ArrayDesignReferenceValueObject instance.
ArrayDesignReferenceValueObject.FromArrayDesignValueObject - Class in ubic.gemma.model.expression.arrayDesign: Project a full ArrayDesignValueObject down to this shape at serialization time.
ArrayDesignRepeatAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
ArrayDesignRepeatAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignRepeatAnalysisEvent
ArrayDesignRepeatScanCli - Class in ubic.gemma.apps: Runs repeatmasker on array designs.
ArrayDesignRepeatScanCli() - Constructor for class ubic.gemma.apps.ArrayDesignRepeatScanCli
ArrayDesignRepeatScanTask - Interface in ubic.gemma.core.tasks.analysis.sequence
ArrayDesignRepeatScanTaskCommand - Class in ubic.gemma.core.tasks.analysis.sequence: A command object to be used by spaces.
ArrayDesignRepeatScanTaskCommand(String, ArrayDesign) - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand: NOTE: we can't pass in a we command as they are defined in the web module, which messes up the configuration.
ArrayDesignRepeatScanTaskCommand(ArrayDesign) - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
ArrayDesignRepeatScanTaskImpl - Class in ubic.gemma.core.tasks.analysis.sequence: An array design repeat scan spaces task
ArrayDesignRepeatScanTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskImpl
ArrayDesignReportCli - Class in ubic.gemma.apps: Regenerate the on-disk platform reports — the per-platform element / sequence / alignment / gene counts that ArrayDesignReportService serializes under ${gemma.appdata.home}/ArrayDesignReports.
ArrayDesignReportCli() - Constructor for class ubic.gemma.apps.ArrayDesignReportCli
arrayDesignReportService - Variable in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
ArrayDesignReportService - Interface in ubic.gemma.core.analysis.report
ArrayDesignReportServiceImpl - Class in ubic.gemma.core.analysis.report
ArrayDesignReportServiceImpl() - Constructor for class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
ArrayDesignReportTask - Interface in ubic.gemma.core.tasks.maintenance: Regenerates the cached platform reports in the background.
ArrayDesignReportTaskCommand - Class in ubic.gemma.core.tasks.maintenance: Regenerate the cached on-disk platform reports, either for every platform or for a single one.
ArrayDesignReportTaskCommand(Boolean) - Constructor for class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskCommand
ArrayDesignReportTaskCommand(ArrayDesign) - Constructor for class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskCommand
ArrayDesignReportTaskImpl - Class in ubic.gemma.core.tasks.maintenance
ArrayDesignReportTaskImpl() - Constructor for class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskImpl
arrayDesignReportTrigger(ArrayDesignReportService, SecurityContext) - Method in class ubic.gemma.core.config.SchedulerConfig: Every first of the month at 01:30.
arrayDesignSearch(String) - Static method in class ubic.gemma.model.common.search.SearchSettings: Convenience method to get pre-configured settings.
ArrayDesignSequenceAlignmentService - Interface in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignSequenceAlignmentServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign: Aligns sequences from array designs to the genome, using blat, and persists the blat results.
ArrayDesignSequenceAlignmentServiceImpl(ArrayDesignReportService, ArrayDesignService, BioSequenceService, GenomePersister, GoldenPathQueryFactory) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
ArrayDesignSequenceAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: The sequence alignment analysis of an ArrayDesign
ArrayDesignSequenceAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent
ArrayDesignSequenceAssociationCli - Class in ubic.gemma.apps: Attach sequences to array design, fetching from BLAST database if requested.
ArrayDesignSequenceAssociationCli() - Constructor for class ubic.gemma.apps.ArrayDesignSequenceAssociationCli
ArrayDesignSequenceManipulatingCli - Class in ubic.gemma.apps: Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.
ArrayDesignSequenceManipulatingCli() - Constructor for class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
ArrayDesignSequenceProcessingService - Interface in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignSequenceProcessingServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign: Handles collapsing the sequences, attaching sequences to DesignElements, either from provided input or via a fetch.
ArrayDesignSequenceProcessingServiceImpl(ArrayDesignReportService, ArrayDesignService, BioSequenceService, ExternalDatabaseService, GenomePersister, String) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
ArrayDesignSequenceRemoveEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Used to indicate that all associations that this array design has with BioSequences have been removed.
ArrayDesignSequenceRemoveEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent
ArrayDesignSequenceUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: The updating of the sequences associated with an ArrayDesign
ArrayDesignSequenceUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceUpdateEvent
arrayDesignService - Variable in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
ArrayDesignService - Interface in ubic.gemma.persistence.service.expression.arrayDesign
ArrayDesignServiceImpl - Class in ubic.gemma.persistence.service.expression.arrayDesign
ArrayDesignServiceImpl(ArrayDesignDao) - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
ArrayDesignsForExperimentCache - Class in ubic.gemma.persistence.persister: Used to hold information for matching to a new experiment, during persisting.
ArrayDesignsForExperimentCache() - Constructor for class ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
ArrayDesignSubsumeCheckEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
ArrayDesignSubsumeCheckEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent
ArrayDesignSubsumptionTesterCli - Class in ubic.gemma.apps: Test two array designs to see if one subsumes the other, and if so update their information.
ArrayDesignSubsumptionTesterCli() - Constructor for class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli
ArrayDesignUrl(String, ArrayDesign) - Constructor for class ubic.gemma.persistence.util.EntityUrlBuilder.ArrayDesignUrl
ArrayDesignValueObject - Class in ubic.gemma.model.expression.arrayDesign: Value object for quickly displaying varied information about Array Designs.
ArrayDesignValueObject() - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
ArrayDesignValueObject(Long) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
ArrayDesignValueObject(ArrayDesign) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: This will only work if the object is thawed (lightly).
ArrayDesignValueObject(ArrayDesign, boolean) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Variant of ArrayDesignValueObject(ArrayDesign) that propagates the skipEvents hint up to AbstractCuratableValueObject, letting the caller batch- hydrate the three last*Event associations off CurationDetails post-fetch (via AbstractCuratableValueObject.applyLastEventTriple(AbstractCuratableValueObject.LastEventTriple)) instead of paying ~3 SELECTs per row at construction time.
ArrayDesignValueObject(ArrayDesignValueObject) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Copies constructor from other ArrayDesignValueObject
ArrayDesignWebUrl(String, ArrayDesign) - Constructor for class ubic.gemma.persistence.util.EntityUrlBuilder.ArrayDesignWebUrl
ArrayDesignWithUsageStatisticsValueObject(ArrayDesignValueObject, Long, Long) - Constructor for class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
ArrayExpressUtil - Class in ubic.gemma.core.loader.expression.arrayExpress.util
ArrayExpressUtil() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.util.ArrayExpressUtil
ArrayExpressUtils - Class in ubic.gemma.core.loader.expression.arrayExpress
ArrayExpressUtils() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.ArrayExpressUtils
ArrayUtils - Class in ubic.gemma.core.util: Utilities and algorithms for arrays.
ArrayUtils() - Constructor for class ubic.gemma.core.util.ArrayUtils
ARXIV - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
asArray() - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
asArray() - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
asArray() - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
asArray() - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
asArray() - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
ASC - Enum constant in enum class ubic.gemma.persistence.util.Sort.Direction
ASC - Enum constant in enum class ubic.gemma.rest.util.args.SortArg.Sort.Direction
asDoubles() - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
asDoubles() - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Attempt to coerce the entries into doubles.
asId(Object) - Static method in class ubic.gemma.core.util.SQLUtils: Convert an arbitrary object to a Long ID.
asRegularGoId(String) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyUtils: Convert various GO IDs formats to the usual format, e.g., GO:0039392.
asRegularGoId(OntologyTerm) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyUtils: Convert various GO IDs formats to the usual format, e.g., GO:0039392.
asRegularGoId(Characteristic) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyUtils: Convert a characteristic to a regular GO ID.
ASSAY - Static variable in class ubic.gemma.model.common.description.Categories
assemble(Serializable, Object) - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
assemble(Serializable, Object) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
assertAccepted(Investigation, PublicationAssertion, PublicationAssociationRole) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationService: Record a single acceptance without disturbing the investigation's other assertions.
assertAccepted(Investigation, PublicationAssertion, PublicationAssociationRole) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
ASSERTED - Enum constant in enum class ubic.gemma.model.common.description.AnnotationRelationStatus: The source states the relation holds.
assertRejected(Investigation, PublicationAssertion) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationService: Record that a publication has been ruled out for an investigation, without disturbing its other assertions.
assertRejected(Investigation, PublicationAssertion) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
assign(Ticket, Contact, Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Assign (or re-assign) the ticket.
assign(Ticket, Contact, Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
assign(V) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
assign(V) - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Set all values in the matrix to the given value.
ASSIGNED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType
assigneeContactId - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueResponse
assigneeContactId - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueSummaryResponse
assignSequencesToDesignElements(Collection, File) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Associate sequences with an array design.
assignSequencesToDesignElements(Collection, File) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
assignSequencesToDesignElements(Collection, InputStream) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
assignSequencesToDesignElements(Collection, InputStream) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl: Associate sequences with an array design.
assignSequencesToDesignElements(Collection, Collection) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Associate sequences with an array design.
assignSequencesToDesignElements(Collection, Collection) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
associateBatchFactor(Map, Map) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Associate dates with bioassays and any new factors with the biomaterials.
associateBatchFactor(Map, Map) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
asStatement(Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Return c as a Statement, converting a plain Characteristic if needed.
AsyncFactoryBean<T> - Interface in ubic.gemma.core.context: Async extension of the FactoryBean interface.
ATAC_FRAGMENT - Enum constant in enum class ubic.gemma.core.loader.expression.cellxgene.FileType
ATAC_INDEX - Enum constant in enum class ubic.gemma.core.loader.expression.cellxgene.FileType
ATAC_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
attach(Investigation, AnnotationSetRole, AnnotationSetSource, AgentCurationKind, String, String, String, String, Date, String, AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: Attach (or return existing) an annotation set to the given investigation.
attach(Investigation, AnnotationSetRole, AnnotationSetSource, AgentCurationKind, String, String, String, String, Date, String, AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
attach(Investigation, AnnotationSetRole, AnnotationSetSource, AgentCurationKind, String, String, AnnotationSetService.RunProvenance, String, AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: As AnnotationSetService.attach(Investigation, AnnotationSetRole, AnnotationSetSource, AgentCurationKind, String, String, String, String, Date, String, AnnotationSet), but carrying the full run provenance rather than the agentVersion / model / ranAt triple.
attach(Investigation, AnnotationSetRole, AnnotationSetSource, AgentCurationKind, String, String, AnnotationSetService.RunProvenance, String, AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
attachAnnotationSet(Long, PreboardedWebService.AttachAnnotationSetRequest) - Method in class ubic.gemma.rest.PreboardedWebService: Attach a new annotation set to a preboarded.
AttachAnnotationSetRequest() - Constructor for class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest
attachBioSequence(CriteriaBuilder, From, String, BioSequence, List) - Static method in class ubic.gemma.persistence.util.BusinessKey: Restricts a parent query so that property propertyName matches a BioSequence by business key.
attachDatabaseEntry(CriteriaBuilder, From, String, DatabaseEntry, List) - Static method in class ubic.gemma.persistence.util.BusinessKey: Restrict a parent query so a DatabaseEntry-typed property at propertyName matches by business key.
AttachedAnnotationSet(AnnotationSet, boolean) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.AttachedAnnotationSet
attempt - Variable in class ubic.gemma.core.util.SimpleRetryContext: Indicate the attempt number (zero for first, 1 for second, etc.)
ATTRIBUTE - Static variable in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationQuietReadProvider: The single config attribute string this provider responds to.
ATTRIBUTE - Static variable in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationStreamFilteringProvider
ATTRIBUTE - Static variable in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectCollectionReadProvider: The single config attribute string this provider responds to.
ATTRIBUTE - Static variable in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectMapReadProvider: The single config attribute string this provider responds to.
ATTRIBUTE - Static variable in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectReadProvider: The single config attribute string this provider responds to.
attributesToRetrieveFromBioMartForProteinQuery(String) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher: Method that based on the taxon supplied constructs an array of attributes that can be queried on.
Audit - Enum constant in enum class ubic.gemma.model.expression.experiment.WorkflowState
AUDIT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: An agent audit run — a batch check of existing curation (dispositions, groundings, publication links, …) that opens a ticket to carry its findings.
AUDIT - Enum constant in enum class ubic.gemma.model.expression.experiment.AgentCurationKind
Auditable - Interface in ubic.gemma.model.common.auditAndSecurity: Created by tesarst on 07/03/17.
AuditAction - Enum Class in ubic.gemma.model.common.auditAndSecurity
Audited - Annotation Interface in ubic.gemma.core.security.audit: Method-level annotation requesting that an AuditEvent of the declared type be written to the audit trail of the first Auditable argument after the method returns normally.
AuditedAspect - Class in ubic.gemma.core.security.audit: Spring AOP aspect that backs the Audited annotation.
AuditedAspect(AuditTrailService, ApplicationEventPublisher) - Constructor for class ubic.gemma.core.security.audit.AuditedAspect
AuditedConditional - Annotation Interface in ubic.gemma.core.security.audit: Conditional cousin of Audited.
AuditedEvent - Class in ubic.gemma.core.security.audit: Spring ApplicationEvent published by AuditedAspect every time an Audited-annotated method completes successfully.
AuditedEvent(Object, Auditable, AuditEventType, AuditEventPayload, AuditEvent) - Constructor for class ubic.gemma.core.security.audit.AuditedEvent
AuditedOnError - Annotation Interface in ubic.gemma.core.security.audit: Throwing cousin of Audited / AuditedConditional.
AuditedOnErrors - Annotation Interface in ubic.gemma.core.security.audit: Container annotation for repeated AuditedOnError declarations on a single method.
AuditEvent - Class in ubic.gemma.model.common.auditAndSecurity: An event in the life of an object.
AuditEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEvent
AuditEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity
AuditEventDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
AuditEventDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
AuditEventDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
auditEventId - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowTransitionResponse
AuditEventPayload - Interface in ubic.gemma.core.security.audit: Marker for typed, JSON-serialised payloads carried by an AuditEvent.
AuditEventPayload.None - Record Class in ubic.gemma.core.security.audit: Sentinel payload for events that carry no extra structured data.
auditEventService - Variable in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
auditEventService - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
AuditEventService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
AuditEventServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
AuditEventServiceImpl(AuditEventDao) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
AuditEventType - Class in ubic.gemma.model.common.auditAndSecurity.eventType
AuditEventType() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType
AuditEventValueObject - Class in ubic.gemma.model.common.auditAndSecurity
AuditEventValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject: Required when using the class as a spring bean.
AuditEventValueObject(Long) - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
AuditEventValueObject(AuditEvent) - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
AuditLogger - Class in ubic.gemma.core.security.audit: Logger for created AuditEvent.
AuditLogger() - Constructor for class ubic.gemma.core.security.audit.AuditLogger
Audit Phase C-2: auto-CREATE / auto-DELETE via Hibernate listeners - Section in class ubic.gemma.persistence.audit.AuditTrailEventListener
Audit Phase C-2: PostInsert / PreDelete wired - Section in class ubic.gemma.persistence.audit.AuditTrailEventListenerConfig
AuditTrail - Class in ubic.gemma.model.common.auditAndSecurity: The trail of events (create or update) that occurred in an objects lifetime.
AuditTrail() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditTrail
AuditTrail.Factory - Class in ubic.gemma.model.common.auditAndSecurity
AuditTrailDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
AuditTrailDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
AuditTrailDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDaoImpl
AuditTrailEventListener - Class in ubic.gemma.persistence.audit: Phase 3 persister retirement (roadmap step 2): a Hibernate PersistEventListener that guarantees every Auditable entity has a non-null AuditTrail attached before session.persist hands it off to the cascade machinery.
AuditTrailEventListener() - Constructor for class ubic.gemma.persistence.audit.AuditTrailEventListener: Legacy no-arg constructor: keeps the persist-side guard behaviour available without pulling in the auto-CREATE / auto-DELETE machinery.
AuditTrailEventListener(UserManager, SessionFactory) - Constructor for class ubic.gemma.persistence.audit.AuditTrailEventListener: Full-fat constructor: persist-side guard PLUS auto-CREATE / auto-DELETE emission (Phase C-2).
AuditTrailEventListenerConfig - Class in ubic.gemma.persistence.audit: Phase 3 persister retirement (roadmap step 2): registers AuditTrailEventListener with Hibernate's EventListenerRegistry so every session.persist of an Auditable flows through a single audit-trail guard, replacing the per-call priming previously hand-coded in PersisterHelperImpl.doPersist.
AuditTrailEventListenerConfig() - Constructor for class ubic.gemma.persistence.audit.AuditTrailEventListenerConfig
auditTrailService - Variable in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
auditTrailService - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
AuditTrailService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity: Create and manipulate audit trails.
AuditTrailServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
AuditTrailServiceImpl(AuditTrailDao, GenericCuratableDao, UserManager, SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
auditTrailUrl - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
auditTrailUrl - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
authenticate(String, String) - Method in class ubic.gemma.cli.authentication.CLIAuthenticationManager
authenticate(String, String) - Method in interface ubic.gemma.core.security.authentication.ManualAuthenticationService: Authenticate using the provided username and password.
authenticate(String, String) - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceImpl
authenticate(FTPClient, String) - Method in class ubic.gemma.core.loader.util.ftp.AnonymousFTPCLientAuthenticator
authenticate(FTPClient, String) - Method in interface ubic.gemma.core.loader.util.ftp.FTPClientAuthenticator
authenticate(FTPClient, String) - Method in class ubic.gemma.core.loader.util.ftp.UsernamePasswordFTPClientAuthenticator
authenticate(FTPClient, String, String, String) - Method in class ubic.gemma.core.loader.util.ftp.AbstractFTPClientAuthenticator
authenticateAnonymously() - Method in class ubic.gemma.cli.authentication.CLIAuthenticationManager
authenticateAnonymously() - Method in interface ubic.gemma.core.security.authentication.ManualAuthenticationService: Perform an anonymous authentication.
authenticateAnonymously() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceImpl
authenticatedUserCount - Variable in class ubic.gemma.rest.AdminWebService.SessionsResponse: Distinct authenticated principals currently tracked by Spring Security's SessionRegistry.
AuthenticationBasedUserIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Strategy for the user ID that uses the authentication object from the SecurityContextHolder.
AuthenticationBasedUserIdRetrievalStrategy(AuthenticationTrustResolver) - Constructor for class ubic.gemma.rest.analytics.ga4.AuthenticationBasedUserIdRetrievalStrategy
AuthenticationExceptionMapper - Class in ubic.gemma.rest.providers: Handles Spring Security AuthenticationException by producing a 403 Forbidden response.
AuthenticationExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.AuthenticationExceptionMapper
authenticationLoggerListener() - Method in class ubic.gemma.core.security.SecurityConfig: Stock Spring Security LoggerListener that logs authentication events at INFO.
authenticationManager(AuthenticationProvider, AuthenticationProvider, AuthenticationProvider) - Method in class ubic.gemma.core.security.SecurityConfig: The Gemma AuthenticationManager.
AUTHOR - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
authorities - Variable in class ubic.gemma.rest.AdminWebService.SessionPrincipalValueObject: Granted authorities, alphabetically sorted; null when the principal isn't a UserDetails.
authorities() - Element in annotation interface ubic.gemma.rest.annotations.CacheControl: Authorities to whom this cache directive applies.
AuthorityConstants - Class in ubic.gemma.core.security: Defines constants used in GrantedAuthories.
AuthorityConstants() - Constructor for class ubic.gemma.core.security.AuthorityConstants
AuthWebService - Class in ubic.gemma.rest: Bearer-token auth endpoints for the curation-UI SPA.
AuthWebService() - Constructor for class ubic.gemma.rest.AuthWebService
AuthWebService.LoginRequest - Class in ubic.gemma.rest: JSON body for POST /login.
AuthWebService.LoginResponse - Class in ubic.gemma.rest: Wire payload for POST /login — {token, user}.
AUTO - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketMode
AUTODETECT - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode
AUTODETECT - Enum constant in enum class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter.Mode: Automatically detect based on the QuantitationType.
AutomatedAnnotationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
this event type was used by the auto-tagger, which has been removed. This event type has been kept so that the audit-trails can still properly display these events, but creation new events of this type should not occur.
AutomatedAnnotationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent: Deprecated.
availableMemory() - Method in record class ubic.gemma.core.util.runtime.MemInfo: Returns the value of the availableMemory record component.
availableProcessors - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse
avoidDownload - Variable in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
awaitBatchExecutorService() - Method in class ubic.gemma.cli.util.AbstractCLI: Await the completion of all batch tasks.
awaitTermination(long, TimeUnit) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
axiomCount - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta
⚠️ A hint, not a contract - Section in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCounts

B

BAC - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType
BACKWARD - Enum constant in enum class ubic.gemma.persistence.util.Cursor.Direction
BALANCED - Enum constant in enum class ubic.gemma.model.common.search.SearchSettings.SearchMode: Normal search mode with trade-offs to make it usable.
BASE_CELLOSAURUS_URI - Static variable in class ubic.gemma.core.ontology.OntologyUtils: Cellosaurus, which is not on an OBO PURL.
BASE_EFO_URI - Static variable in class ubic.gemma.core.ontology.OntologyUtils: Base URI used by EFO.
BASE_GEMMA_ONTOLOGY_URI - Static variable in class ubic.gemma.core.ontology.OntologyUtils: Base URI used by Gemma's internal ontologies.
BASE_METADATA - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
BASE_PURL_URI - Static variable in class ubic.gemma.core.ontology.OntologyUtils: Base URI used by PURL ontologies.
BaseAclAdvice - Class in ubic.gemma.core.security.acl: Adds security controls to newly created objects (including those created by updates to other objects via cascades), and removes them for objects that are deleted.
BaseAclAdvice(AclService, SessionFactory, ObjectIdentityRetrievalStrategy) - Constructor for class ubic.gemma.core.security.acl.BaseAclAdvice
baseCodeConfigurer(PropertySources) - Static method in class ubic.gemma.core.config.SettingsConfig
BaseCodeConfigurer - Class in ubic.gemma.core.config: Configure the baseCode library from a given property sources.
BaseCodeConfigurer() - Constructor for class ubic.gemma.core.config.BaseCodeConfigurer
BaseCodeOntologySearchException - Exception Class in ubic.gemma.core.search: Exception that wraps a baseCode OntologySearchException.
BaseCodeOntologySearchException(OntologySearchException) - Constructor for exception class ubic.gemma.core.search.BaseCodeOntologySearchException
BaseDao<T> - Interface in ubic.gemma.persistence.service: Interface that supports basic CRUD operations.
BaseImmutableService<O> - Interface in ubic.gemma.persistence.service: Base service class for an immutable entity.
Baseline - Class in ubic.gemma.model.analysis.expression.diff: Represents a baseline for a single factor or an interaction of factors.
BaselineSelection - Class in ubic.gemma.core.analysis.expression.diff: Utilities for deciding if a factor value is a baseline condition.
BaselineSelection() - Constructor for class ubic.gemma.core.analysis.expression.diff.BaselineSelection
BaseReadOnlyService<O> - Interface in ubic.gemma.persistence.service: Interface for read-only services.
bases(Set) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
BaseScanDateExtractor - Class in ubic.gemma.core.analysis.preprocess.batcheffects
BaseScanDateExtractor() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
BaseService<O> - Interface in ubic.gemma.persistence.service: Interface that supports basic CRUD operations.
baseUrl - Variable in class ubic.gemma.persistence.util.EntityUrlBuilder.AllEntitiesUrl
baseUrl - Variable in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl
baseUrl - Variable in class ubic.gemma.persistence.util.EntityUrlBuilder.SomeEntitiesUrl
BaseUserService - Interface in ubic.gemma.core.security.authentication
BaseValueObject - Class in ubic.gemma.model.common
BaseValueObject() - Constructor for class ubic.gemma.model.common.BaseValueObject
BaseVoEnabledDao<O,VO> - Interface in ubic.gemma.persistence.service: Created by tesarst on 01/06/17.
BaseVoEnabledService<O,VO> - Interface in ubic.gemma.persistence.service: Created by tesarst on 01/06/17.
BashCompletionGenerator - Class in ubic.gemma.cli.completion
BashCompletionGenerator(String, Set) - Constructor for class ubic.gemma.cli.completion.BashCompletionGenerator
BasicLineMapParser<K,T> - Class in ubic.gemma.core.loader.util.parser: A line parser that produces a Map instead of a Collection.
BasicLineMapParser() - Constructor for class ubic.gemma.core.loader.util.parser.BasicLineMapParser
BasicLineParser<T> - Class in ubic.gemma.core.loader.util.parser: A simple LineParser implementation that doesn't do anything.
BasicLineParser() - Constructor for class ubic.gemma.core.loader.util.parser.BasicLineParser
basis(AnnotationRelationBasis) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
batch - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode
batch(List, int) - Static method in class ubic.gemma.core.util.ListUtils
BATCH_CONF_HAS - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
BATCH_CONF_NO_HAS - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
BATCH_CORRECTED_SUCCESS - Enum constant in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that there was a significant batch effect that was corrected.
BATCH_EFF_NONE - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
BATCH_EFF_STRONG - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
BATCH_EFF_WEAK - Static variable in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
BATCH_EFFECT_FAILURE - Enum constant in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that there is a batch effect.
BATCH_EFFECT_UNDETERMINED_FAILURE - Enum constant in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that all information necessary is present, but the batch effect could not be determined.
BATCH_FACTOR_CATEGORIES - Static variable in class ubic.gemma.model.expression.experiment.ExperimentFactorUtils: A list of all categories considered to be batch.
BATCH_FACTOR_NAME - Static variable in class ubic.gemma.model.expression.experiment.ExperimentFactorUtils: Name used by a batch factor.
BATCH_FACTOR_NAME_PREFIX - Static variable in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl: Prefix to use when generating batch factor names.
BATCH_INFO_NEEDED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: Batch information is missing or ambiguous and the EE can't be analyzed until it's resolved.
BatchConfound - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Represents a summary of a batch effect confound.
BatchConfound(BioAssaySet, ExperimentalFactor, double, int, double, int) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound: Creates a new BatchConfound instance.
BatchConfoundUtils - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Test if an experimental design is confounded with batches.
BatchConfoundUtils() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtils
BatchConfoundValueObject(BatchConfound) - Constructor for class ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
batchCorrect(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorHelperService: If possible, batch-correct the processed data vectors via ComBat.
batchCorrect(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.PreprocessorHelperServiceImpl: If possible, batch correct the processed data vectors.
BatchCorrectionEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
BatchCorrectionEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BatchCorrectionEvent
BatchEffectDetails - Class in ubic.gemma.core.analysis.preprocess.batcheffects: provide some basic information about the properties and strength of a batch effect, if any.
BatchEffectDetails(BatchInformationEvent, boolean, boolean) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
BatchEffectDetails.BatchEffectStatistics - Class in ubic.gemma.core.analysis.preprocess.batcheffects
BatchEffectPopulationCli - Class in ubic.gemma.apps: For bulk processing of batch-info-fetching.
BatchEffectPopulationCli() - Constructor for class ubic.gemma.apps.BatchEffectPopulationCli
BatchEffectStatisticsValueObject(BatchEffectDetails.BatchEffectStatistics) - Constructor for class ubic.gemma.rest.DatasetsWebService.BatchEffectStatisticsValueObject
BatchEffectType - Enum Class in ubic.gemma.model.expression.experiment: Represents a batch effect.
BatchEffectUtils - Class in ubic.gemma.core.analysis.preprocess.batcheffects
BatchEffectUtils() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectUtils
batchIdentifiableParameterList(Collection, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
BatchInfoFetchTask - Interface in ubic.gemma.core.tasks.analysis.expression
BatchInfoFetchTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
BatchInfoFetchTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskCommand
BatchInfoFetchTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression: Task to try to get 'batch' information about an experiment.
BatchInfoFetchTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskImpl
batchInfoJobDetail(ExpressionExperimentService, ExpressionExperimentReportService, AuditEventService, SecurityContext) - Method in class ubic.gemma.core.config.SchedulerConfig
BatchInfoMissingException - Exception Class in ubic.gemma.core.analysis.preprocess.batcheffects: Indicate that batch information is missing.
BatchInfoMissingException(ExpressionExperiment, String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException
BatchInfoMissingException(ExpressionExperiment, String, Throwable) - Constructor for exception class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException
BatchInfoParser - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Parse information on batch from raw data files.
BatchInfoParser() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
BatchInfoPopulationException - Exception Class in ubic.gemma.core.analysis.preprocess.batcheffects: Used to indicate a problem with the population of batch information for a given ExpressionExperiment.
BatchInfoPopulationException(ExpressionExperiment, String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException
BatchInfoPopulationException(ExpressionExperiment, String, Throwable) - Constructor for exception class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException
BatchInfoPopulationException(ExpressionExperiment, Throwable) - Constructor for exception class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException
BatchInfoPopulationHelperService - Interface in ubic.gemma.core.analysis.preprocess.batcheffects
BatchInfoPopulationHelperServiceImpl - Class in ubic.gemma.core.analysis.preprocess.batcheffects
BatchInfoPopulationHelperServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl
BatchInfoPopulationService - Interface in ubic.gemma.core.analysis.preprocess.batcheffects: Retrieve batch information from the data source, if possible, and populate it into experiments.
BatchInfoPopulationServiceImpl - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Retrieve batch information from the data source, if possible, and populate it into experiments.
BatchInfoPopulationServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl
BatchInfoRepopulationJob - Class in ubic.gemma.core.scheduler: Schedule job that populates batch information for all experiments that have been updated since the last run.
BatchInfoRepopulationJob() - Constructor for class ubic.gemma.core.scheduler.BatchInfoRepopulationJob
BatchInformationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Abstract class for events related to batch information.
BatchInformationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationEvent
BatchInformationFetchingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that batch information was successfully obtained.
BatchInformationFetchingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationFetchingEvent
BatchInformationMissingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicate that batch information has been looked for and was missing.
BatchInformationMissingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationMissingEvent
BatchInformationValueObject(BatchEffectType, BatchEffectDetails, List, Map) - Constructor for class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
batchInfoTrigger(JobDetail) - Method in class ubic.gemma.core.config.SchedulerConfig: Every day at 00:30.
batchMarkSampleOutliers(DatasetArg, DatasetsWebService.BatchOutlierRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Batch outlier mark / unmark.
BatchOutlierRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.BatchOutlierRequest
BatchOutlierResponse() - Constructor for class ubic.gemma.rest.DatasetsWebService.BatchOutlierResponse
batchParameterList(Collection, int) - Static method in class ubic.gemma.persistence.util.QueryUtils: Partition a parameter list into a collection of batches of a given size.
BatchProblemsUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event that tracks when batch effects or problems are detected.
BatchProblemsUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BatchProblemsUpdateEvent
BatchTaskExecutorService - Class in ubic.gemma.cli.batch: A task executor that automatically reports errors in batch tasks.
BatchTaskExecutorService(ExecutorService, BatchTaskProgressReporter) - Constructor for class ubic.gemma.cli.batch.BatchTaskExecutorService
BatchTaskProcessingResult - Class in ubic.gemma.cli.batch: Represents an individual result in a batch processing.
BatchTaskProgressReporter - Class in ubic.gemma.cli.batch: Report progress on batch tasks.
BatchTaskProgressReporter(BatchTaskSummaryWriter, Console) - Constructor for class ubic.gemma.cli.batch.BatchTaskProgressReporter
BatchTaskSummaryWriter - Interface in ubic.gemma.cli.batch
BCRYPT_PREFIX - Static variable in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder: Prefix Spring Security's DelegatingPasswordEncoder uses for bcrypt hashes.
BeanFactoryUtils - Class in ubic.gemma.core.context: Utilities for working with bean factories.
BeanFactoryUtils() - Constructor for class ubic.gemma.core.context.BeanFactoryUtils
beanInitializationTimeMonitor() - Static method in class ubic.gemma.core.profiling.ProfilingConfig
BeanInitializationTimeMonitor - Class in ubic.gemma.core.profiling: Hook into the bean post-processing lifecycle and record bean initialization time.
BeanInitializationTimeMonitor() - Constructor for class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
BeanNameGenerator - Class in ubic.gemma.core.context: Our \@Service etc.
BeanNameGenerator() - Constructor for class ubic.gemma.core.context.BeanNameGenerator
BearerTokenAuthenticationFilter - Class in ubic.gemma.rest.security: Spring Security filter that resolves an Authorization: Bearer <opaque> header to a Authentication previously issued by AuthWebService.login(AuthWebService.LoginRequest) and stored in TokenStore.
BearerTokenAuthenticationFilter(TokenStore) - Constructor for class ubic.gemma.rest.security.BearerTokenAuthenticationFilter
beforeCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.BashCompletionGenerator
beforeCompletion(PrintWriter) - Method in interface ubic.gemma.cli.completion.CompletionGenerator: Executed before any completions has been generated.
beforeCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.FishCompletionGenerator
beforeCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.WikiCompletionGenerator
belongsTo - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Relate a FactorValue to the ExpressionExperiment that owns it.
benjaminiHochberg(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.MultipleTestCorrection
benjaminiHochberg(DoubleMatrix1D) - Static method in class ubic.gemma.core.util.math.MultipleTestCorrection
benjaminiHochbergCut(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.MultipleTestCorrection: Benjamini-Hochberg method.
BenjaminiYekuteliCut(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.MultipleTestCorrection: Benjamini-Yekuteli method.
best - Enum constant in enum class ubic.gemma.rest.DatasetsWebService.CorrelationMatrixChoice
BIBLIOGRAPHIC_REFERENCE - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetType: A BibliographicReference (PubMed-style publication).
BibliographicReference - Class in ubic.gemma.model.common.description: Hibernate Search 7 indexed root.
BibliographicReference() - Constructor for class ubic.gemma.model.common.description.BibliographicReference
BibliographicReference.Factory - Class in ubic.gemma.model.common.description
BibliographicReferenceDao - Interface in ubic.gemma.persistence.service.common.description
BibliographicReferenceDaoImpl - Class in ubic.gemma.persistence.service.common.description
BibliographicReferenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
BibliographicReferenceReadService - Interface in ubic.gemma.persistence.service.common.description: Read-only retrieval service for BibliographicReference.
BibliographicReferenceReadServiceImpl - Class in ubic.gemma.persistence.service.common.description: Implementation of BibliographicReferenceReadService.
BibliographicReferenceReadServiceImpl(BibliographicReferenceDao, SearchService, ExpressionExperimentService) - Constructor for class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
bibliographicReferenceSearch(String) - Static method in class ubic.gemma.model.common.search.SearchSettings: Convenience method to get pre-configured settings.
BibliographicReferenceService - Interface in ubic.gemma.persistence.service.common.description
BibliographicReferenceServiceImpl - Class in ubic.gemma.persistence.service.common.description: Implementation of BibliographicReferenceService.
BibliographicReferenceServiceImpl(BibliographicReferenceDao) - Constructor for class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
BibliographicReferenceValueObject - Class in ubic.gemma.model.common.description: represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists in web
BibliographicReferenceValueObject() - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject: Required when using the class as a spring bean.
BibliographicReferenceValueObject(Long) - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject
BibliographicReferenceValueObject(Long, String, String, String, String, String, String, Date, String, String, String, Collection) - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject
BibliographicReferenceValueObject(BibliographicReference) - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject: does not set related experiments field
BibRefAnnotation - Class in ubic.gemma.model.common.description: Base class for Keyword and MedicalSubjectHeading; the @Indexed annotation lives on the concrete subclasses.
BibRefAnnotation() - Constructor for class ubic.gemma.model.common.description.BibRefAnnotation
BibRefUpdaterCli - Class in ubic.gemma.apps: Refreshes the information in all the bibliographic references in the system.
BibRefUpdaterCli() - Constructor for class ubic.gemma.apps.BibRefUpdaterCli
Bin(double, double, long) - Constructor for class ubic.gemma.rest.PvalueDistributionValueObject.Bin
BinaryFunctionContributor - Class in ubic.gemma.persistence.hibernate: Registers binary-aware HQL functions for working with BLOB-mapped columns.
BinaryFunctionContributor() - Constructor for class ubic.gemma.persistence.hibernate.BinaryFunctionContributor
binarySearchFirst(double[], double) - Static method in class ubic.gemma.core.util.ArrayUtils: A binary search that returns the index of the first occurrence of the value in the array.
bindTo(MeterRegistry) - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
bindTo(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.database.HikariCPMetrics
bindTo(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.GenericExecutorMetrics
bindTo(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.GenericTaskExecutorMetrics
bindTo(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.jpa.Hibernate4Metrics
bindTo(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.jpa.Hibernate4QueryMetrics
bindTo(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.ThreadPoolExecutorMetrics
bindTo(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.ThreadPoolTaskExecutorMetrics
bindTo(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetrics
binFromRange(int, int) - Static method in class ubic.gemma.core.analysis.sequence.SequenceBinUtils: return bin that this start-end segment is in
binFromRange(int, int) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
BIO_MATERIAL_RNAME_PREFIX - Static variable in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
BIO_PROCESS_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
BIO_STUDIES - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
bioAssay() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns the value of the bioAssay record component.
BioAssay - Class in ubic.gemma.model.expression.bioAssay: Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).
BioAssay() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssay
BioAssay.Factory - Class in ubic.gemma.model.expression.bioAssay
BioAssayCategories - Class in ubic.gemma.model.expression.bioAssay: Categories for BioAssays.
BioAssayCategories() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayCategories
BioAssayDao - Interface in ubic.gemma.persistence.service.expression.bioAssay
BioAssayDaoImpl - Class in ubic.gemma.persistence.service.expression.bioAssay
BioAssayDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
BioAssayDimension - Class in ubic.gemma.model.expression.bioAssayData: Stores the order of BioAssays referred to in DataVectors.
BioAssayDimension() - Constructor for class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
BioAssayDimension.Factory - Class in ubic.gemma.model.expression.bioAssayData
BioAssayDimensionDao - Interface in ubic.gemma.persistence.service.expression.bioAssayData
BioAssayDimensionDaoImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.bioAssayData.BioAssayDimension.
BioAssayDimensionDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl
BioAssayDimensionService - Interface in ubic.gemma.persistence.service.expression.bioAssayData
BioAssayDimensionServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData: Spring Service base class for BioAssayDimensionService, provides access to all services and entities referenced by this service.
BioAssayDimensionServiceImpl(BioAssayDimensionDao) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl
BioAssayDimensionValueObject - Class in ubic.gemma.model.expression.bioAssayData
BioAssayDimensionValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject: Required when using the class as a spring bean.
BioAssayDimensionValueObject(Long) - Constructor for class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject: Do not use this constructor unless this represents a subset of a persistent BioAssayDimension.
BioAssayDimensionValueObject(BioAssayDimension) - Constructor for class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
BioAssayMapper - Interface in ubic.gemma.core.loader.util.mapper: Strategy used for comparing BioAssay to sample names from the data.
BioAssayOutlierProcessingTask - Interface in ubic.gemma.core.tasks.analysis.expression
BioAssayOutlierProcessingTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
BioAssayOutlierProcessingTaskCommand(Collection) - Constructor for class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
BioAssayOutlierProcessingTaskCommand(Collection, boolean) - Constructor for class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
BioAssayOutlierProcessingTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression: Handle 'flagging' a sample as an outlier.
BioAssayOutlierProcessingTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskImpl
BioAssayReadService - Interface in ubic.gemma.persistence.service.expression.bioAssay: Read-only retrieval service for BioAssay.
BioAssayReadServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssay: Implementation of BioAssayReadService.
BioAssayReadServiceImpl(BioAssayDao, ArrayDesignDao, BioMaterialReadService) - Constructor for class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
bioAssays() - Method in record class ubic.gemma.core.security.audit.payload.SampleRemovalPayload: Returns the value of the bioAssays record component.
bioAssays() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentWebUrl
BioAssayService - Interface in ubic.gemma.persistence.service.expression.bioAssay
BioAssayServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssay
BioAssayServiceImpl(BioAssayDao, BioMaterialDao) - Constructor for class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
BioAssaySet - Class in ubic.gemma.model.expression.experiment: Represents a set of BioAssays.
BioAssaySet() - Constructor for class ubic.gemma.model.expression.experiment.BioAssaySet
BioAssaySetValueObject - Interface in ubic.gemma.model.expression.experiment: Interface for VOs deriving from BioAssaySet.
BioAssayUtils - Class in ubic.gemma.model.expression.bioAssay
BioAssayUtils() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayUtils
BioAssayValueObject - Class in ubic.gemma.model.expression.bioAssay
BioAssayValueObject() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: Required when using the class as a spring bean.
BioAssayValueObject(Long) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
BioAssayValueObject(BioAssay) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
BioAssayValueObject(BioAssay, boolean) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
BioAssayValueObject(BioAssay, boolean, boolean) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
BioAssayValueObject(BioAssay, Map, BioAssay, boolean, boolean) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
BIOLOGICAL_PROCESS - Enum constant in enum class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect
BIOLOGICAL_SEX - Static variable in class ubic.gemma.model.common.description.Categories
biologicalReplicate - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType
BiomartEnsembleNcbiParser - Class in ubic.gemma.core.loader.util.biomart: Parser for BioMart file.
BiomartEnsembleNcbiParser(Taxon, String[]) - Constructor for class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser: Class needs to be initialised with taxon and which attributes have been used in query for biomart and thus what columns are in this file.
biomartEnsemblNcbiFetcher - Variable in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator: Fetcher is called to download files if bioMartFileName is null
BiomartEnsemblNcbiFetcher - Class in ubic.gemma.core.loader.util.biomart: BioMart is a query-oriented data management system.
BiomartEnsemblNcbiFetcher() - Constructor for class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher
BiomartEnsemblNcbiObjectGenerator - Class in ubic.gemma.core.loader.util.biomart: Class that is responsible for generating a map of BioMartEnsembleNcbiObject value objects which are keyed on ensemble protein id.
BiomartEnsemblNcbiObjectGenerator() - Constructor for class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator: Constructor ensuring that fetcher is set.
bioMartEnsemblNcbiParser - Variable in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator: A biomart parser which is constructed a new for each taxon due to slight file taxon differences
bioMartFileName - Variable in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator: If this file name is set then implies that file is local and no remote call should be made to biomart service
BIOMARTPATH - Static variable in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher
BioMaterial - Class in ubic.gemma.model.expression.biomaterial: In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
BioMaterial() - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterial
BioMaterial.Factory - Class in ubic.gemma.model.expression.biomaterial
BioMaterialDao - Interface in ubic.gemma.persistence.service.expression.biomaterial
BioMaterialDaoImpl - Class in ubic.gemma.persistence.service.expression.biomaterial
BioMaterialDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
BioMaterialFactorValueAssignment() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.BioMaterialFactorValueAssignment
BioMaterialFactorValueAssignment(Long, String, List) - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.BioMaterialFactorValueAssignment
BioMaterialMappingUpdate - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that the biomaterial to bioassay mapping of the expression experiment was modified.
BioMaterialMappingUpdate() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate
BioMaterialReadService - Interface in ubic.gemma.persistence.service.expression.biomaterial: Read-only retrieval service for BioMaterial.
BioMaterialReadServiceImpl - Class in ubic.gemma.persistence.service.expression.biomaterial: Implementation of BioMaterialReadService.
BioMaterialReadServiceImpl(BioMaterialDao) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
bioMaterials() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentWebUrl
BioMaterialService - Interface in ubic.gemma.persistence.service.expression.biomaterial
BioMaterialServiceImpl - Class in ubic.gemma.persistence.service.expression.biomaterial
BioMaterialServiceImpl(BioMaterialDao, FactorValueDao, BioAssayDao, ExperimentalFactorDao, CharacteristicService, BioMaterialReadService) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
BioMaterialUtils - Class in ubic.gemma.persistence.service.expression.biomaterial
BioMaterialUtils() - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialUtils
BioMaterialValueObject - Class in ubic.gemma.model.expression.biomaterial
BioMaterialValueObject() - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Required when using the class as a spring bean.
BioMaterialValueObject(Long) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
BioMaterialValueObject(BioMaterial) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
BioMaterialValueObject(BioMaterial, boolean, boolean) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
BioMaterialValueObject(BioMaterial, BioAssay) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
bioProcess - Enum constant in enum class ubic.gemma.rest.PlatformsWebService.AnnotationFileType: Biological-process terms only.
BIOPROCESS - Enum constant in enum class ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType
BIORXIV - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
BioSequence - Class in ubic.gemma.model.genome.biosequence: The sequence of a biological polymer such as a protein or DNA.
BioSequence() - Constructor for class ubic.gemma.model.genome.biosequence.BioSequence
BioSequence.Factory - Class in ubic.gemma.model.genome.biosequence
BioSequence2GeneProduct - Class in ubic.gemma.model.association: An association between a BioSequence and a Gene Product.
BioSequence2GeneProduct() - Constructor for class ubic.gemma.model.association.BioSequence2GeneProduct
BioSequenceCleanupCli - Class in ubic.gemma.apps: Goes through the biosequences for array designs in the database and removes duplicates.
BioSequenceCleanupCli() - Constructor for class ubic.gemma.apps.BioSequenceCleanupCli
BioSequenceDao - Interface in ubic.gemma.persistence.service.genome.biosequence
BioSequenceDaoImpl - Class in ubic.gemma.persistence.service.genome.biosequence
BioSequenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
BioSequenceLite(String, Long) - Constructor for record class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao.BioSequenceLite: Creates an instance of a BioSequenceLite record class.
BioSequenceReadService - Interface in ubic.gemma.persistence.service.genome.biosequence: Read-only retrieval service for BioSequence.
BioSequenceReadServiceImpl - Class in ubic.gemma.persistence.service.genome.biosequence: Implementation of BioSequenceReadService.
BioSequenceReadServiceImpl(BioSequenceDao) - Constructor for class ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl
BioSequenceService - Interface in ubic.gemma.persistence.service.genome.biosequence
BioSequenceServiceImpl - Class in ubic.gemma.persistence.service.genome.biosequence: Spring Service base class for BioSequenceService, provides access to all services and entities referenced by this service.
BioSequenceServiceImpl(BioSequenceDao) - Constructor for class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
BioSequenceValueObject - Class in ubic.gemma.model.genome.sequenceAnalysis
BioSequenceValueObject() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject: Required when using the class as a spring bean.
BISULFITE_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
bitand(Dialect, String, String) - Static method in class ubic.gemma.persistence.util.BitwiseUtils: Emit a native-SQL bitwise-AND expression appropriate for the given Hibernate Dialect.
BITFIELD - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
BitwiseUtils - Class in ubic.gemma.persistence.util: Helpers for emitting portable native-SQL bitwise operations.
BLACKBODY_COLORMAP - Static variable in class ubic.gemma.core.util.graphics.ColorMap
BlacklistCli - Class in ubic.gemma.apps: Add entries to the blacklist
BlacklistCli() - Constructor for class ubic.gemma.apps.BlacklistCli
BlacklistedEntity - Class in ubic.gemma.model.blacklist: Represents a blacklisted entity that should not be loaded into Gemma.
BlacklistedEntity() - Constructor for class ubic.gemma.model.blacklist.BlacklistedEntity
BlacklistedEntityDao - Interface in ubic.gemma.persistence.service.blacklist
BlacklistedEntityDaoImpl - Class in ubic.gemma.persistence.service.blacklist
BlacklistedEntityDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
BlacklistedEntityService - Interface in ubic.gemma.persistence.service.blacklist
BlacklistedEntityServiceImpl - Class in ubic.gemma.persistence.service.blacklist
BlacklistedEntityServiceImpl(BlacklistedEntityDao) - Constructor for class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
BlacklistedExperiment - Class in ubic.gemma.model.blacklist: TODO Document Me
BlacklistedExperiment() - Constructor for class ubic.gemma.model.blacklist.BlacklistedExperiment
BlacklistedPlatform - Class in ubic.gemma.model.blacklist
BlacklistedPlatform() - Constructor for class ubic.gemma.model.blacklist.BlacklistedPlatform
BlacklistedValueObject - Class in ubic.gemma.model.blacklist
BlacklistedValueObject() - Constructor for class ubic.gemma.model.blacklist.BlacklistedValueObject: Required when using the class as a spring bean.
blacklistExpressionExperiment(ExpressionExperiment, String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService: Blacklist a given dataset.
blacklistExpressionExperiment(ExpressionExperiment, String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
BlacklistListResponse() - Constructor for class ubic.gemma.rest.AdminWebService.BlacklistListResponse
blacklistPlatform(ArrayDesign, String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService: Blacklist a given platform.
blacklistPlatform(ArrayDesign, String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
BlacklistRequest() - Constructor for class ubic.gemma.rest.AdminWebService.BlacklistRequest
Blas - Class in ubic.gemma.core.util.math.linalg: This class contains Java versions of a number of the LINPACK basic linear algebra subroutines (blas): isamax_j daxpy_j ddot_j dscal_j dswap_j dnrm2_j dcopy_j drotg_j It also contains utility routines that the translator found useful while translating the FORTRAN code to Java code.
Blas() - Constructor for class ubic.gemma.core.util.math.linalg.Blas
Blat - Interface in ubic.gemma.core.analysis.sequence
BlatAssociation - Class in ubic.gemma.model.genome.sequenceAnalysis
BlatAssociation() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
BlatAssociation.Factory - Class in ubic.gemma.model.genome.sequenceAnalysis
BlatAssociationDao - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
BlatAssociationDaoImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type BlatAssociation.
BlatAssociationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl
BlatAssociationReadService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis: Read-only retrieval service for BlatAssociation.
BlatAssociationReadServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis: Implementation of BlatAssociationReadService.
BlatAssociationReadServiceImpl(BlatAssociationDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadServiceImpl
BlatAssociationScorer - Class in ubic.gemma.core.analysis.sequence: Given a set of BlatAssociations that might be redundant, clean them up and score them.
BlatAssociationScorer() - Constructor for class ubic.gemma.core.analysis.sequence.BlatAssociationScorer
BlatAssociationService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
BlatAssociationServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis: Spring Service base class for BlatAssociationService, provides access to all services and entities referenced by this service.
BlatAssociationServiceImpl(BlatAssociationDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl
blatFormatChromosomeName(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Puts "chr" prefix on the chromosome name, if need be.
blatLocationsToIntArray(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Convert a psl-formatted list (comma-delimited) to an int[].
blatQuery(Collection, boolean, Taxon) - Method in interface ubic.gemma.core.analysis.sequence.Blat
blatQuery(Collection, boolean, Taxon) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
blatQuery(Collection, Taxon) - Method in interface ubic.gemma.core.analysis.sequence.Blat
blatQuery(Collection, Taxon) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
blatQuery(BioSequence) - Method in interface ubic.gemma.core.analysis.sequence.Blat: Run a BLAT search using the gfClient.
blatQuery(BioSequence) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
blatQuery(BioSequence, Taxon, boolean) - Method in interface ubic.gemma.core.analysis.sequence.Blat: Run a BLAT search using the gfClient.
blatQuery(BioSequence, Taxon, boolean) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
BlatResult - Class in ubic.gemma.model.genome.sequenceAnalysis: Represents the result of a BLAT search.
BlatResult() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
BlatResult.Factory - Class in ubic.gemma.model.genome.sequenceAnalysis
BlatResult2Psl - Class in ubic.gemma.core.analysis.sequence: Used to convert BlatResult objects into PSL lines that can be displayed in the UCSC Genome Browser.
BlatResult2Psl() - Constructor for class ubic.gemma.core.analysis.sequence.BlatResult2Psl
blatResult2PslTrack(BlatResult, String) - Static method in class ubic.gemma.core.analysis.sequence.BlatResult2Psl: Creates text that can be displayed directly as a track in UCSC, using their hgTracks program.
BlatResultDao - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
BlatResultDaoImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.sequenceAnalysis.BlatResult.
BlatResultDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl
BlatResultParser - Class in ubic.gemma.core.loader.genome: Loader to handle results generated by Jim Kent's Blat.
BlatResultParser() - Constructor for class ubic.gemma.core.loader.genome.BlatResultParser
BlatResultReadService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis: Read-only retrieval service for BlatResult.
BlatResultReadServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis: Implementation of BlatResultReadService.
BlatResultReadServiceImpl(BlatResultDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadServiceImpl
blatResults2PslTrack(Collection, String, String) - Static method in class ubic.gemma.core.analysis.sequence.BlatResult2Psl: Creates a single custom track carrying every supplied alignment.
BlatResultService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
BlatResultServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis: Spring Service base class for BlatResultService, provides access to all services and entities referenced by this service.
BlatResultServiceImpl(BlatResultDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl
BlatResultValueObject - Class in ubic.gemma.model.genome.sequenceAnalysis
BlatResultValueObject() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject: Required when using the class as a spring bean.
BlatResultValueObject(Long) - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
BlatResultValueObject(Long, TaxonValueObject, Integer, String, Integer, Integer, Integer, Integer, Integer, Integer, BioSequenceValueObject, Integer, String, Integer, Double, Double, String, String, String, Long, Integer, Integer, Long, String) - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
BlatResultValueObject(BlatResult, Double, Double) - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
blobToString(Blob, Charset) - Static method in class ubic.gemma.core.util.SQLUtils: Convert a blob to a string.
BLOCK - Static variable in class ubic.gemma.model.common.description.Categories
blockComplete(Collection, Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil: A variant that judges from a given set of samples rather than every sample in the experiment.
blockComplete(BioAssaySet, Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil: Returns true if the block design is complete and there are at least 2 biological replicates for each "group", false otherwise.
blocked(DesignPreflightReport) - Static method in class ubic.gemma.rest.util.args.DatasetArgService.DesignChangeResult
Blocker() - Constructor for class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
Blocker(String, String) - Constructor for class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
blockingReport - Variable in class ubic.gemma.rest.util.args.DatasetArgService.DesignChangeResult
BODY - Enum constant in enum class ubic.gemma.rest.util.LocationType
BonferroniCut(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.MultipleTestCorrection: Determine the Bonferroni pvalue threshold to maintain the family wise error rate (assuming pvalues are independent).
BOOLEAN - Enum constant in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType
booleanArrayToBytes(boolean[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
booleanArrayToBytes(boolean[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
BooleanVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData: Value object for a BulkExpressionDataVector containing booleans.
BooleanVectorValueObject(BulkExpressionDataVector, ExpressionExperimentValueObject, QuantitationTypeValueObject, BioAssayDimensionValueObject, ArrayDesignValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
BootstrappedDataSourceFactory - Class in ubic.gemma.persistence.initialization: A bootstrapped data source that strips the database from the JDBC URL.
BootstrappedDataSourceFactory(DataSource) - Constructor for class ubic.gemma.persistence.initialization.BootstrappedDataSourceFactory
both - Enum constant in enum class ubic.gemma.rest.DatasetsWebService.PcLoadingDirection
boundingLayerOf - Static variable in class ubic.gemma.core.ontology.jena.RO
BrainKeywordMatcher - Class in ubic.gemma.core.geoscrape: Cheesy v1 brain-related keyword matcher.
BrainKeywordMatcher() - Constructor for class ubic.gemma.core.geoscrape.BrainKeywordMatcher: Test seam: no-arg constructor uses the curated set only.
BrainKeywordMatcher(UberonOntologyService) - Constructor for class ubic.gemma.core.geoscrape.BrainKeywordMatcher
branchingPartOf - Static variable in class ubic.gemma.core.ontology.jena.RO
BRIEF - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoAmount: Add only metadata, no data tables.
BROAD - Enum constant in enum class ubic.gemma.core.ontology.model.OntologyXref.Strength: The foreign term names something wider than the declaring term.
BROAD_SYNONYM - Enum constant in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia
browse(int, int) - Method in interface ubic.gemma.persistence.service.BrowsingDao
browse(int, int) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
browse(int, int) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
browse(int, int) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
browse(int, int) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
browse(int, int) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
browse(int, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Browse through the characteristics, excluding GO annotations.
browse(int, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
browse(int, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Browse through the characteristics, excluding GO annotations.
browse(int, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
browse(int, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Browse through the characteristics, excluding GO annotations.
browse(int, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
browse(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
browse(int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
browse(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
browse(int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
browse(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
browse(int, int, String, boolean) - Method in interface ubic.gemma.persistence.service.BrowsingDao
browse(int, int, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
browse(int, int, String, boolean) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
browse(int, int, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
browse(int, int, String, boolean) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
browse(int, int, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
browse(int, int, String, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Browse through the characteristics, excluding GO annotations, with sorting.
browse(int, int, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
browse(int, int, String, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Browse through the characteristics, excluding GO annotations.
browse(int, int, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
browse(int, int, String, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Browse through the characteristics, excluding GO annotations.
browse(int, int, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
browse(int, int, String, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
BrowsingDao<T> - Interface in ubic.gemma.persistence.service: Support for paging through the data.
Bucket() - Constructor for class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket
build() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder
build() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExperimentSubSetsCreationConfig.SingleCellExperimentSubSetsCreationConfigBuilder
build() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder
build() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder
build() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig.GeoRetrieveConfigBuilder
build() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig.GeoUpdateConfigBuilder
build() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder
build() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata.SequencingMetadataBuilder
build() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
build() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder
build() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder
build() - Method in class ubic.gemma.core.logging.log4j.ProgressUpdateAppender.Builder
build() - Method in class ubic.gemma.core.logging.log4j.SlackAppender.Builder
build() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder
build() - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder
build() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder
build() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
build() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder
build() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig.SingleCellVectorInitializationConfigBuilder
build() - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder
build() - Method in class ubic.gemma.rest.util.BuildInfoValueObject.BuildInfoValueObjectBuilder
build() - Method in class ubic.gemma.rest.util.ResponseErrorObject.ResponseErrorObjectBuilder
build() - Method in class ubic.gemma.rest.util.WellComposedError.WellComposedErrorBuilder
build() - Method in class ubic.gemma.rest.util.WellComposedErrorBody.WellComposedErrorBodyBuilder
build() - Method in class ubic.gemma.rest.util.WellComposedWarning.WellComposedWarningBuilder
build(Iterable, Set) - Static method in class ubic.gemma.core.ontology.lexical.LexicalOntologyIndex: Build a fresh in-memory Lucene 9 index over the given terms.
build(Collection) - Static method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex: Invert a collection of cross-references.
build(GeoSeries, GeoSourceMetadataBuilder.ExperimentIdentity, Date) - Method in class ubic.gemma.core.loader.expression.geo.GeoSourceMetadataBuilder: Build the document.
BUILD_INFO_CONTEXT_KEY - Static variable in class ubic.gemma.core.logging.log4j.BuildInfoThreadContextPopulator: Context key used to store the build information.
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignBlatCli
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignMergeCli
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignProbeCleanupCLI
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli
buildArrayDesignOptions(Options) - Method in class ubic.gemma.apps.BioSequenceCleanupCli
BuildBlock(String, String, String) - Constructor for class ubic.gemma.rest.monitoring.InfoWebService.BuildBlock
buildDesignMatrix(List, List, boolean) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Build a design matrix for the given factors and samples.
builder() - Static method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig
builder() - Static method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExperimentSubSetsCreationConfig
builder() - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig
builder() - Static method in class ubic.gemma.core.loader.expression.DataLoaderConfig
builder() - Static method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig
builder() - Static method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig
builder() - Static method in class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig
builder() - Static method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata
builder() - Static method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
builder() - Static method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig
builder() - Static method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig
builder() - Static method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig
builder() - Static method in class ubic.gemma.model.common.search.SearchSettings
builder() - Static method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
builder() - Static method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
builder() - Static method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig
builder() - Static method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig
builder() - Static method in class ubic.gemma.rest.util.BuildInfoValueObject
builder() - Static method in class ubic.gemma.rest.util.ResponseErrorObject
builder() - Static method in class ubic.gemma.rest.util.WellComposedError
builder() - Static method in class ubic.gemma.rest.util.WellComposedErrorBody
builder() - Static method in class ubic.gemma.rest.util.WellComposedWarning
Builder() - Constructor for class ubic.gemma.core.logging.log4j.ProgressUpdateAppender.Builder
Builder() - Constructor for class ubic.gemma.core.logging.log4j.SlackAppender.Builder
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.AffyDataFromCelCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.BatchEffectPopulationCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.DeleteExperimentsCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisWriterCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExperimentalDesignImportCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionDataCorrMatCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.GeeqCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.LockExpressionDataFileCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ProcessedDataComputeCLI
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.RefreshExperimentCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ReplaceDataCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.RNASeqDataAddCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.SingleCellCellTypeFactorCreatorCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataLoaderCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.SplitExperimentCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.SVDCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.UpdateEe2AdCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.UpdateEE2CCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.VectorMergingCli
buildExperimentOptions(Options) - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCli
buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.CellLevelMetadataWriterCli
buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.RawExpressionDataWriterCli
buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli
buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataDeleterCli
buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataUpdaterCli
buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataWriterCli
buildHeatmapData(ExpressionExperiment, Collection, Collection, Long, double, Integer, int, int, String, Long, QuantitationType, boolean) - Method in class ubic.gemma.rest.HeatmapDataService: Build a heatmap payload for ee given a vector-selection mode.
buildInfo(BuildInfoValueObject) - Method in class ubic.gemma.rest.util.ResponseErrorObject.ResponseErrorObjectBuilder: Build information.
BuildInfo - Class in ubic.gemma.core.util
BuildInfo() - Constructor for class ubic.gemma.core.util.BuildInfo
BuildInfo(String, String, String) - Constructor for class ubic.gemma.core.util.BuildInfo
BuildInfoThreadContextPopulator - Class in ubic.gemma.core.logging.log4j: Populate build information in the Log4j ThreadContext.
BuildInfoThreadContextPopulator(BuildInfo) - Constructor for class ubic.gemma.core.logging.log4j.BuildInfoThreadContextPopulator
BuildInfoValueObject - Class in ubic.gemma.rest.util
BuildInfoValueObject.BuildInfoValueObjectBuilder - Class in ubic.gemma.rest.util
buildOptions(Options) - Method in class ubic.gemma.apps.AclLinterCli
buildOptions(Options) - Method in class ubic.gemma.apps.AffyProbeCollapseCli
buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli
buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
buildOptions(Options) - Method in class ubic.gemma.apps.BibRefUpdaterCli
buildOptions(Options) - Method in class ubic.gemma.apps.BlacklistCli
buildOptions(Options) - Method in class ubic.gemma.apps.CellXGeneDataAdderCli
buildOptions(Options) - Method in class ubic.gemma.apps.CellXGeneDataDownloaderCli
buildOptions(Options) - Method in class ubic.gemma.apps.CellXGeneGrabberCli
buildOptions(Options) - Method in class ubic.gemma.apps.CompleteCli
buildOptions(Options) - Method in class ubic.gemma.apps.ExperimentalDesignViewCli
buildOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
buildOptions(Options) - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli
buildOptions(Options) - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli
buildOptions(Options) - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli
buildOptions(Options) - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI
buildOptions(Options) - Method in class ubic.gemma.apps.FactorValueOntologyWriterCli
buildOptions(Options) - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli
buildOptions(Options) - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli
buildOptions(Options) - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator
buildOptions(Options) - Method in class ubic.gemma.apps.GeoGrabberCli
buildOptions(Options) - Method in class ubic.gemma.apps.GeoSingleCellDataDownloaderCli
buildOptions(Options) - Method in class ubic.gemma.apps.IndexGemmaCLI
buildOptions(Options) - Method in class ubic.gemma.apps.InitializeDatabaseCli
buildOptions(Options) - Method in class ubic.gemma.apps.LoadExpressionDataCli
buildOptions(Options) - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli
buildOptions(Options) - Method in class ubic.gemma.apps.MergeDuplicateBibRefsCli
buildOptions(Options) - Method in class ubic.gemma.apps.MultifunctionalityCli
buildOptions(Options) - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI
buildOptions(Options) - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI
buildOptions(Options) - Method in class ubic.gemma.apps.ProtocolAdderCli
buildOptions(Options) - Method in class ubic.gemma.apps.ProtocolDeleterCli
buildOptions(Options) - Method in class ubic.gemma.apps.PubMedLoaderCli
buildOptions(Options) - Method in class ubic.gemma.apps.PubMedSearcher
buildOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataTransformCli
buildOptions(Options) - Method in class ubic.gemma.apps.TaxonLoaderCli
buildOptions(Options) - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli
buildOptions(Options) - Method in class ubic.gemma.apps.UpdateDatabaseCli
buildOptions(Options) - Method in class ubic.gemma.apps.UpdateExternalRelationsCli
buildOptions(Options) - Method in class ubic.gemma.apps.UpdateGene2CsCli
buildOptions(Options) - Method in class ubic.gemma.apps.UpdateOntologyRelationsCli
buildOptions(Options) - Method in class ubic.gemma.apps.UpdatePubMedCli
buildOptions(Options) - Method in class ubic.gemma.cli.util.AbstractCLI: Build option implementation.
buildRDesignMatrix(List, List, boolean) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Build an R-friendly design matrix.
buildRDesignMatrix(List, List, Map, boolean) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: A variant of DiffExAnalyzerUtils.buildRDesignMatrix(List, List, boolean) that allows for reusing baselines for repeated calls.
BulkDataSlicerUtils - Class in ubic.gemma.core.analysis.preprocess.slice: Slice bulk data vectors.
BulkDataSlicerUtils() - Constructor for class ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtils
BulkExpressionDataDoubleMatrix - Class in ubic.gemma.core.datastructure.matrix
BulkExpressionDataDoubleMatrix(List) - Constructor for class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
BulkExpressionDataIntMatrix - Class in ubic.gemma.core.datastructure.matrix: A bulk expression data matrix that can be efficiently accessed as a primitive int matrix.
BulkExpressionDataIntMatrix(List) - Constructor for class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
BulkExpressionDataMatrix<T> - Interface in ubic.gemma.core.datastructure.matrix: Interface for bulk expression data matrices.
BulkExpressionDataMatrixUtils - Class in ubic.gemma.core.datastructure.matrix
BulkExpressionDataMatrixUtils() - Constructor for class ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrixUtils
BulkExpressionDataMatrixWriter - Interface in ubic.gemma.core.datastructure.matrix.io
BulkExpressionDataPrimitiveDoubleMatrix - Interface in ubic.gemma.core.datastructure.matrix: Interface for bulk expression data matrices that can be efficiently accessed as a primitive double matrix.
BulkExpressionDataPrimitiveIntMatrix - Interface in ubic.gemma.core.datastructure.matrix: Interface for bulk expression data matrices that can be efficiently accessed as a primitive int matrix.
BulkExpressionDataVector - Class in ubic.gemma.model.expression.bioAssayData: A data vector storing bulk expression data.
BulkExpressionDataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector
BulkExpressionDataVectorService<T> - Interface in ubic.gemma.persistence.service.expression.bioAssayData
bundle(Path, OutputStream) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixBundler
BusinessKey - Class in ubic.gemma.persistence.util: Methods to test business-key-related issues on objects.
BusinessKey() - Constructor for class ubic.gemma.persistence.util.BusinessKey
by(String, String, Class, Filter.Operator, Collection) - Static method in class ubic.gemma.persistence.util.Filter: Create a new filter without an original property and a collection right hand side.
by(String, String, Class, Filter.Operator, Collection) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Class, Filter.Operator, Collection, String) - Static method in class ubic.gemma.persistence.util.Filter: Create a new filter with a collection right hand side.
by(String, String, Class, Filter.Operator, Collection, String) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Class, Filter.Operator, T) - Static method in class ubic.gemma.persistence.util.Filter: Create a new filter without an original property.
by(String, String, Class, Filter.Operator, T) - Static method in class ubic.gemma.persistence.util.Filters: Create a singleton Filters from an explicit clause.
by(String, String, Class, Filter.Operator, T, String) - Static method in class ubic.gemma.persistence.util.Filter: Create a new filter.
by(String, String, Class, Filter.Operator, T, String) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Class, Filter.Operator, Subquery) - Static method in class ubic.gemma.persistence.util.Filter
by(String, String, Class, Filter.Operator, Subquery) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Class, Filter.Operator, Subquery, String) - Static method in class ubic.gemma.persistence.util.Filter: Create a new filter with a subquery right hand side.
by(String, String, Class, Filter.Operator, Subquery, String) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Sort.Direction, Sort.NullMode) - Static method in class ubic.gemma.persistence.util.Sort: Create a sort without an original property.
by(String, String, Sort.Direction, Sort.NullMode, String) - Static method in class ubic.gemma.persistence.util.Sort: Create a Sort for a given alias, property and direction.
by(Filter...) - Static method in class ubic.gemma.persistence.util.Filters: Create a singleton Filters from a Filter.
by(Filters) - Static method in class ubic.gemma.persistence.util.Filters: Copy constructor.
byRole - Variable in class ubic.gemma.rest.AdminWebService.ProposalsBlock: Lifetime per-role counts (proposal / draft / snapshot).
byShortName() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ArrayDesignWebUrl
byShortName() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentWebUrl
ByteArrayConverter - Class in ubic.gemma.persistence.util: Class to convert byte arrays (e.g., Blobs) to and from other types of arrays.
ByteArrayConverter() - Constructor for class ubic.gemma.persistence.util.ByteArrayConverter
byteArrayToBooleans(byte[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
byteArrayToBooleans(byte[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToChars(byte[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
byteArrayToChars(byte[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToDoubleMatrix(byte[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter: Convert a byte array to a double matrix, assuming it is square.
byteArrayToDoubleMatrix(byte[], int) - Method in class ubic.gemma.persistence.util.ByteArrayConverter: Convert a byte array to a double matrix.
byteArrayToDoubles(byte[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
byteArrayToDoubles(byte[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToFloats(byte[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
byteArrayToFloats(byte[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToInts(byte[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
byteArrayToInts(byte[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToLongs(byte[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
byteArrayToLongs(byte[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToObjects(byte[], Class) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToObjects(byte[], Class, Charset) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
byteArrayToStrings(byte[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToStrings(byte[], Charset) - Method in class ubic.gemma.persistence.util.ByteArrayConverter: Convert a byte array into a array of Strings.
byteArrayToStrings(byte[], Charset) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToTabbedString(byte[], Class, Charset) - Method in class ubic.gemma.persistence.util.ByteArrayConverter: Convert a byte array to a tab-delimited string.
byteArrayToTabbedStrings(byte[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteArrayToTabbedStrings(byte[], Charset) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
byteArrayToTabbedStrings(byte[], Charset) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
ByteArrayType - Class in ubic.gemma.persistence.hibernate: Represents a vector of scalars stored as a byte array in a single column.
ByteArrayType() - Constructor for class ubic.gemma.persistence.hibernate.ByteArrayType
ByteArrayUtils - Class in ubic.gemma.persistence.util: Utilities for working with byte arrays.
ByteArrayUtils() - Constructor for class ubic.gemma.persistence.util.ByteArrayUtils
bytePerSecondToDisplaySize(double) - Static method in class ubic.gemma.core.util.NetUtils
bytesToDoubleMatrix(byte[], int) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
byteToCorrel(int) - Static method in class ubic.gemma.core.util.math.CorrelationStats
byteToPvalue(int) - Static method in class ubic.gemma.core.util.math.CorrelationStats
byType - Variable in class ubic.gemma.rest.TicketsWebService.OpenTicketSummaryResponse: Per-type open counts.

C

C - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Create
CACHE_NAME - Static variable in class ubic.gemma.core.ontology.chembl.ChemblCodeResolverImpl: Admin-evictable cache of code → ChemblCompound.
CACHE_NAME - Static variable in class ubic.gemma.core.ontology.ols.OlsTermResolverImpl: Admin-evictable cache of IRI → OlsTerm.
CacheControl - Annotation Interface in ubic.gemma.rest.annotations
CacheControlHeaderDecorator - Class in ubic.gemma.rest.providers
CacheControlHeaderDecorator() - Constructor for class ubic.gemma.rest.providers.CacheControlHeaderDecorator
CacheControls - Annotation Interface in ubic.gemma.rest.annotations
CachedFilteringDao<O> - Interface in ubic.gemma.persistence.service
CachedFilteringVoEnabledDao<O,VO> - Interface in ubic.gemma.persistence.service
CacheHealthIndicator - Class in ubic.gemma.rest.monitoring.health: Cache health probe.
CacheHealthIndicator(CacheManager) - Constructor for class ubic.gemma.rest.monitoring.health.CacheHealthIndicator
CacheKeyLock - Interface in ubic.gemma.persistence.cache: Represents a lock over a cache key.
CacheKeyLock.LockAcquisition - Interface in ubic.gemma.persistence.cache: Represents an acquired lock on a cache key.
CacheListResponse() - Constructor for class ubic.gemma.rest.AdminWebService.CacheListResponse
cacheManagerAliasRegistrar() - Static method in class ubic.gemma.persistence.hibernate.HibernateConfig: Register an alias cacheManager → ehcache so that Spring's @EnableCaching infrastructure (which looks up a bean named cacheManager by default) and any legacy injection point on the name cacheManager resolve to the CacheManager published by EhcacheConfig under the id ehcache.
caches - Variable in class ubic.gemma.rest.AdminWebService.CacheListResponse: Per-cache stats roll-up; same ordering as AdminWebService.CacheListResponse.names.
CacheStatRow() - Constructor for class ubic.gemma.rest.AdminWebService.CacheStatRow
CacheUtils - Class in ubic.gemma.persistence.cache: Common helpers for Spring Cache manipulation.
CacheUtils() - Constructor for class ubic.gemma.persistence.cache.CacheUtils
calculateGoTermOverlap(Long, Collection) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
calculateGoTermOverlap(Long, Collection) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
calculateGoTermOverlap(Gene, Collection) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Given a query Gene, and a collection of gene ids calculates the go term overlap for each pair of queryGene and gene in the given collection.
calculateGoTermOverlap(Gene, Collection) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
calculateGoTermOverlap(Gene, Gene) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
calculateGoTermOverlap(Gene, Gene) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
calculateScore(ExpressionExperiment, GeeqService.ScoreMode) - Method in interface ubic.gemma.persistence.service.expression.experiment.GeeqService: Calculates the GEEQ score in the given mode for the experiment with the given id.
calculateScore(ExpressionExperiment, GeeqService.ScoreMode) - Method in class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
calculateSize(Path) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixBundler: Calculate the size of the resulting TAR without actually producing it.
call() - Method in interface ubic.gemma.core.loader.entrez.EntrezUtils.EntrezCall
call() - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextCallable
call() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.GeeqTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapperTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.MultifunctionalityTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskImpl
call() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskImpl
call(SimpleRetryContext) - Method in interface ubic.gemma.core.util.SimpleRetryCallable
CALLER_IDENTITY - Enum constant in enum class ubic.gemma.model.annotations.WithheldFromApi.Reason: The value depends on who is asking rather than on the entity — an authorization flag, an ownership check, a per-principal count.
cancel(SchedulerHandle) - Method in class ubic.gemma.core.pipeline.LuigiPipelineScheduler
cancel(SchedulerHandle) - Method in class ubic.gemma.core.pipeline.MockPipelineScheduler
cancel(SchedulerHandle) - Method in class ubic.gemma.core.pipeline.NextflowPipelineScheduler
cancel(SchedulerHandle) - Method in interface ubic.gemma.core.pipeline.PipelineScheduler: Request cancellation of a running job.
cancelBatch(Long) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService: Request cancellation of every non-terminal job in the batch.
cancelBatch(Long) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl
cancelBatch(Long) - Method in class ubic.gemma.rest.AdminPipelineWebService
cancelInitializationThread() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService: Cancel the initialization thread.
cancelInitializationThread() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
cancelInitializationThread() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
cancelInitializationThread() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Cancel a running initialization thread.
cancelJob(Long) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService: Request cancellation of one job mid-batch.
cancelJob(Long) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl
cancelJob(Long, Long) - Method in class ubic.gemma.rest.AdminPipelineWebService
CANCELLED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType
CANCELLED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketState
CANCELLED - Enum constant in enum class ubic.gemma.model.expression.experiment.GeoScrapeWatermark.Status
CANCELLED - Enum constant in enum class ubic.gemma.model.pipeline.JobState
CANCELLED - Enum constant in enum class ubic.gemma.model.pipeline.PipelineJobBatch.BatchState
cancelling - Variable in class ubic.gemma.rest.AdminWebService.JobsListResponse
CANCELLING - Enum constant in enum class ubic.gemma.core.job.SubmittedTask.Status
CANCELLING - Enum constant in enum class ubic.gemma.model.pipeline.JobState
cancelTask(String) - Method in class ubic.gemma.rest.TasksWebService: Cooperative task cancellation.
canDelete(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
canDelete(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
canDelete(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
canDelete(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
canDelete(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao
canDelete(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
Candidate - Enum constant in enum class ubic.gemma.model.expression.experiment.WorkflowState
canEqual(Object) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
canEqual(Object) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
canEqual(Object) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
canEqual(Object) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
canEqual(Object) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket
canEqual(Object) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleContactMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraBase
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackageSet
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExternalId
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFiles
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPlatform
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPool
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
canEqual(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
canEqual(Object) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
canEqual(Object) - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject
canEqual(Object) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
canEqual(Object) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
canEqual(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
canEqual(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
canEqual(Object) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
canEqual(Object) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
canEqual(Object) - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
canEqual(Object) - Method in class ubic.gemma.model.analysis.ProtocolValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.BaseValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.IdentifiableValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
canEqual(Object) - Method in class ubic.gemma.model.common.search.SearchResult
canEqual(Object) - Method in class ubic.gemma.model.common.search.SearchSettings
canEqual(Object) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
canEqual(Object) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject
canEqual(Object) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
canEqual(Object) - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
canEqual(Object) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject
canEqual(Object) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
canEqual(Object) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
canEqual(Object) - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject
canEqual(Object) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
canEqual(Object) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
canEqual(Object) - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLock
canEqual(Object) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
canEqual(Object) - Method in class ubic.gemma.persistence.util.Filters
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.EntityRef
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermRef
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.Section
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
canEqual(Object) - Method in class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject
canEqual(Object) - Method in class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject
canEqual(Object) - Method in class ubic.gemma.rest.GeneWebService.GeneDifferentialExpressionGroupValueObject
canEqual(Object) - Method in class ubic.gemma.rest.util.SortValueObject
canonicalLabel(String, String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: The label that goes with CharacteristicUtils.canonicalUri(String).
canonicalUri(String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: The URI Gemma should report for a term, which is not always the one stored.
CanonicalUriValueObject(String, String, String, String, String) - Constructor for class ubic.gemma.rest.AnnotationsWebService.CanonicalUriValueObject
canSkipAclCheck(Object) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice: Check for special cases of objects that don't need to be examined for associations at all, for efficiency when following associations.
canSkipAclCheck(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
canTransitionTo(WorkflowState) - Method in enum class ubic.gemma.model.expression.experiment.WorkflowState
cardinality() - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
cardinality() - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
CARDINALITY - Enum constant in enum class ubic.gemma.core.ontology.model.OntologyCardinalityRestriction.CardinalityType
categorical - Enum constant in enum class ubic.gemma.model.expression.experiment.FactorType
categorical(FactorValue) - Static method in class ubic.gemma.model.analysis.expression.diff.Baseline: Create a baseline for a single categorical factor.
categorical(FactorValue) - Static method in class ubic.gemma.model.analysis.expression.diff.Contrast: Create a contrast for a categorical factor.
CATEGORICAL - Enum constant in enum class ubic.gemma.model.common.quantitationtype.GeneralType: For categorical data.
CATEGORICAL - Static variable in enum class ubic.gemma.model.expression.experiment.FactorType: Aliases for consistency.
CategoricalArray<T> - Class in ubic.gemma.core.loader.util.anndata: Represents a categorical array.
CategoricalArray(H5Group, Class) - Constructor for class ubic.gemma.core.loader.util.anndata.CategoricalArray
Categories - Class in ubic.gemma.model.common.description: Enumeration of commonly used categories for referring to in the code.
Categories() - Constructor for class ubic.gemma.model.common.description.Categories
category - Variable in class ubic.gemma.model.common.description.Category
category - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
Category - Class in ubic.gemma.model.common.description: Represents a category.
Category(String, String) - Constructor for class ubic.gemma.model.common.description.Category
CategoryStat() - Constructor for class ubic.gemma.core.analysis.report.HomeStats.CategoryStat
CategoryStat(String, String, String, long) - Constructor for class ubic.gemma.core.analysis.report.HomeStats.CategoryStat
categoryUri - Variable in class ubic.gemma.model.common.description.Category
categoryUri - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
CategoryWithUsageStatisticsValueObject(String, String, Long) - Constructor for class ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject: Creates a new CategoryWithUsageStatisticsValueObject instance.
cdf(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Stats: Convert an array into a cumulative density function (CDF).
Cell() - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
CELL - Enum constant in enum class ubic.gemma.core.visualization.SingleCellSparsityHeatmap.SingleCellHeatmapType
CELL_BROWSER_SC_DATA_SUFFIX - Static variable in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
CELL_BROWSER_SC_METADATA_SUFFIX - Static variable in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
CELL_ID_COLUMN_NAME_KEYWORDS - Static variable in class ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer: TODO
CELL_TYPE - Static variable in class ubic.gemma.model.common.description.Categories
CELL_TYPE_ANNOTATION_PIPELINE_REPORT - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
CELL_TYPE_ANNOTATION_PIPELINE_REPORT_DATA - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
CELL_TYPE_ANNOTATION_PIPELINE_REPORT_LOG - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
CELL_TYPE_FACTOR_RECREATED - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome
CELL_TYPE_FACTOR_REMOVED - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome
CELL_TYPE_FACTOR_UNCHANGED - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome
CELL_TYPE_FACTOR_UNCHANGED_BUT_MISALIGNED - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome: The factor was left unchanged, but is now misaligned with the preferred cell type assignment.
CellBrowserMetadataWriter - Class in ubic.gemma.core.visualization.cellbrowser: Write metadata file for the Cell Browser visualization tool.
CellBrowserMetadataWriter() - Constructor for class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter
CellBrowserService - Interface in ubic.gemma.core.visualization.cellbrowser
CellBrowserServiceImpl - Class in ubic.gemma.core.visualization.cellbrowser
CellBrowserServiceImpl() - Constructor for class ubic.gemma.core.visualization.cellbrowser.CellBrowserServiceImpl
CellBrowserTabularMatrixReader - Class in ubic.gemma.core.visualization.cellbrowser
CellBrowserTabularMatrixReader() - Constructor for class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixReader
CellBrowserTabularMatrixWriter - Class in ubic.gemma.core.visualization.cellbrowser: Generate a tabular matrix format compatible with Cell Browser.
CellBrowserTabularMatrixWriter() - Constructor for class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter
CellBrowserTabularMetadataReader - Class in ubic.gemma.core.datastructure.matrix
CellBrowserTabularMetadataReader() - Constructor for class ubic.gemma.core.datastructure.matrix.CellBrowserTabularMetadataReader
CellBrowserUtils - Class in ubic.gemma.core.visualization.cellbrowser
CellBrowserUtils() - Constructor for class ubic.gemma.core.visualization.cellbrowser.CellBrowserUtils
CellIdOverlapBioAssayMapper - Class in ubic.gemma.core.loader.util.mapper: Strategy for mapping sample name to BioAssay that relies on overlapping cell IDs.
CellIdOverlapBioAssayMapper(Map, Map) - Constructor for class ubic.gemma.core.loader.util.mapper.CellIdOverlapBioAssayMapper
CellLevelCharacteristics - Interface in ubic.gemma.model.expression.bioAssayData: Characteristics applicable to individual cells in a SingleCellDimension.
CellLevelCharacteristics.Factory - Class in ubic.gemma.model.expression.bioAssayData
CellLevelCharacteristicsAddedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when a cell-level characteristics is removed.
CellLevelCharacteristicsAddedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CellLevelCharacteristicsAddedEvent
CellLevelCharacteristicsEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when a cell-level characteristics is modified (either added or removed).
CellLevelCharacteristicsEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CellLevelCharacteristicsEvent
CellLevelCharacteristicsMappingUtils - Class in ubic.gemma.core.analysis.singleCell: Utilities for creating, reading and writing mappings of CellLevelCharacteristics to ExperimentalFactor.
CellLevelCharacteristicsMappingUtils() - Constructor for class ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils
CellLevelCharacteristicsRemovedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when a cell-level characteristics is removed.
CellLevelCharacteristicsRemovedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CellLevelCharacteristicsRemovedEvent
CellLevelCharacteristicsValueObject - Class in ubic.gemma.model.expression.bioAssayData
CellLevelCharacteristicsValueObject(CellLevelCharacteristics, boolean) - Constructor for class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
CellLevelCharacteristicsWriter - Class in ubic.gemma.core.loader.expression.singleCell.metadata
CellLevelCharacteristicsWriter() - Constructor for class ubic.gemma.core.loader.expression.singleCell.metadata.CellLevelCharacteristicsWriter
CellLevelMetadataWriterCli - Class in ubic.gemma.apps
CellLevelMetadataWriterCli() - Constructor for class ubic.gemma.apps.CellLevelMetadataWriterCli
cellLine - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
cellLineOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
CellLineOntologyService - Class in ubic.gemma.core.ontology.providers: Cell Line Ontology
CellLineOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.CellLineOntologyService
cellLineType() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Returns the value of the cellLineType record component.
CellMetadataFileOptionValue - Class in ubic.gemma.cli.options: Options to write cell metadata file.
CellMetadataFileOptionValue(boolean, boolean, Path, Path, boolean, boolean, boolean, String, boolean) - Constructor for class ubic.gemma.cli.options.CellMetadataFileOptionValue
CellMetadataFileOptionValue(DataFileOptionValue, boolean, boolean, boolean) - Constructor for class ubic.gemma.cli.options.CellMetadataFileOptionValue
CELLOSAURUS - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
cellosaurusOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
CellosaurusOntologyService - Class in ubic.gemma.core.ontology.providers: Cellosaurus served as a flat lexical cell-line name-resolution source, as a backup for the Cell Line Ontology (CLO) in cell-line searches.
CellosaurusOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.CellosaurusOntologyService
cellosaurusRelationProducer(List, AnnotationRelationDao, PlatformTransactionManager, TaxonService) - Method in class ubic.gemma.core.ontology.OntologyConfig: Cellosaurus as EXTERNAL relations — donor disease and derived-from site.
CellosaurusRelationProducer - Class in ubic.gemma.core.ontology.relation: Turns Cellosaurus into AnnotationRelationBasis.EXTERNAL relations: which disease a cell line's donor had, and which part of the body it came from.
CellosaurusRelationProducer(List, AnnotationRelationDao, TransactionTemplate, TaxonService) - Constructor for class ubic.gemma.core.ontology.relation.CellosaurusRelationProducer
CellRangerBasedTransformation - Interface in ubic.gemma.core.loader.expression.singleCell.transform
cellType - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
CellTypeAssignment - Class in ubic.gemma.model.expression.bioAssayData: Represents a cell type assignment where cells from a given dataset are assigned cell types.
CellTypeAssignment() - Constructor for class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment
CellTypeAssignment.Factory - Class in ubic.gemma.model.expression.bioAssayData
CellTypeAssignmentAddedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when a CellTypeAssignmentEvent is added.
CellTypeAssignmentAddedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CellTypeAssignmentAddedEvent
cellTypeAssignmentDescription(String) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: A description to use for the cell type assignment.
CellTypeAssignmentEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when a cell type assignment is modified (either added or removed).
CellTypeAssignmentEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CellTypeAssignmentEvent
cellTypeAssignmentFile(Path) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: A location where cell type can be found in a format covered by GenericMetadataSingleCellDataLoader.
cellTypeAssignmentName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: A name to use for the cell type assignment.
cellTypeAssignmentProtocol(Protocol) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: A protocol to use for the cell type assignment.
CellTypeAssignmentRemovedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when a CellTypeAssignmentEvent is removed.
CellTypeAssignmentRemovedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CellTypeAssignmentRemovedEvent
CellTypeAssignmentValueObject - Class in ubic.gemma.model.analysis
CellTypeAssignmentValueObject(CellTypeAssignment, boolean) - Constructor for class ubic.gemma.model.analysis.CellTypeAssignmentValueObject
cellTypeFactor() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellSubSetsCreatedPayload: Returns the value of the cellTypeFactor record component.
cellTypeFactorName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
cellTypeOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
CellTypeOntologyService - Class in ubic.gemma.core.ontology.providers: Cell Ontology
CellTypeOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.CellTypeOntologyService
cellTypes() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellSubSetsCreatedPayload: Returns the value of the cellTypes record component.
cellTypeToFactorValueMapping() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellSubSetsCreatedPayload: Returns the value of the cellTypeToFactorValueMapping record component.
cellTypeUriFactorName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
CELLULAR_COMPONENT - Enum constant in enum class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect
CELLXGENE - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
CellXGeneAnnDataSingleCellDataConfigurer - Class in ubic.gemma.core.loader.expression.cellxgene: Configures a AnnDataSingleCellDataLoader for CELLxGENE datasets.
CellXGeneAnnDataSingleCellDataConfigurer(Path, SingleCellDataTransformationFactory) - Constructor for class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataConfigurer
CellXGeneAnnDataSingleCellDataConfigurer(Path, SingleCellDataTransformationFactory, Path) - Constructor for class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataConfigurer
CellXGeneAnnDataSingleCellDataLoader - Class in ubic.gemma.core.loader.expression.cellxgene
CellXGeneAnnDataSingleCellDataLoader(Path, boolean, boolean) - Constructor for class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoader
CellXGeneAnnDataSingleCellDataLoaderConfig - Class in ubic.gemma.core.loader.expression.cellxgene: A configuration for loading CELLxGENE data from AnnData files.
CellXGeneAnnDataSingleCellDataLoaderConfig(CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder) - Constructor for class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig
CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C,B> - Class in ubic.gemma.core.loader.expression.cellxgene
CellXGeneAnnDataSingleCellDataLoaderConfigBuilder() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder
CellXGeneConverter - Class in ubic.gemma.core.loader.expression.cellxgene: Convert CELLxGENE dataset metadata into an ExpressionExperiment.
CellXGeneConverter(ExternalDatabaseService, TaxonReadService, PubMedSearch) - Constructor for class ubic.gemma.core.loader.expression.cellxgene.CellXGeneConverter
CellXGeneDataAdderCli - Class in ubic.gemma.apps
CellXGeneDataAdderCli() - Constructor for class ubic.gemma.apps.CellXGeneDataAdderCli
CellXGeneDataDownloaderCli - Class in ubic.gemma.apps
CellXGeneDataDownloaderCli() - Constructor for class ubic.gemma.apps.CellXGeneDataDownloaderCli
CellXGeneDataLoaderService - Interface in ubic.gemma.core.loader.expression.cellxgene: High-level service for fetching and loading CELLxGENE datasets.
CellXGeneDataLoaderServiceImpl - Class in ubic.gemma.core.loader.expression.cellxgene
CellXGeneDataLoaderServiceImpl(Persister, ArrayDesignService, ExpressionExperimentService, SingleCellExpressionExperimentService, ExternalDatabaseService, TaxonReadService, SingleCellDataTransformationFactory, PlatformTransactionManager, Path, Path, String) - Constructor for class ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderServiceImpl
CellXGeneFetcher - Class in ubic.gemma.core.loader.expression.cellxgene: Fetch data from CELLxGENE.
CellXGeneFetcher(SimpleRetryPolicy, Path) - Constructor for class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher
CellXGeneGrabberCli - Class in ubic.gemma.apps
CellXGeneGrabberCli() - Constructor for class ubic.gemma.apps.CellXGeneGrabberCli
CellXGeneUtils - Class in ubic.gemma.core.loader.expression.cellxgene
CellXGeneUtils() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils
ChainedEntityMapper<T> - Class in ubic.gemma.core.loader.util.mapper: Implementation of a chain of entity mappers.
ChainedEntityMapper(EntityMapper...) - Constructor for class ubic.gemma.core.loader.util.mapper.ChainedEntityMapper
CHANGE - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementType
changeMyPassword(RootWebService.ChangePasswordRequest) - Method in class ubic.gemma.rest.RootWebService: Self-service password change for the authenticated user.
changePassword(String, String) - Method in interface ubic.gemma.core.security.authentication.UserManager
changePassword(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
changePasswordForUser(String, String, String) - Method in interface ubic.gemma.core.security.authentication.UserDetailsManager
changePasswordForUser(String, String, String) - Method in interface ubic.gemma.core.security.authentication.UserManager
changePasswordForUser(String, String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
ChangePasswordRequest() - Constructor for class ubic.gemma.rest.RootWebService.ChangePasswordRequest
changePreferredCellTypeAssignment(ExpressionExperiment, QuantitationType, CellTypeAssignment, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
changePreferredCellTypeAssignment(ExpressionExperiment, QuantitationType, CellTypeAssignment, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
changePreferredCellTypeAssignment(ExpressionExperiment, SingleCellDimension, CellTypeAssignment, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Change the preferred cell type assignment to the given one.
changePreferredCellTypeAssignment(ExpressionExperiment, SingleCellDimension, CellTypeAssignment, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
channelNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
ChannelUtils - Class in ubic.gemma.persistence.util: Determine if a quantitation type (by name) represents background or signal.
ChannelUtils() - Constructor for class ubic.gemma.persistence.util.ChannelUtils
CHAR - Enum constant in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType
Characteristic - Class in ubic.gemma.model.common.description: Instances of this are used to describe other entities.
Characteristic() - Constructor for class ubic.gemma.model.common.description.Characteristic: No-arg constructor added to satisfy javabean contract
Characteristic.Factory - Class in ubic.gemma.model.common.description
characteristic2CharacteristicVO(Collection) - Static method in class ubic.gemma.model.common.description.CharacteristicValueObject
CharacteristicDao - Interface in ubic.gemma.persistence.service.common.description
CharacteristicDao.PriorCurationUsage - Class in ubic.gemma.persistence.service.common.description: A term prior curators chose for some value string, and how many distinct experiments they chose it on.
CharacteristicDao.UsageExample - Class in ubic.gemma.persistence.service.common.description: One representative, ACL-visible usage of a term (keyed by its value URI), for showing a search hit in the context it has actually been applied (e.g.
CharacteristicDaoImpl - Class in ubic.gemma.persistence.service.common.description
CharacteristicDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
CharacteristicReadService - Interface in ubic.gemma.persistence.service.common.description: Read-only retrieval service for Characteristic and Statement.
CharacteristicReadServiceImpl - Class in ubic.gemma.persistence.service.common.description: Implementation of CharacteristicReadService.
CharacteristicReadServiceImpl(CharacteristicDao, StatementDao) - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
CharacteristicService - Interface in ubic.gemma.persistence.service.common.description
CharacteristicServiceImpl - Class in ubic.gemma.persistence.service.common.description
CharacteristicServiceImpl(CharacteristicDao) - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
CharacteristicUpdateCommand - Class in ubic.gemma.core.tasks.maintenance
CharacteristicUpdateCommand() - Constructor for class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
CharacteristicUpdateTask - Interface in ubic.gemma.core.tasks.maintenance
CharacteristicUpdateTaskImpl - Class in ubic.gemma.core.tasks.maintenance: This handles characteristic updates from the client: experiment tags, characteristic browser
CharacteristicUpdateTaskImpl(BioMaterialService, CharacteristicService, ExpressionExperimentService, FactorValueService, SecurityService) - Constructor for class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTaskImpl
CharacteristicUtils - Class in ubic.gemma.model.common.description
CharacteristicUtils() - Constructor for class ubic.gemma.model.common.description.CharacteristicUtils
CharacteristicValueObject - Class in ubic.gemma.model.common.description: Value object representation of a Characteristic.
CharacteristicValueObject() - Constructor for class ubic.gemma.model.common.description.CharacteristicValueObject: Required when using the class as a spring bean.
CharacteristicValueObject(Long) - Constructor for class ubic.gemma.model.common.description.CharacteristicValueObject
CharacteristicValueObject(String, String) - Constructor for class ubic.gemma.model.common.description.CharacteristicValueObject
CharacteristicValueObject(String, String, String, String) - Constructor for class ubic.gemma.model.common.description.CharacteristicValueObject
CharacteristicValueObject(Characteristic) - Constructor for class ubic.gemma.model.common.description.CharacteristicValueObject
CharacteristicWithUsageStatisticsAndOntologyTerm(Characteristic, Long, OntologyTerm) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm: Creates a new CharacteristicWithUsageStatisticsAndOntologyTerm instance.
charArrayToBytes(char[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
charArrayToBytes(char[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
ChartThemeUtils - Class in ubic.gemma.core.visualization
ChartThemeUtils() - Constructor for class ubic.gemma.core.visualization.ChartThemeUtils
ChartUtils - Class in ubic.gemma.core.visualization
ChartUtils() - Constructor for class ubic.gemma.core.visualization.ChartUtils
chebiOntologyService(OntologySlimExtractor, ChebiSeedResolver) - Method in class ubic.gemma.core.ontology.OntologyConfig: Bean for the CHEBI ontology with slim-cache wiring.
ChebiOntologyService - Class in ubic.gemma.core.ontology.providers: Chemical Entities of Biological Interest
ChebiOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.ChebiOntologyService
ChebiSeedResolver - Class in ubic.gemma.core.ontology.providers.chebi: Resolves the corpus-side seed set for the CHEBI slim build (consumed by ubic.gemma.core.ontology.providers.OntologySlimExtractor): every CHEBI URI the gemd corpus uses, in any of the subject, object or second-object slots.
ChebiSeedResolver(SessionFactory) - Constructor for class ubic.gemma.core.ontology.providers.chebi.ChebiSeedResolver
check() - Method in class ubic.gemma.rest.monitoring.health.CacheHealthIndicator
check() - Method in class ubic.gemma.rest.monitoring.health.DbHealthIndicator
check() - Method in class ubic.gemma.rest.monitoring.health.DiskSpaceHealthIndicator
check() - Method in interface ubic.gemma.rest.monitoring.health.HealthIndicator: Run the probe and report the result.
check(Supplier, MethodInvocation) - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManager
checkColRange(int, int) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
checkCorrectability(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService: Check if the given experiment is correctable for batch effects.
checkCorrectability(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
checkEntity(AbstractEntityArg, T) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService: Checks whether the given object is null, and throws an appropriate exception if necessary.
checkForFile(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
checkForFile(FTPClient, String) - Static method in class ubic.gemma.core.util.NetUtils: Determine if a file exists on the remote server.
checkHasBatchInfo(Collection) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService: Batch counterpart to ExpressionExperimentBatchInformationService.checkHasBatchInfo(ExpressionExperiment).
checkHasBatchInfo(Collection) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
checkHasBatchInfo(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService: Check if the given experiment has batch information.
checkHasBatchInfo(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
checkHasUsableBatchInfo(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService: Check if the given experiment has usable batch information.
checkHasUsableBatchInfo(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
checkKey(Contact) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(User) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(BibliographicReference) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(Characteristic) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(DatabaseEntry) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(ExternalDatabase) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(QuantitationType) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(BioAssayDimension) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(DesignElementDataVector) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(ExpressionExperimentSubSet) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(FactorValue) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkKey(Gene) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkRowRange(int, int) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
checkValidForLm(Collection, ExperimentalFactor) - Static method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil: A variant that judges from a given set of samples rather than every sample in the experiment.
checkValidForLm(BioAssaySet, ExperimentalFactor) - Static method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil: Check that the factorValues are measurements, or that there are at least two assays for at least one factor value.
checkValidKey(Gene2GOAssociation) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkValidKey(DatabaseEntry) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkValidKey(Unit) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkValidKey(ArrayDesign) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkValidKey(ExperimentalFactor) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkValidKey(BioSequence) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkValidKey(Chromosome) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkValidKey(Gene) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkValidKey(GeneProduct) - Static method in class ubic.gemma.persistence.util.BusinessKey
checkValidKey(Taxon) - Static method in class ubic.gemma.persistence.util.BusinessKey
ChemblCodeResolver - Interface in ubic.gemma.core.ontology.chembl: Identifies a drug developmental / trial code against ChEMBL's synonym table.
ChemblCodeResolverImpl - Class in ubic.gemma.core.ontology.chembl: Resolves a trial code against ChEMBL's synonym table (GET {base}/chembl/api/data/molecule?molecule_synonyms__molecule_synonym__iexact=...).
ChemblCodeResolverImpl() - Constructor for class ubic.gemma.core.ontology.chembl.ChemblCodeResolverImpl
ChemblCompound - Class in ubic.gemma.core.ontology.chembl: A compound ChEMBL identifies for a developmental / trial code, together with the provenance of that identification.
ChemblCompound(String, String, String, String, String) - Constructor for class ubic.gemma.core.ontology.chembl.ChemblCompound
CHIA_PET - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
CHIP_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
ChIPChip - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
CHM_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
chol2inv() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition: Used for computing standard errors of parameter estimates for least squares; copies functionality of R chol2inv.
chompExtension(String) - Static method in class ubic.gemma.core.util.FileTools
choosePrivate(Collection) - Method in interface ubic.gemma.core.security.SecurityService: Pick private securables.
choosePrivate(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
choosePublic(Collection) - Method in interface ubic.gemma.core.security.SecurityService: Pick public securables.
choosePublic(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
Chromosome - Class in ubic.gemma.model.genome: Immutable representation of a chromosome
Chromosome() - Constructor for class ubic.gemma.model.genome.Chromosome
Chromosome.Factory - Class in ubic.gemma.model.genome
ChromosomeDao - Interface in ubic.gemma.persistence.service.genome
ChromosomeDaoImpl - Class in ubic.gemma.persistence.service.genome: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.Chromosome.
ChromosomeDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.ChromosomeDaoImpl
ChromosomeFeature - Class in ubic.gemma.model.genome: Some part of a chromosome
ChromosomeFeature() - Constructor for class ubic.gemma.model.genome.ChromosomeFeature
ChromosomeLocation - Class in ubic.gemma.model.genome
ChromosomeLocation() - Constructor for class ubic.gemma.model.genome.ChromosomeLocation
ChromosomeService - Interface in ubic.gemma.persistence.service.genome
ChromosomeServiceImpl - Class in ubic.gemma.persistence.service.genome: Spring Service base class for ChromosomeService, provides access to all services and entities referenced by this service.
ChromosomeServiceImpl(ChromosomeDao) - Constructor for class ubic.gemma.persistence.service.genome.ChromosomeServiceImpl
ChromosomeUtils - Class in ubic.gemma.persistence.service.genome: A utility class for Chromosome
ChromosomeUtils() - Constructor for class ubic.gemma.persistence.service.genome.ChromosomeUtils
CitationValueObject - Class in ubic.gemma.model.common.description: Represents a BibliographicReference as a citation string (which is really super light value object).
CitationValueObject() - Constructor for class ubic.gemma.model.common.description.CitationValueObject
claimDatabaseCreation() - Static method in class ubic.gemma.persistence.initialization.TestBootstrapState: Atomically claim the right to (drop and) create the test database.
claimDataSeeding() - Static method in class ubic.gemma.persistence.initialization.TestBootstrapState: Atomically claim the right to seed initial data.
claimSchemaExtras() - Static method in class ubic.gemma.persistence.initialization.TestBootstrapState: Atomically claim the right to run the schema-extras populator (ACL seed INSERTs, indices, additional tables defined in sql/init-acls.sql + sql/init-entities.sql + sql/<vendor>/init-entities.sql).
claimSchemaMaterialization() - Static method in class ubic.gemma.persistence.initialization.TestBootstrapState: Atomically claim the right to let Hibernate materialize the schema (via hbm2ddl=create).
classCount - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta
className - Variable in class ubic.gemma.rest.AdminWebService.IndexStatusValueObject: Java simple class name.
className - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject: Java simple class name (always available, even if inspection fails).
ClasspathOntologyService - Class in ubic.gemma.core.ontology.jena: An ontology service that loads an ontology from a classpath resource.
ClasspathOntologyService(String, String, boolean, String) - Constructor for class ubic.gemma.core.ontology.jena.ClasspathOntologyService
clause() - Method in class ubic.gemma.rest.util.args.FilterArgParser
clause() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
clause(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
ClauseContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
cleanForFileName(String) - Static method in class ubic.gemma.core.util.FileTools: Avoid getting file names with spaces, slashes, quotes, # etc; replace them with "_".
cleanUp(File) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
cleanUpQueryName(String) - Static method in class ubic.gemma.core.loader.genome.BlatResultParser
clear() - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter: Clear the state of the converter.
clear() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
clear() - Method in class ubic.gemma.model.util.UninitializedCollection
clear(GeoPlatform) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: Remove the data for a given platform (use to save memory)
clear(GeoPlatform, List, Integer) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: If possible, null out the data for a quantitation type on a given platform.
clearAllCaches() - Method in class ubic.gemma.rest.AdminWebService: Clears every registered cache.
clearAllowedUriPrefixes() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
clearAllowedUriPrefixes() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
clearAllowedUriPrefixes() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
clearAllowedUriPrefixes() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Clear the list of allowed URI prefixes.
clearAuthentication() - Method in interface ubic.gemma.cli.authentication.CLIAuthenticationAware
clearAuthentication() - Method in class ubic.gemma.cli.authentication.GemmaRestApiClientAuthenticator
clearAuthentication() - Method in class ubic.gemma.cli.logging.log4j.UserDetailsThreadContextPopulator
clearAuthentication() - Method in class ubic.gemma.cli.metrics.MeterRegistryCliConfigurer
clearAuthentication() - Method in interface ubic.gemma.core.util.GemmaRestApiClient: Clear any credentials.
clearAuthentication() - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
clearBioAssays() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
clearCache() - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
clearCache() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
clearCache(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache: Remove all elements from the cache for the given result set, if the cache exists.
clearCache(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
clearCache(String) - Method in class ubic.gemma.rest.AdminWebService: Clears a single named cache.
clearCaches() - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Primarily here for testing, to recover memory.
clearCaches() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
clearCachesForOntology(OntologyService) - Method in interface ubic.gemma.core.ontology.OntologyService: Drop every OntologyCache entry tied to the given ontology service.
clearCachesForOntology(OntologyService) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
clearDescriptions() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder
clearDispositions(Long) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Erase every per-finding ruling on an annotation set so it can be dispositioned again from scratch.
clearDispositions(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionService: Erase every ruling on one set, so it can be dispositioned again from scratch.
clearDispositions(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionServiceImpl
ClearDispositionsResponse() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.ClearDispositionsResponse
clearFactorValueNeedsAttention(DatasetArg, Long, String) - Method in class ubic.gemma.rest.DatasetsWebService: Resolve every open needs-attention ticket on a factor value.
clearNeedsAttentionFlag(FactorValue, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionService: Clear a needs attention flag on a given factor value.
clearNeedsAttentionFlag(FactorValue, String) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceImpl
clearPreferredCellTypeAssignment(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
clearPreferredCellTypeAssignment(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
clearPreferredCellTypeAssignment(ExpressionExperiment, SingleCellDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Clear the preferred cell type assignment.
clearPreferredCellTypeAssignment(ExpressionExperiment, SingleCellDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
clearProgress() - Static method in class ubic.gemma.cli.util.AnsiEscapeCodes: Clear a progress indicator.
clearPropertyDirect(String) - Method in class ubic.gemma.core.config.PropertySourcesConfiguration: Deprecated.
clearResultObject() - Method in class ubic.gemma.model.common.search.SearchResult: Clear the result object.
clearResultSetCountsCache(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache: Evict a single result-set entry from the counts cache (called on analysis deletion).
clearResultSetCountsCache(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
clearResultTypes() - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder
clearScalarConversionThreadLocalStorage() - Static method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils: Clear the thread-local storage used for converting scalars.
clearTopHitCache(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache: Remove all elements from the top hits cache for the given result set, if the cache exists.
clearTopHitCache(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
CLI - Interface in ubic.gemma.cli.util: Interface for CLI tools.
CLI - Static variable in class ubic.gemma.core.context.EnvironmentProfiles: Independent feature toggles.
CLI_ARGUMENTS_CONTEXT_KEY - Static variable in class ubic.gemma.cli.main.GemmaCLI: Key used in the Log4j context data.
CLI.CommandGroup - Enum Class in ubic.gemma.cli.util
CliArrayDesignAuditService - Interface in ubic.gemma.cli.audit: Co-bean that owns the audit-emission step for the ArrayDesign-targeted CLI tools.
CliArrayDesignAuditServiceImpl - Class in ubic.gemma.cli.audit: Default CliArrayDesignAuditService implementation.
CliArrayDesignAuditServiceImpl() - Constructor for class ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl
CliAuthConfig - Class in ubic.gemma.cli.authentication
CliAuthConfig() - Constructor for class ubic.gemma.cli.authentication.CliAuthConfig
CLIAuthenticationAware - Interface in ubic.gemma.cli.authentication: Interface for a component that should receive the username/password authentication token from the CLI.
cliAuthenticationManager() - Method in class ubic.gemma.cli.authentication.CliAuthConfig
CLIAuthenticationManager - Class in ubic.gemma.cli.authentication: Manages authentication from the CLI.
CLIAuthenticationManager(ManualAuthenticationService, List) - Constructor for class ubic.gemma.cli.authentication.CLIAuthenticationManager
CliComponentScanConfig - Class in ubic.gemma.cli.config: Component-scan configuration for the gemma-cli module, replacing the XML <context:component-scan> blocks previously declared in applicationContext-component-scan.xml.
CliComponentScanConfig() - Constructor for class ubic.gemma.cli.config.CliComponentScanConfig
CLIContext - Interface in ubic.gemma.cli.util
ClientIdRetrievalStrategy - Interface in ubic.gemma.rest.analytics.ga4: Strategy for retrieving a client ID.
CliExpressionExperimentAuditService - Interface in ubic.gemma.cli.audit: Co-bean owning the audit-emission step for ExpressionExperiment-targeted CLI tools.
CliExpressionExperimentAuditServiceImpl - Class in ubic.gemma.cli.audit: Default CliExpressionExperimentAuditService implementation.
CliExpressionExperimentAuditServiceImpl() - Constructor for class ubic.gemma.cli.audit.CliExpressionExperimentAuditServiceImpl
clInferredLocationProducer(AnnotationRelationDao, PlatformTransactionManager) - Method in class ubic.gemma.core.ontology.OntologyConfig: The entailed CL cell type → anatomical structure locations, from a reviewed file.
ClInferredLocationProducer - Class in ubic.gemma.core.ontology.relation: Cell type → anatomical structure relations that CL entails rather than asserts.
ClInferredLocationProducer(AnnotationRelationDao, TransactionTemplate) - Constructor for class ubic.gemma.core.ontology.relation.ClInferredLocationProducer: 🛑 Constructor-injected and declared as a @Bean in OntologyConfig, NOT a @Service.
clone() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
CLONE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
CLONEEND - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
close() - Method in class ubic.gemma.cli.batch.BatchTaskExecutorService
close() - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter: Print out a summary of what the program did.
close() - Method in interface ubic.gemma.cli.batch.BatchTaskSummaryWriter: Close the writer and write any remaining results.
close() - Method in class ubic.gemma.cli.batch.CompositeBatchTaskSummaryWriter
close() - Method in class ubic.gemma.cli.batch.LoggingBatchTaskSummaryWriter
close() - Method in class ubic.gemma.cli.batch.SuppressBatchTaskSummaryWriter
close() - Method in class ubic.gemma.cli.batch.TextBatchTaskSummaryWriter
close() - Method in class ubic.gemma.cli.batch.TsvBatchTaskSummaryWriter
close() - Method in class ubic.gemma.cli.util.ConsoleProgressReporter
close() - Method in class ubic.gemma.core.goldenpath.GoldenPath
close() - Method in interface ubic.gemma.core.job.progress.ProgressUpdateContext
close() - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
close() - Method in interface ubic.gemma.core.loader.expression.DataLoader: Free any resources that the loaded has setup.
close() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
close() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
close() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
close() - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
close() - Method in class ubic.gemma.core.loader.util.anndata.AnnData
close() - Method in interface ubic.gemma.core.loader.util.anndata.Array
close() - Method in class ubic.gemma.core.loader.util.anndata.CategoricalArray
close() - Method in class ubic.gemma.core.loader.util.anndata.Dataframe
close() - Method in class ubic.gemma.core.loader.util.anndata.DenseMatrix
close() - Method in class ubic.gemma.core.loader.util.anndata.EnumArray
close() - Method in class ubic.gemma.core.loader.util.anndata.Mapping
close() - Method in interface ubic.gemma.core.loader.util.anndata.Matrix: Release the underlying H5 resource for this matrix.
close() - Method in class ubic.gemma.core.loader.util.anndata.NullableArray
close() - Method in class ubic.gemma.core.loader.util.anndata.SparseMatrix
close() - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
close() - Method in class ubic.gemma.core.loader.util.hdf5.H5Attribute
close() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
close() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset.H5Dataspace
close() - Method in class ubic.gemma.core.loader.util.hdf5.H5File
close() - Method in class ubic.gemma.core.loader.util.hdf5.H5Group
close() - Method in class ubic.gemma.core.loader.util.hdf5.H5Type
close() - Method in class ubic.gemma.core.logging.log4j.ProgressUpdateAppender.ProgressUpdateContextImpl
close() - Method in class ubic.gemma.core.metrics.binder.jpa.Hibernate4QueryMetrics
close() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
close() - Method in class ubic.gemma.core.ontology.jena.TdbOntologyService
close() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
close() - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyIndex
close() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
close() - Method in class ubic.gemma.core.ontology.search.JenaTextOntologySearchService: Best-effort cleanup of the underlying dataset.
close() - Method in class ubic.gemma.core.profiling.StopWatchUtils.StopWatchRegion
close() - Method in interface ubic.gemma.core.security.util.ActingIdentity.Scope
close() - Method in interface ubic.gemma.core.util.locking.LockedPath: Release the lock.
close() - Method in class ubic.gemma.core.util.LoggingProgressReporter
close() - Method in class ubic.gemma.core.util.ProgressInputStream
close() - Method in interface ubic.gemma.core.util.ProgressReporter: Clear any progress that was rendered.
close() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition
close(RetryContext, RetryCallback, Throwable) - Method in class ubic.gemma.persistence.retry.RetryLogger
closeAndGetPath() - Method in interface ubic.gemma.core.util.locking.LockedPath: Release the lock and obtain the underlying Path object.
CLOSED - Enum constant in enum class ubic.gemma.model.pipeline.PipelineJobBatch.BatchState
code(int) - Method in class ubic.gemma.rest.util.WellComposedErrorBody.WellComposedErrorBodyBuilder
colaxpy_j(int, double, double[][], int, int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method multiplies a constant times a portion of a column of a matrix and adds the product to the corresponding portion of another column of the matrix --- a portion of col2 is replaced by the corresponding portion of a*col1 + col2.
coldot_j(int, double[][], int, int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method calculates the dot product of portions of two columns of a matrix.
colisamax_j(int, double[][], int, int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method finds the index of the element of a portion of a column of a matrix that has the maximum absolute value.
collapse(Collection) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Convert a CompositeSequence's immobilizedCharacteristics into a single sequence, using a simple merge-join strategy.
COLLAPSED_NAME_SUFFIX - Static variable in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Suffix appended to a CompositeSequence's name to name the SequenceType.AFFY_COLLAPSED BioSequence built from its reporters.
collection() - Method in class ubic.gemma.rest.util.args.FilterArgParser
collection() - Method in class ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
COLLECTION_OF_MATERIAL_URI - Static variable in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
CollectionContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
CollectionMetadata - Class in ubic.gemma.core.loader.expression.cellxgene.model
CollectionMetadata() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
collectionOperator() - Method in class ubic.gemma.rest.util.args.FilterArgParser
collectionOperator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
collectionOperator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
CollectionOperatorContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
colNameMap - Variable in class ubic.gemma.core.util.matrix.MatrixWriter
colnrm2_j(int, double[][], int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method calculates the Euclidean norm of a portion of a column of a matrix.
colorMap - Variable in class ubic.gemma.core.util.graphics.ColorMatrix
ColorMap - Class in ubic.gemma.core.util.graphics
ColorMap() - Constructor for class ubic.gemma.core.util.graphics.ColorMap
ColorMap(int) - Constructor for class ubic.gemma.core.util.graphics.ColorMap
ColorMap(int, Color[]) - Constructor for class ubic.gemma.core.util.graphics.ColorMap: Pre-condition: suggestedNumberOfColors > colorMap.length
ColorMap(Color[]) - Constructor for class ubic.gemma.core.util.graphics.ColorMap
ColorMatrix<A,B> - Class in ubic.gemma.core.util.graphics: Creates a color matrix from a matrix of doubles
ColorMatrix(DoubleMatrix) - Constructor for class ubic.gemma.core.util.graphics.ColorMatrix
ColorMatrix(DoubleMatrix, Color[], Color) - Constructor for class ubic.gemma.core.util.graphics.ColorMatrix
colors - Variable in class ubic.gemma.core.util.graphics.ColorMatrix
colrot_j(int, double[][], int, int, double, double) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method "applies a plane rotation." It is a modification of the LINPACK function DROT.
colscal_j(int, double, double[][], int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method scales a portion of a column of a matrix by a constant.
colSums(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixStats: NaN values are omitted from calculations.
colswap_j(int, double[][], int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method interchanges two columns of a matrix.
ColumnMeta() - Constructor for class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta
columns() - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
columns() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
columns() - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
columns() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Obtain the total number of columns.
columns() - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
columns() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
columns() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
columns() - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
columns() - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
columns() - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
columns() - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
columns() - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Get the number of columns the matrix has.
columns() - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
columns() - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
columns() - Method in class ubic.gemma.core.util.matrix.StringMatrix
columns(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
columns(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix: Number of columns that use the given design element.
columnsAfter() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage: Returns the value of the columnsAfter record component.
colvaxpy_j(int, double, double[][], double[], int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method multiplies a constant times a portion of a column of a matrix x[][] and adds the product to the corresponding portion of a vector y[] --- a portion of y[] is replaced by the corresponding portion of ax[][j] + y[].
colvdot_j(int, double[][], double[], int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method calculates the dot product of a portion of a column of a matrix and the corresponding portion of a vector.
colvraxpy_j(int, double, double[], double[][], int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method multiplies a constant times a portion of a vector y[] and adds the product to the corresponding portion of a column of a matrix x[][] --- a portion of column j of x[][] is replaced by the corresponding portion of ay[] + x[][j].
comBat(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService: Run ComBat using default settings (parametric)
comBat(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
comBat(ExpressionExperiment, ExpressionDataDoubleMatrix) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService: Run ComBat with a specific data matrix.
comBat(ExpressionExperiment, ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
CommandMeta(String, String) - Constructor for class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator.CommandMeta
commence(HttpServletRequest, HttpServletResponse, AuthenticationException) - Method in class ubic.gemma.rest.security.RestAuthEntryPoint
comment() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Returns the value of the comment record component.
comment() - Method in record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Returns the value of the comment record component.
comment() - Element in annotation interface ubic.gemma.model.annotations.WithheldFromApi: The specific hazard, the projection to use instead, or what to check before exposing this.
COMMENT - Static variable in class ubic.gemma.core.util.TsvUtils
COMMENT_EDITED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType: Deferred — see Decision 4 in the recce doc.
COMMENT_MARK - Static variable in class ubic.gemma.core.loader.util.parser.BasicLineMapParser: Lines starting with this will be ignored.
COMMENTED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType
CommentedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: An event indicating a comment was added to the auditable.
CommentedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent
COMMIT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetRole
commitCuration(ExpressionExperiment, CurationCommitRequest, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Apply an all-or-none curation commit to ee, reconciling the sections carried in request in a single transaction (phase 1: basics + publications).
commitCuration(ExpressionExperiment, CurationCommitRequest, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
commitCuration(DatasetArg, Boolean, String, DatasetsWebService.CurationDocument) - Method in class ubic.gemma.rest.DatasetsWebService
committedBytes - Variable in class ubic.gemma.rest.AdminWebService.MemoryBlock
CommonalityRankingStrategy - Class in ubic.gemma.rest.ranking: Orders hits by how commonly prior curators wrote the query string to mean each candidate.
CommonalityRankingStrategy(double, double) - Constructor for class ubic.gemma.rest.ranking.CommonalityRankingStrategy: Convenience constructor pinning the shape weight to the production default.
CommonalityRankingStrategy(double, double, double) - Constructor for class ubic.gemma.rest.ranking.CommonalityRankingStrategy
CommonPersister - Class in ubic.gemma.persistence.persister: Persister for ubic.gemma.model.common package classes.
CommonPersister() - Constructor for class ubic.gemma.persistence.persister.CommonPersister
commonPrefix(Collection) - Static method in class ubic.gemma.core.util.StringUtil: Given a set of strings, identify any prefix they have in common.
CommonQueries - Class in ubic.gemma.persistence.util: Contains methods to perform 'common' queries that are needed across DAOs.
CommonQueries() - Constructor for class ubic.gemma.persistence.util.CommonQueries
commonSuffix(Collection) - Static method in class ubic.gemma.core.util.StringUtil: Given a set of strings, identify any suffix they have in common.
CompactAuditEventValueObject - Class in ubic.gemma.rest: Wire payload for GET /datasets/{id}/auditEvents?compact=true.
CompactAuditEventValueObject(AuditEventValueObject, int, Date) - Constructor for class ubic.gemma.rest.CompactAuditEventValueObject
COMPARATOR - Static variable in class ubic.gemma.model.common.measurement.Measurement
COMPARATOR - Static variable in interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics
COMPARATOR - Static variable in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment
COMPARATOR - Static variable in class ubic.gemma.model.expression.biomaterial.BioMaterial
COMPARATOR - Static variable in class ubic.gemma.model.expression.experiment.ExperimentalFactor
compare(double, int, double, int) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Statistical comparison of two Pearson correlations.
compare(OntologySearchResult, OntologySearchResult) - Method in class ubic.gemma.core.ontology.search.OntologySearchResult
compare(DifferentialExpressionAnalysisResult, DifferentialExpressionAnalysisResult) - Method in class ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator
compare(Describable, Describable) - Method in class ubic.gemma.persistence.util.DescribableComparator
compare(FactorValue, FactorValue) - Method in class ubic.gemma.persistence.util.FactorValueComparator
compareTerm(String, String, String, String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Compare a pair of ontology terms.
compareTo(CompositeSequenceMapValueObject) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
compareTo(ExpressionDataMatrixRowElement) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
compareTo(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
compareTo(SearchResultDisplayObject) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
compareTo(AclEntry) - Method in class ubic.gemma.core.security.acl.domain.AclEntry
compareTo(Characteristic) - Method in class ubic.gemma.model.common.description.Characteristic
compareTo(Characteristic) - Method in class ubic.gemma.model.expression.experiment.Statement
compareTo(CharacteristicValueObject) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
compareTo(CitationValueObject) - Method in class ubic.gemma.model.common.description.CitationValueObject
compareTo(ExternalDatabaseValueObject) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
compareTo(SearchResult) - Method in class ubic.gemma.model.common.search.SearchResult
compareTo(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
compareTo(StatementValueObject) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
compile(String) - Static method in class ubic.gemma.core.util.XMLUtils: Compile an XPath expression.
CompleteCli - Class in ubic.gemma.apps: This CLI provide various runtime completions that can be re-used by other CLIs.
CompleteCli() - Constructor for class ubic.gemma.apps.CompleteCli
completed - Variable in class ubic.gemma.rest.AdminWebService.JobsListResponse
completed() - Method in class ubic.gemma.cli.pipeline.PipelineJobReporter: Terminal success.
COMPLETED - Enum constant in enum class ubic.gemma.core.job.SubmittedTask.Status
COMPLETED - Enum constant in enum class ubic.gemma.model.expression.experiment.GeoScrapeWatermark.Status
Completion(String, String) - Constructor for class ubic.gemma.cli.completion.CompletionSource.Completion
CompletionGenerator - Interface in ubic.gemma.cli.completion
CompletionSource - Interface in ubic.gemma.cli.completion: Defines a source of completions.
CompletionSource.Completion - Class in ubic.gemma.cli.completion
CompletionsWebService - Class in ubic.gemma.rest: Prefix-aware completion suggestions for CLI / curation-UI / REST clients.
CompletionsWebService() - Constructor for class ubic.gemma.rest.CompletionsWebService
CompletionsWebService.CompletionValueObject - Class in ubic.gemma.rest: Wire shape for a single completion suggestion.
CompletionType - Enum Class in ubic.gemma.cli.completion
CompletionUtils - Class in ubic.gemma.cli.completion: Utilities for generating completions.
CompletionUtils() - Constructor for class ubic.gemma.cli.completion.CompletionUtils
CompletionValueObject(String, String) - Constructor for class ubic.gemma.rest.CompletionsWebService.CompletionValueObject: Creates a new CompletionValueObject instance.
ComponentScanConfig - Class in ubic.gemma.core.config: Phase 3 XML->Java migration: replaces applicationContext-component-scan.xml.
ComponentScanConfig() - Constructor for class ubic.gemma.core.config.ComponentScanConfig
ComponentValueObject(String, Map) - Constructor for class ubic.gemma.rest.monitoring.HealthWebService.ComponentValueObject
CompositeBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch
CompositeBatchTaskSummaryWriter(List) - Constructor for class ubic.gemma.cli.batch.CompositeBatchTaskSummaryWriter
CompositeClientIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Composite strategy for retrieving client ID.
CompositeClientIdRetrievalStrategy(List) - Constructor for class ubic.gemma.rest.analytics.ga4.CompositeClientIdRetrievalStrategy
CompositeMeterRegistryFactory - Class in ubic.gemma.core.metrics: Static factories for Micrometer registries that need a wiring step Spring XML cannot express directly (because the constructors take Clock or PrometheusConfig statics that are public fields, not factory methods).
CompositeRankingStrategy - Class in ubic.gemma.rest.ranking: Combined ranker that blends all three primary signals into a single score per hit:
CompositeRankingStrategy(double, double, double) - Constructor for class ubic.gemma.rest.ranking.CompositeRankingStrategy
CompositeSearchSource - Class in ubic.gemma.core.search.source: A search source constituted of multiple other sources.
CompositeSearchSource(List) - Constructor for class ubic.gemma.core.search.source.CompositeSearchSource
CompositeSequence - Class in ubic.gemma.model.expression.designElement: A "Probe set" (Affymetrix) or a "Probe" (other types of arrays).
CompositeSequence() - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequence
CompositeSequence.Factory - Class in ubic.gemma.model.expression.designElement
CompositeSequenceArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for Composite Sequence arguments.
CompositeSequenceArg(String, Class, T) - Constructor for class ubic.gemma.rest.util.args.CompositeSequenceArg
CompositeSequenceArgService - Class in ubic.gemma.rest.util.args
CompositeSequenceArgService(CompositeSequenceService) - Constructor for class ubic.gemma.rest.util.args.CompositeSequenceArgService
CompositeSequenceArrayArg - Class in ubic.gemma.rest.util.args
CompositeSequenceDao - Interface in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceDao.BioSequenceLite - Record Class in ubic.gemma.persistence.service.expression.designElement: Lightweight (sequence, length) projection used to hydrate CompositeSequenceValueObject.getSequence() + CompositeSequenceValueObject.getSequenceLength() on opt-in platform-elements requests.
CompositeSequenceDaoImpl - Class in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
CompositeSequenceGeneMapperService - Class in ubic.gemma.core.analysis.service
CompositeSequenceGeneMapperService() - Constructor for class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService
CompositeSequenceIdArg - Class in ubic.gemma.rest.util.args: Composite Sequence argument for CS ID.
CompositeSequenceMapSummary - Class in ubic.gemma.core.analysis.sequence: This is a convenience object to hold the results of CompositeSequence mapping results.
CompositeSequenceMapSummary(CompositeSequence) - Constructor for class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
CompositeSequenceMapValueObject - Class in ubic.gemma.core.analysis.sequence
CompositeSequenceMapValueObject() - Constructor for class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
CompositeSequenceNameArg - Class in ubic.gemma.rest.util.args: Composite Sequence argument for CS name.
CompositeSequenceParser - Class in ubic.gemma.core.loader.expression.arrayDesign: Parse the "old" array description format.
CompositeSequenceParser() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
CompositeSequenceReadService - Interface in ubic.gemma.persistence.service.expression.designElement: Read-only retrieval service for CompositeSequence.
CompositeSequenceReadServiceImpl - Class in ubic.gemma.persistence.service.expression.designElement: Implementation of CompositeSequenceReadService.
CompositeSequenceReadServiceImpl(CompositeSequenceDao) - Constructor for class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
compositeSequenceSearch(String, ArrayDesign) - Static method in class ubic.gemma.model.common.search.SearchSettings: Convenience method to get pre-configured settings.
CompositeSequenceService - Interface in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceServiceImpl - Class in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceServiceImpl(CompositeSequenceDao, BioSequenceService, GeneProductService, BlatResultService, ArrayDesignService, CompositeSequenceReadService) - Constructor for class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
CompositeSequenceSummaryValueObject(CompositeSequenceValueObject, List, int, Integer) - Constructor for class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject
CompositeSequenceValueObject - Class in ubic.gemma.model.expression.designElement
CompositeSequenceValueObject() - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Required when using the class as a spring bean.
CompositeSequenceValueObject(Long) - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
CompositeSequenceValueObject(CompositeSequence) - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
CompositeSequenceValueObject(CompositeSequence, ArrayDesignValueObject) - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Constructor that reuses an existing ArrayDesignValueObject.
Compound - Class in ubic.gemma.model.expression.biomaterial: Hibernate Search 7 mapping: chemicals attached to BibliographicReference via @IndexedEmbedded; name is tokenized, registryNumber is keyword (CAS).
Compound() - Constructor for class ubic.gemma.model.expression.biomaterial.Compound
COMPOUND - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
Compound.Factory - Class in ubic.gemma.model.expression.biomaterial
CompoundDao - Interface in ubic.gemma.persistence.service.expression.biomaterial
CompoundDaoImpl - Class in ubic.gemma.persistence.service.expression.biomaterial: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.biomaterial.Compound.
CompoundDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.CompoundDaoImpl
CompoundService - Interface in ubic.gemma.persistence.service.expression.biomaterial
CompoundServiceImpl - Class in ubic.gemma.persistence.service.expression.biomaterial: Spring Service base class for CompoundService, provides access to all services and entities referenced by this service.
CompoundServiceImpl(CompoundDao) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.CompoundServiceImpl
compress(List) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType: Compress the given list of strings into a gzip-compressed input stream.
compressedsparse(int, int) - Static method in class ubic.gemma.core.util.matrix.DoubleMatrixFactory
CompressedSparseDoubleMatrix<R,C> - Class in ubic.gemma.core.util.matrix: Supports sparse matrices (where sparse means most values are zero, not that they are missing).
CompressedSparseDoubleMatrix(double[][]) - Constructor for class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
CompressedSparseDoubleMatrix(int, int) - Constructor for class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
CompressedStringListType - Class in ubic.gemma.persistence.hibernate: Type that transparently stores a List of String as gzip-compressed blob.
CompressedStringListType() - Constructor for class ubic.gemma.persistence.hibernate.CompressedStringListType
CompRowMatrixUtils - Class in ubic.gemma.core.datastructure.sparse: Utilities for CompRowMatrix.
CompRowMatrixUtils() - Constructor for class ubic.gemma.core.datastructure.sparse.CompRowMatrixUtils
compute(ExpressionExperiment, PreparedCoexMatrices) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService: Computes sample correlation matrices for the given experiment.
compute(ExpressionExperiment, PreparedCoexMatrices) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl: Unfortunately, this method breaks under high contention (see #400, so we need to fully lock the database while undergoing using Isolation.SERIALIZABLE transaction isolation level.
computeMatrixSimilarity(Gene, Gene, DoubleMatrix, GoMetric.Metric) - Method in interface ubic.gemma.core.ontology.GoMetric
computeMatrixSimilarity(Gene, Gene, DoubleMatrix, GoMetric.Metric) - Method in class ubic.gemma.core.ontology.GoMetricImpl
computeMaxSimilarity(Gene, Gene, Map, GoMetric.Metric) - Method in interface ubic.gemma.core.ontology.GoMetric
computeMaxSimilarity(Gene, Gene, Map, GoMetric.Metric) - Method in class ubic.gemma.core.ontology.GoMetricImpl
computeMergedOverlap(List, List, Map) - Method in interface ubic.gemma.core.ontology.GoMetric
computeMergedOverlap(List, List, Map) - Method in class ubic.gemma.core.ontology.GoMetricImpl: Tailored to handle computing overlap between two gene lists which may contain duplicate genes of the same name but different IDs.
computeMissingValues(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
computeMissingValues(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl
computeMissingValues(ExpressionExperiment, double, Collection) - Method in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
computeMissingValues(ExpressionExperiment, double, Collection) - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl
computeOverlap(long, long, long, long) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
computeOverlap(Collection, Collection) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
computeOverlap(Collection, Collection) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
computeOverlap(PhysicalLocation, PhysicalLocation) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Compute the overlap between two physical locations.
computeOverlapFraction(BlatAssociation) - Static method in class ubic.gemma.core.analysis.sequence.BlatAssociationScorer: Compute how much the BLAT alignment with the target gene product is as a fraction of the query sequence length.
computeSampleCorrelation(ExpressionExperiment) - Method in interface ubic.gemma.cli.audit.CliExpressionExperimentAuditService: Runs the sample-correlation compute step for an experiment.
computeSampleCorrelation(ExpressionExperiment) - Method in class ubic.gemma.cli.audit.CliExpressionExperimentAuditServiceImpl
computeSimilarity(Gene, Gene, Map, GoMetric.Metric) - Method in interface ubic.gemma.core.ontology.GoMetric
computeSimilarity(Gene, Gene, Map, GoMetric.Metric) - Method in class ubic.gemma.core.ontology.GoMetricImpl
computeSimpleOverlap(Gene, Gene, Map) - Method in interface ubic.gemma.core.ontology.GoMetric
computeSimpleOverlap(Gene, Gene, Map) - Method in class ubic.gemma.core.ontology.GoMetricImpl
computeSize(boolean, boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay: compute the size of the matrix in pixels.
computeUnmaskedProcessedDataMatrix(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Rebuild the processed data matrix from raw WITHOUT masking assays flagged as outliers, persisting nothing.
computeUnmaskedProcessedDataMatrix(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
CONC - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementKind: Concentration
CONCENTRATION - Static variable in enum class ubic.gemma.model.common.measurement.MeasurementKind: Alias for readability.
cond() - Method in class ubic.gemma.core.util.math.linalg.SingularValueDecomposition
Condition(Long, Long) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
Condition(ExpressionExperimentValueObject, DifferentialExpressionAnalysisValueObject, DiffExResultSetSummaryValueObject, FactorValueValueObject) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
CONFIDENCEINDICATOR - Enum constant in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Indicate a confidence level.
config() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Returns the value of the config record component.
configExperimentalFactorValueObject(ExperimentalFactor) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService
configExperimentalFactorValueObject(ExperimentalFactor) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
Configuration - Class in ubic.gemma.core.config: Configuration of ontology services and other things.
Configuration() - Constructor for class ubic.gemma.core.config.Configuration
ConfigurationLinter - Class in ubic.gemma.cli.config: Lint various aspects of the configuration for the CLI profile.
ConfigurationLinter() - Constructor for class ubic.gemma.cli.config.ConfigurationLinter
configure(MeterRegistry) - Method in class ubic.gemma.cli.metrics.MeterRegistryCliConfigurer
configure(MeterRegistry) - Method in class ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer
configure(MeterRegistry) - Method in class ubic.gemma.core.metrics.GenericMeterRegistryConfigurer
configure(MeterRegistry) - Method in class ubic.gemma.core.metrics.MeterRegistryJCacheConfigurer
configureAllLoggers(int) - Method in class ubic.gemma.cli.logging.log4j.Log4jConfigurer
configureAllLoggers(int) - Method in interface ubic.gemma.cli.logging.LoggingConfigurer: Set the logging level of all loggers.
configureAllLoggers(String) - Method in interface ubic.gemma.cli.logging.LoggingConfigurer: Set the logging level of all loggers using a named level.
configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao: Register filterable properties.
configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
configureLoader(C) - Method in interface ubic.gemma.core.loader.expression.DataLoaderConfigurer: Create a DataLoader from the given configuration.
configureLoader(SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataConfigurer
configureLoader(SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer: Automatically configure a loader for an AnnData file.
configureLoader(SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer
configureLoader(SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfigurer
configureLoader(SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderConfigurer
configureLoader(SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer
configureLoader(SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoaderConfigurer
configureLoader(SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.SequencingMetadataFileSingleCellDataLoaderConfigurer
configureLogger(String, int) - Method in class ubic.gemma.cli.logging.log4j.Log4jConfigurer: Set up logging according to the user-selected (or default) verbosity level.
configureLogger(String, int) - Method in interface ubic.gemma.cli.logging.LoggingConfigurer: Set the logging level of a specific logger.
configureLogger(String, String) - Method in interface ubic.gemma.cli.logging.LoggingConfigurer: Set the logging level of a specific logger using a named level.
ConfigUtils - Class in ubic.gemma.core.config: Shared configuration helpers.
ConfigUtils - Class in ubic.gemma.core.util: Convenience methods for loading configurations.
ConfluenceWikiHtmlGenerator - Class in ubic.gemma.cli.completion: Generate Wiki pages according to Confluence Storage Format
ConfluenceWikiHtmlGenerator(Path) - Constructor for class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator
ConfluenceWikiHtmlGenerator.CommandMeta - Class in ubic.gemma.cli.completion
conjunction(BooleanArrayList, BooleanArrayList) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil: Compute the conjuction (logical 'and') of two boolean vectors
CONJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
CONJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
CONJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
CONJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
CONJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
CONJUNCTION(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
CONJUNCTION(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
connect(int) - Method in class ubic.gemma.core.util.NetDatasourceUtil
connect(int, String, String, String) - Static method in class ubic.gemma.core.util.NetUtils: Convenience method to get an FTP connection.
connectionTimeoutMillis - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
CONSIDER_URI - Static variable in class ubic.gemma.core.ontology.OntologyUtils: oboInOwl:consider — a pointer to terms a CURATOR might consider in place of an obsolete one.
console(Console) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder
console(Console) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Console to use for reporting progress.
ConsoleProgressReporter - Class in ubic.gemma.cli.util
ConsoleProgressReporter(Object, Console) - Constructor for class ubic.gemma.cli.util.ConsoleProgressReporter
ConsoleProgressReporterFactory - Class in ubic.gemma.cli.util: A console-based progress reporter factory.
ConsoleProgressReporterFactory(Console) - Constructor for class ubic.gemma.cli.util.ConsoleProgressReporterFactory
Constants - Class in ubic.gemma.core.util: Constants used across Gemma.
Constants - Class in ubic.gemma.core.util.math: Numeric constants used in some ports of statistical code.
Constants() - Constructor for class ubic.gemma.core.util.Constants
Constants() - Constructor for class ubic.gemma.core.util.math.Constants
constantTimeHexEquals(String, String) - Static method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder: Constant-time, case-insensitive comparison of two hex strings of equal length.
constructAssayName(BioAssay, boolean, boolean) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils: Construct a BioAssay column name, unprefixed by the BioMaterial from which it originates.
constructAssaysName(Collection, boolean, boolean, char) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils
constructCellId(BioAssay, String, boolean, boolean) - Static method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserUtils: Construct a cell ID for the Cell Browser.
constructCellIdName(BioAssay, String, boolean, boolean) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils: Construct a BioAssay column name, unprefixed by the BioMaterial from which it originates.
constructCitation(BibliographicReference) - Static method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
constructCitations(Collection) - Static method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
constructConditionId(long, long) - Static method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
constructDatasetName(ExpressionExperiment) - Static method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserUtils
constructExperimentalFactorName(ExperimentalFactor) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils: Construct an ExperimentalFactor column name.
constructExperimentalFactorNames(List) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils: Construct an ExperimentalFactor column names for a list of factors.
constructSampleName(BioMaterial, boolean, boolean) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils
constructSampleName(BioMaterial, Collection, boolean, boolean, char) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils: Construct a BioAssay column name prefixed by the BioMaterial from which it originates.
constructSampleName(BioMaterial, BioAssay, boolean, boolean) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils: Construct a sample name in case there is only one BioAssay attached to the corresponding BioMaterial.
Contact - Class in ubic.gemma.model.common.auditAndSecurity: Representing a person or organization that can be contacted about, or is the source of, data in the system.
Contact() - Constructor for class ubic.gemma.model.common.auditAndSecurity.Contact
Contact.Factory - Class in ubic.gemma.model.common.auditAndSecurity
ContactDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
ContactDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
ContactDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.ContactDaoImpl
contactName - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
ContactUtils - Class in ubic.gemma.model.common.auditAndSecurity: Helpers for reading a Contact the way a person is displayed.
contains(Object) - Method in class ubic.gemma.model.util.UninitializedCollection
contains(String) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper.StatefulEntityMapper: Check if any of the candidates can be mapped to the identifier.
contains(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.ChainedEntityMapper
contains(Collection, String) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper: Check if any of the candidates can be mapped to the identifier.
contains(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
contains(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper
containsAll(Collection) - Method in class ubic.gemma.model.util.UninitializedCollection
containsAny(Collection) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper.StatefulEntityMapper: Check if any of the candidates can be mapped to any of the identifiers.
containsAny(Collection, Collection) - Method in class ubic.gemma.core.loader.util.mapper.ChainedEntityMapper
containsAny(Collection, Collection) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper: Check if any of the candidates can be mapped to any of the identifiers.
containsAny(Collection, Collection) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
containsAny(Collection, Collection) - Method in class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper
containsAnyAlias(Filters, Sort, String...) - Static method in class ubic.gemma.persistence.util.FiltersUtils: Check if an alias is mentioned in a set of Filter.
containsColumnName(C) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
containsColumnName(C) - Method in interface ubic.gemma.core.util.matrix.Matrix2D
containsGene(Gene, GeneSet) - Static method in class ubic.gemma.model.genome.gene.GeneSet
containsKey(Integer) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParser
containsKey(String) - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
containsKey(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
containsKey(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
containsKey(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
containsKey(String) - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParser
containsKey(String) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser: Method that returns a particular BioMartEnsembleNcbi based on a peptide id.
containsKey(K) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
containsKey(Cache, Object) - Static method in class ubic.gemma.persistence.cache.CacheUtils
containsKey(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
containsKeyInternal(String) - Method in class ubic.gemma.core.config.PropertySourcesConfiguration: Deprecated.
containsNearlyZeros(DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
containsRowName(R) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
containsRowName(R) - Method in interface ubic.gemma.core.util.matrix.Matrix2D
containsValueInternal(Object) - Method in class ubic.gemma.core.config.PropertySourcesConfiguration: Deprecated.
contentTokens(String) - Static method in class ubic.gemma.rest.ranking.QueryTokens: Tokenise an arbitrary user query into "content" tokens: lowercase, split on runs of non-alphanumeric characters, drop tokens shorter than QueryTokens.MIN_CONTENT_TOKEN_LENGTH, drop stop-words.
contextDestroyed(ServletContextEvent) - Method in class ubic.gemma.rest.servlet.JdbcDriverDeregistrationListener
contextDestroyed(ServletContextEvent) - Method in class ubic.gemma.rest.servlet.JerseyClientAbortLogFilter
contextDestroyed(ServletContextEvent) - Method in class ubic.gemma.rest.servlet.StartupLogNoiseFilter
contextInitialized(ServletContextEvent) - Method in class ubic.gemma.rest.servlet.JerseyClientAbortLogFilter
contextInitialized(ServletContextEvent) - Method in class ubic.gemma.rest.servlet.StartupLogNoiseFilter
continuous - Enum constant in enum class ubic.gemma.model.expression.experiment.FactorType
continuous(ExperimentalFactor) - Static method in class ubic.gemma.model.analysis.expression.diff.Contrast: Create a contrast for a continuous factor.
CONTINUOUS - Static variable in enum class ubic.gemma.model.expression.experiment.FactorType: Aliases for consistency.
Contrast - Class in ubic.gemma.model.analysis.expression.diff: Represents a contrast.
ContrastResult - Class in ubic.gemma.model.analysis.expression.diff: Represents a contrast between "conditions".
ContrastResult() - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastResult
ContrastResult.Factory - Class in ubic.gemma.model.analysis.expression.diff
ContrastResultValueObject - Class in ubic.gemma.model.analysis.expression.diff: Represents a contrast result.
ContrastResultValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
ContrastResultValueObject(ContrastResult, boolean) - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject: Create a contrast value object from a given ContrastResult.
ContrastsValueObject - Class in ubic.gemma.model.analysis.expression.diff: Stores selected details of the contrasts for a single DifferentialExpressionResult
ContrastsValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
ContrastsValueObject(Long) - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
ContrastsValueObject(DifferentialExpressionAnalysisResult) - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
ContrastVO - Class in ubic.gemma.model.analysis.expression.diff: Helper object, not for general use.
ContrastVO() - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastVO
ContrastVO(Long, Long, Long, Double, Double) - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastVO
ContrastVO(ContrastResult) - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastVO
contributeFunctions(FunctionContributions) - Method in class ubic.gemma.persistence.hibernate.BinaryFunctionContributor
conversionService() - Method in class ubic.gemma.core.config.SettingsConfig: The default Spring conversion service has limited support for Java 8 types.
convert(Object) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
convert(Object, TypeDescriptor, TypeDescriptor) - Method in class ubic.gemma.persistence.util.ServiceBasedEntityConverter
convert(Object, TypeDescriptor, TypeDescriptor) - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverter
convert(Collection) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
convert(Collection) - Method in interface ubic.gemma.core.loader.util.converter.Converter
convert(Collection) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convert(Collection) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(Collection, Class) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter: Convert a collection of GeoData objects, retaining only elements of the specified data type.
convert(Collection, Class) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(BlockingQueue, BlockingQueue) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
convert(S) - Method in interface ubic.gemma.core.loader.util.converter.Converter
convert(CollectionMetadata, DatasetMetadata, ArrayDesign, Collection, String, SingleCellDataLoader, boolean) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneConverter
convert(GeoData) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convert(GeoData) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(GeoDataset, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convert(GeoDataset, boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(GeoPlatform) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convert(GeoPlatform) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(GeoSeries) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convert(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(GeoSeries, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convert(GeoSeries, boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(SimpleExpressionExperimentMetadata, DoubleMatrix) - Method in interface ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService: Convert simple experiment metadata and data into Gemma objects.
convert(SimpleExpressionExperimentMetadata, DoubleMatrix) - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl
convert(NCBIGene2Accession, Gene) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
convert(NCBIGeneInfo) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
convert(NcbiGeneData) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
convert(ArrayDesignValueObject) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject.FromArrayDesignValueObject
convert2CitationValueObject(BibliographicReference) - Static method in class ubic.gemma.model.common.description.CitationValueObject
convert2CitationValueObjects(Collection) - Static method in class ubic.gemma.model.common.description.CitationValueObject
convert2ValueObject(Gene) - Static method in class ubic.gemma.model.genome.gene.GeneValueObject: Converts a Gene to a GeneValueObject
convert2ValueObjects(Collection) - Static method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject: does not set related experiments field
convertData(double[], QuantitationType, ScaleType) - Static method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils: Convert a vector of double data to the target scale.
convertData(double[], StandardQuantitationType, ScaleType, ScaleType) - Static method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils
convertData(float[], QuantitationType, ScaleType) - Static method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils: Convert a vector of float data to the target scale.
convertData(int[], ScaleType) - Static method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils: Convert a vector of counting data to the target scale.
convertData(long[], ScaleType) - Static method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils: Convert a vector of counting data to the target scale.
convertData(DataVector, ScaleType) - Static method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils: Convert a vector to the target scale.
Converter<S,T> - Interface in ubic.gemma.core.loader.util.converter: Defines a class that can convert objects from one type to another.
convertH5Exception(HDF5Exception) - Static method in class ubic.gemma.core.loader.util.hdf5.H5Utils: Convert an HDF5 exception to an IOException or a H5Exception.
convertibleTypes - Variable in class ubic.gemma.persistence.util.ServiceBasedEntityConverter
convertMembers2GeneValueObjects(Collection) - Static method in class ubic.gemma.model.genome.gene.GeneValueObject: A static method for easily converting GeneSetMembers into GeneValueObjects
convertScalar(Number, QuantitationType, ScaleType) - Static method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils: Convert a single number.
convertSearchResults2SearchResultDisplayObjects(List) - Static method in class ubic.gemma.core.search.SearchResultDisplayObject: Creates a collection of SearchResultDisplayObjects from a collection of objects.
convertStringToDate(String, String) - Static method in class ubic.gemma.core.util.DateUtil: This method generates a string representation of a date/time in the format you specify on input.
convertStringToExperimentType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset: gene expression array-based, gene expression SAGE-based, gene expression MPSS-based, gene expression RT-PCR-based, protein expression array-based, protein expression MS-based, array CGH, ChIP-chip, SNP
convertStringToMolecule(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
convertStringToPlatformType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
convertStringToRepeatType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication: Convert a string e.g.
convertStringToSampleType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
convertStringToSeriesType(String) - Static method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParser: See also GeoDataset.convertStringToExperimentType
convertStringToType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable: Convert a string found in the GEO sample descriptions e.g., "age" to the corresponding category, represented here by VariableType.
convertStringToValueType(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset: count, log ratio, log2 ratio, log10 ratio, logE ratio, log e ratio, transformed count
convertSubsetToExperimentalFactor(ExpressionExperiment, GeoSubset) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter: Converts Geo subsets to experimental factors.
convertSubsetToExperimentalFactor(ExpressionExperiment, GeoSubset) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convertToEntity(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper
convertToEntity(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl: Tries to load an existing experiment set with the param's id, if no experiment can be loaded, create a new one with id = null.
convertToGOValueObject(GeneSet, String, String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper: Method to create a GO group object from an ad hoc entity
convertToGOValueObject(GeneSet, String, String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
convertToLightValueObject(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper: Constructor to build value object from GeneSet.
convertToLightValueObject(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
convertToLightValueObjects(Collection, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper: results will be sorted by size
convertToLightValueObjects(Collection, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
convertToLog2(DoubleMatrix, double) - Static method in class ubic.gemma.core.util.math.MatrixStats: Convert a log_b-transformed data set to log 2.
convertToLog2Cpm(DoubleMatrix, DoubleMatrix1D) - Static method in class ubic.gemma.core.util.math.MatrixStats: Convert a count matrix to log2 counts per million.
convertToValueObject(GeneDifferentialExpressionMetaAnalysis) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperService: Convert the given meta-analysis into detail value object.
convertToValueObject(GeneDifferentialExpressionMetaAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperServiceImpl
convertToValueObject(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper: Constructor to build value object from GeneSet.
convertToValueObject(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
convertToValueObjects(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
convertToValueObjects(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
convertToValueObjects(Collection, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
convertToValueObjects(Collection, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
convertVectors(Collection, PrimitiveType, Class) - Static method in class ubic.gemma.core.analysis.preprocess.convert.RepresentationConversionUtils: Convert a collection of vectors to a desired representation.
convertVectors(Collection, ScaleType, Class) - Static method in class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils
Coordinate - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser.model
Coordinate() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
COORDINATE - Enum constant in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Used to represent a value for a spatial coordinate.
copy() - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
copy() - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
copy() - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
copy() - Method in class ubic.gemma.core.util.matrix.DoubleMatrix: Create a deep copy of this
copy() - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
copy() - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
copy() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: Create a copy of this vector.
copy() - Method in class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject
copy(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao
copy(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
copy(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService: Copy a BioMaterial.
copy(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
copy(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Copies a bioMaterial.
copy(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
copyMetadataFile(ExpressionExperiment, Path, String, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Copy a generic metadata file.
copyMetadataFile(ExpressionExperiment, Path, String, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
copyMetadataFile(ExpressionExperiment, Path, ExpressionExperimentMetaFileType, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Copy a metadata file to the location of a given metadata type.
copyMetadataFile(ExpressionExperiment, Path, ExpressionExperimentMetaFileType, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
copyMultiQCReport(ExpressionExperiment, Path, ExpressionExperimentMetaFileType, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Copy a MultiQC report.
copyMultiQCReport(ExpressionExperiment, Path, ExpressionExperimentMetaFileType, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
CORPUS - Enum constant in enum class ubic.gemma.model.common.description.AnnotationRelationBasis: Nobody asserts it; our own curation attests it by co-occurrence, and the specificity of that co-occurrence is measurable.
correctedPvalue - Variable in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneDiffExStats
correl(double[], double[]) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Compute the Pearson correlation, missing values are permitted.
correlAsByte(double) - Static method in class ubic.gemma.core.util.math.CorrelationStats
correlation(double[], double[], double[], double[], boolean[], boolean[]) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Highly optimized version of the correlation computation, where as much information is precomputed as possible.
correlation(DoubleArrayList, DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Calculate the pearson correlation of two arrays.
CORRELATION - Enum constant in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Indicate a correlation value.
CorrelationEffectMetaAnalysis - Class in ubic.gemma.core.util.math.metaanalysis: Implementation of meta-analysis of correlations along the lines of chapter 18 of Cooper and Hedges, "Handbook of Research Synthesis".
CorrelationEffectMetaAnalysis() - Constructor for class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
CorrelationEffectMetaAnalysis(boolean, boolean) - Constructor for class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
correlationForPvalue(double, int) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Find the approximate Pearson correlation required to meet a particular pvalue.
correlationMatrix(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixStats: Compute the correlation matrix of the rows of a matrix.
correlationMatrix(DoubleMatrix, double) - Static method in class ubic.gemma.core.util.math.MatrixStats
correlationOfStandardized(double[], double[]) - Static method in class ubic.gemma.core.util.math.Distance: Highly optimized implementation of the Pearson correlation.
correlationOfStandardized(DoubleArrayList, DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Distance: Like correlationofNormedFast, but takes DoubleArrayLists as inputs, handles missing values correctly, and does more error checking.
CorrelationStats - Class in ubic.gemma.core.util.math: Statistical evaluation and transformation tools for correlations.
CorrelationStats() - Constructor for class ubic.gemma.core.util.math.CorrelationStats
correlationTstat(double, int) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Compute the t-statistic associated with a Pearson correlation.
correlFast(double[], double[], double, double, double, double) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Compute Pearson correlation when there are no missing values.
CorsFilter - Class in ubic.gemma.rest.servlet: Filter for adding CORS headers to the RESTful API responses.
CorsFilter() - Constructor for class ubic.gemma.rest.servlet.CorsFilter
cosine - Enum constant in enum class ubic.gemma.core.ontology.GoMetric.Metric
count - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
count - Variable in class ubic.gemma.rest.AdminWebService.BlacklistListResponse: Number of entries actually returned in entries.
count - Variable in class ubic.gemma.rest.AdminWebService.CacheListResponse
count - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchResponse: Number of tasks actually submitted (post-blank-skip).
count - Variable in class ubic.gemma.rest.AdminWebService.OntologiesResponse
count - Variable in class ubic.gemma.rest.AdminWebService.SearchIndicesResponse
count(DataVector) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive: Count the number of values in a vector.
count(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive: Count the number of values in each assay.
count(Filters) - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
count(Filters) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
count(Filters) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
count(Filters) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
count(Filters) - Method in interface ubic.gemma.persistence.service.FilteringDao: Count VOs matching the given filters.
count(Filters) - Method in interface ubic.gemma.persistence.service.FilteringService
COUNT - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
COUNT - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementKind
COUNT - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Indicates value was (originally) an integer count of something, such as RNAseq reads.
COUNT - Enum constant in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Indicates value is a count, such as the number of sequencing reads.
COUNT_FAST - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
countAboveThreshold(SingleCellExpressionDataVector, double) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive: Compute the number of cells expressed strictly above the given threshold.
countAll() - Method in class ubic.gemma.persistence.service.AbstractDao
countAll() - Method in class ubic.gemma.persistence.service.AbstractService
countAll() - Method in interface ubic.gemma.persistence.service.BaseDao: Counts all entities of T in the persistent storage.
countAll() - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
countAll() - Method in interface ubic.gemma.persistence.service.common.description.DatabaseEntryReadService
countAll() - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryReadServiceImpl
countBioMaterials(Filters) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Count the number of biomaterials of datasets satisfying the given filters.
countBioMaterials(Filters) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
countBioMaterials(Filters) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
countBioMaterials(Filters) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
countBioMaterials(Filters) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
countBioMaterials(Filters) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
countBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: returns the number of bioSequences associated with this ArrayDesign id
countBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: returns the number of BlatResults (BioSequence2GeneProduct) entries associated with this ArrayDesign id.
countBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countByGoTermUris(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao: Count distinct genes annotated to any of the given GO term URIs.
countByGoTermUris(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
countByGoTermUris(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao: Taxon-scoped variant of Gene2GOAssociationDao.countByGoTermUris(Collection).
countByGoTermUris(Collection, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
countByGOTermUris(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationReadService: Count distinct genes annotated to any of the given GO term URIs.
countByGOTermUris(Collection, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl
countByGOTermUris(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService: Count distinct genes annotated to any of the given GO term URIs.
countByGOTermUris(Collection, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
countByInvestigation(Investigation, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: Count rows attached to the given investigation matching the role filter (or all roles if null).
countByInvestigation(Investigation, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
countByInvestigation(Investigation, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
countByInvestigation(Investigation, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
countByRoleSince(Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: Group rows by role, counting per bucket.
countByRoleSince(Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
countByRoleSince(Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
countByRoleSince(Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
countByValueUri(Collection, Collection, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
countByValueUri(Collection, Collection, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
countByValueUri(Collection, Collection, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
countByValueUri(Collection, Collection, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
countByValueUriGroupedByNormalizedValue(Collection, Collection, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Count characteristics matching the provided value URIs.
countByValueUriGroupedByNormalizedValue(Collection, Collection, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
countByVerdict() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDao: Corpus-wide tally by verdict, for the triage queue's counts.
countByVerdict() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDaoImpl
countByVerdict() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService: Corpus-wide tally by verdict.
countByVerdict() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
countCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countCompositeSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countCompositeSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
countCompositeSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countCompositeSequencesWithBioSequences() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countCompositeSequencesWithBioSequences() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countCompositeSequencesWithBioSequences() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countCompositeSequencesWithBioSequences() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countCompositeSequencesWithBioSequences() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Function to return a count of all compositeSequences with bioSequence associations
countCompositeSequencesWithBioSequences() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countCompositeSequencesWithBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countCompositeSequencesWithBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countCompositeSequencesWithBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countCompositeSequencesWithBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countCompositeSequencesWithBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
countCompositeSequencesWithBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countCompositeSequencesWithBlatResults() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countCompositeSequencesWithBlatResults() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countCompositeSequencesWithBlatResults() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countCompositeSequencesWithBlatResults() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countCompositeSequencesWithBlatResults() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Function to return all composite sequences with blat results
countCompositeSequencesWithBlatResults() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countCompositeSequencesWithBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countCompositeSequencesWithBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countCompositeSequencesWithBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countCompositeSequencesWithBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countCompositeSequencesWithBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
countCompositeSequencesWithBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countCompositeSequencesWithGenes(boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countCompositeSequencesWithGenes(boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countCompositeSequencesWithGenes(boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countCompositeSequencesWithGenes(boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countCompositeSequencesWithGenes(boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Function to return a count of all composite sequences with associated genes.
countCompositeSequencesWithGenes(boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countCompositeSequencesWithGenes(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countCompositeSequencesWithGenes(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countCompositeSequencesWithGenes(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countCompositeSequencesWithGenes(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countCompositeSequencesWithGenes(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countCompositeSequencesWithGenes(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countCompositeSequencesWithGenes(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
countCompositeSequencesWithGenes(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countDistinctExperiments() - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao: Count distinct ExpressionExperiments that have at least one single-cell dimension recorded.
countDistinctExperiments() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl
countDistinctRunIdsSince(Date, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: Number of distinct runIds seen on rows with createdAt >= since (or all-time if null).
countDistinctRunIdsSince(Date, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
countDistinctRunIdsSince(Date, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
countDistinctRunIdsSince(Date, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
countDistinctWithRelatedExperiments() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao: Count the number of distinct references that are linked to experiments.
countDistinctWithRelatedExperiments() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
countDistinctWithRelatedExperiments() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
countDistinctWithRelatedExperiments() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
countDistinctWithRelatedExperiments() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
countDistinctWithRelatedExperiments() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
countExperimentsByUris(Collection, boolean, boolean, boolean, boolean, Taxon, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: As CharacteristicDao.countExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, Collection), but able to count usage in the CATEGORY slot as well.
countExperimentsByUris(Collection, boolean, boolean, boolean, boolean, Taxon, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
countExperimentsByUris(Collection, boolean, boolean, boolean, boolean, Taxon, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
countExperimentsByUris(Collection, boolean, boolean, boolean, boolean, Taxon, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
countExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Count the distinct experiments referencing each of the given URIs.
countExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
countExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
countExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
countExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
countExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
countExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Obtain the number of associated expression experiments.
countExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
countExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countFast(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive: Quickly count the non-zeroes for each assay.
countFast(SingleCellExpressionDataVector, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
countFast(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
countFast(SingleCellExpressionDataVector, CellLevelCharacteristics) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
countFastWithUnknown(SingleCellExpressionDataVector, CellLevelCharacteristics) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
countGenes(boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countGenes(boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countGenes(boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countGenes(boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countGenes(boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Returns a count of the number of genes associated with an array design.
countGenes(boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countGenes(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
countGenes(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countGenes(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countGenes(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countGenes(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Returns the number of unique Genes associated with this ArrayDesign id
countGenes(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countGenesByGoTerm(String, TaxonArg, boolean, int) - Method in class ubic.gemma.rest.GoTermsWebService: Distinct-gene count for the given GO term, optionally including descendants.
countMissing(DataVector) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive: Count the number of missing values.
countNewExpressionExperiments(Date) - Method in interface ubic.gemma.core.analysis.report.WhatsNewService: Count the public experiments first created in Gemma since a given date.
countNewExpressionExperiments(Date) - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
countOpen() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Count tickets in a non-terminal state (OPEN + IN_PROGRESS), EXCLUDING TicketType.SCRATCHPAD.
countOpen() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
countOpen() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
countOpen() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
countOpenByType() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Count open (OPEN + IN_PROGRESS) tickets grouped by TicketType.
countOpenByType() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
countOpenByType() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
countOpenByType() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
countResults(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Count the number of results in a given result set.
countResults(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
countResults(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
countResults(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
countResults(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Count the number of results in a given result set below a given corrected P-value threshold.
countResults(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
countResults(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
countResults(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
countSamplesWithData(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilterUtils: Count the number of samples in the given matrix.
countsByPrefix() - Method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex: Distinct foreign identifiers per prefix — DOID, NCIT, UMLS, … — for reporting what a load actually covers.
countSince(Date, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: Count rows with createdAt on or after since (or all rows if since is null).
countSince(Date, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
countSince(Date, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
countSince(Date, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
countSummaries(AnnotationSetRole, AnnotationSetSource, String, AgentCurationKind, String, List) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: Cross-experiment count.
countSummaries(AnnotationSetRole, AnnotationSetSource, String, AgentCurationKind, String, List) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
countSummaries(AnnotationSetRole, AnnotationSetSource, String, AgentCurationKind, String, List) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
countSummaries(AnnotationSetRole, AnnotationSetSource, String, AgentCurationKind, String, List) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
countSwitchedExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Count the number of switched ExpressionExperiment from a given platform.
countSwitchedExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
countSwitchedExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countSwitchedExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countSwitchedExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
countSwitchedExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countTickets(boolean, Long, TicketPriority) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Count tickets matching the same filters as TicketDao.findTickets(boolean, Long, TicketPriority, int, int).
countTickets(boolean, Long, TicketPriority) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
countTickets(boolean, Long, TicketPriority) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
countTickets(boolean, Long, TicketPriority) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
countTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Count tickets matching the same extended filter set as TicketDao.findTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, int, int).
countTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
countTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
countTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
countWithCache(Filters) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
countWithCache(Filters) - Method in interface ubic.gemma.persistence.service.CachedFilteringDao
countWithCache(Filters) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
countWithCache(Filters) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
countWithCache(Filters) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
countWithCache(Filters) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countWithCache(Filters, Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
countWithCache(Filters, Set) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
countWithCache(Filters, Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Count the number of experiments that match the given filters.
countWithCache(Filters, Set) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
countWithRelatedExperiments() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao: Count the number of references-experiment pairs.
countWithRelatedExperiments() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
countWithRelatedExperiments() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
countWithRelatedExperiments() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
countWithRelatedExperiments() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
countWithRelatedExperiments() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
cov2cor(DoubleMatrix2D) - Static method in class ubic.gemma.core.util.math.MatrixStats: Scale a covariance matrix to the corresponding correlation matrix.
covariance(DoubleArrayList, DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the SAMPLE covariance of two data sequences.
CpuInfo - Record Class in ubic.gemma.core.util.runtime: Information about a CPU.
CpuInfo(String[]) - Constructor for record class ubic.gemma.core.util.runtime.CpuInfo: Creates an instance of a CpuInfo record class.
create(C) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService
create(Runnable) - Static method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextRunnable
create(String, String, Collection, long, long, int) - Static method in class ubic.gemma.core.ontology.providers.OntologySlimMeta
create(String, Collection, long, long, int) - Static method in class ubic.gemma.core.ontology.providers.OntologySlimMeta
create(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService
create(Collection) - Method in class ubic.gemma.persistence.service.AbstractService
create(Collection) - Method in interface ubic.gemma.persistence.service.BaseImmutableService
create(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseImmutableService
create(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService
create(Collection) - Method in class ubic.gemma.persistence.service.AbstractDao
create(Collection) - Method in interface ubic.gemma.persistence.service.BaseDao: Create all the given entities in the persistent storage.
create(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
create(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
create(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
create(Collection) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
create(Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
create(Collection) - Static method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
create(Callable) - Static method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextCallable
create(O) - Method in class ubic.gemma.persistence.service.AbstractService
create(O) - Method in interface ubic.gemma.persistence.service.BaseImmutableService
create(O) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseImmutableService
create(O) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService
create(T) - Method in class ubic.gemma.persistence.service.AbstractDao
create(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Create an entity in the persistent storage.
create(SimpleExpressionExperimentMetadata, DoubleMatrix) - Method in interface ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService: Parses, converts (into Gemma objects), and loads data into the database.
create(SimpleExpressionExperimentMetadata, DoubleMatrix) - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl
create(User) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
create(User) - Method in interface ubic.gemma.core.security.authentication.UserService
create(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
create(UserGroup) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
create(UserGroup) - Method in interface ubic.gemma.core.security.authentication.UserService
create(UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
create(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
create(Gene2GOAssociation) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
create(AuditTrail) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
create(UserGroup) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
create(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
create(Characteristic) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
create(ExternalDatabase) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
create(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
create(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
create(QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
create(QuantitationType, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
create(QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService: Create a new QuantitationType for the given vector type.
create(QuantitationType, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
create(ArrayDesign, Boolean, boolean) - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService: Create (or update) all the annotation files for the given platform.
create(ArrayDesign, Boolean, boolean) - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
create(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
create(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
create(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
create(ExpressionExperiment) - Method in class ubic.gemma.persistence.persister.EeWriteServiceImpl: No-cache overload: synthesises the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction.
create(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.EeWriteService: Persist an ExpressionExperiment graph, synthesising the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction.
create(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.preprocess.MeanVarianceService: Retrieve (and if necessary compute) the mean-variance relationship for the experiment
create(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceImpl
create(ExpressionExperiment, DoubleMatrix, double[], DoubleMatrix, BioAssayDimension, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
create(ExpressionExperiment, DoubleMatrix, double[], DoubleMatrix, BioAssayDimension, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl
create(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in class ubic.gemma.persistence.persister.EeWriteServiceImpl
create(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in interface ubic.gemma.persistence.service.expression.experiment.EeWriteService: Persist an ExpressionExperiment graph.
create(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper: Create an experiment set from a VO.
create(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
create(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
create(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
create(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneWriteService: Create-path body for a brand-new gene with its products.
create(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl
create(Taxon) - Method in interface ubic.gemma.core.goldenpath.GoldenPathQueryFactory: Construct a new GoldenPathQuery for the given taxon.
create(Taxon) - Method in class ubic.gemma.core.goldenpath.GoldenPathQueryFactoryImpl
create(Taxon) - Method in interface ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysisFactory: Construct a new GoldenPathSequenceAnalysis for the given taxon.
create(Taxon) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysisFactoryImpl
create(Taxon) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
CREATE - Static variable in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Aliases, for readability.
createAcl(ObjectIdentity) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
createAggregateImage(SingleCellSparsityHeatmap.SingleCellHeatmapType) - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
createAggregator(SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod, CellLevelCharacteristics, boolean) - Static method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils: Create an aggregator that can be used on a Stream of vectors.
createAnnotations() - Method in class ubic.gemma.core.visualization.SingleCellDataBoxplot: Obtain annotations to include in the plot.
createBADMap(List) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
createBatchFactor(ExpressionExperiment, Map) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService
createBatchFactor(ExpressionExperiment, Map) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl
createBioAssayToSourceBioAssayMap(BioAssaySet, Collection) - Static method in class ubic.gemma.model.expression.bioAssay.BioAssayUtils: Create a mapping between assays and their source assays from a given BioAssaySet.
createBioMartEnsembleNcbi(String[]) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser: Given an array of strings representing the line to parse then create a BioMartEnsembleNcbi value object with some validation.
createBooleanSlicer(List, boolean) - Static method in class ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtils: Create a slicer function for bulk data vectors that can be applied on a Stream.
createBootstrappedDataSource(DataSource) - Static method in class ubic.gemma.persistence.initialization.BootstrappedDataSourceFactory
createCellTypeFactor(ExpressionExperiment, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Recreate the cell type factor based on the preferred cell type assignment of the preferred single-cell vectors.
createCellTypeFactor(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
createCharacteristicMap(Collection) - Static method in class ubic.gemma.model.expression.bioAssay.BioAssayUtils: Create a mapping of biomaterial to characteristics for each category.
createCharacteristicMap(Collection) - Static method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialUtils: Create a mapping of biomaterial to characteristics for each category.
createColorPalette(int, Color[]) - Method in class ubic.gemma.core.util.graphics.ColorMap: Allocates colors across a range.
createContext(ProgressUpdateCallback) - Static method in interface ubic.gemma.core.job.progress.ProgressUpdateContext
createContext(ProgressUpdateCallback) - Static method in class ubic.gemma.core.logging.log4j.ProgressUpdateAppender: Create a new context for observing progress.
CREATED_AT - Enum constant in enum class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao.SummarySort: When the row was stored.
createdAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
createdAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
createDatabaseEntity(GeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: create an entity in the database based on the value object parameter
createDatabaseEntity(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
createDatabaseInitializerStub() - Method in class ubic.gemma.core.config.DataSourceConfig: Dummy createDatabaseInitializer stub.
CreateDatabasePopulator - Class in ubic.gemma.persistence.initialization: Create a new database and drop an existing one if desired.
CreateDatabasePopulator(String) - Constructor for class ubic.gemma.persistence.initialization.CreateDatabasePopulator
createDataset() - Method in class ubic.gemma.core.visualization.SingleCellDataBoxplot: Create a dataset.
createdBy - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
createdBy - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
createdBy - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
createdBy - Variable in class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest
createDir(String) - Static method in class ubic.gemma.core.util.FileTools: Creates the directory if it does not exist.
createDocumentBuilder(EntityResolver) - Static method in class ubic.gemma.core.util.XMLUtils: Create a new DocumentBuilder with some good presets for general usage.
createDoubleSlicer(List, boolean) - Static method in class ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtils: Create a slicer function for bulk data vectors that can be applied on a Stream.
createEmptyRow(int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader
createEnvironmentVariables() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation: Replicate as much as possible the environment from sourceme.bash.
createEnvironmentVariables() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedAnnDataTransformation
createEnvironmentVariables() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractScriptBasedTransformation
createErrorMessage(InputStream, URL) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation
createErrorMessage(InputStream, URL) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedTransformation
createErrorMessage(InputStream, URL) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractScriptBasedTransformation: Create an error message from a failing script.
createExperimentSet(ExperimentSetsWebService.ExperimentSetRequest) - Method in class ubic.gemma.rest.ExperimentSetsWebService
createExpressionHandler() - Method in class ubic.gemma.core.security.MethodSecurityConfig: Build a MethodSecurityExpressionHandler wired with the lab's permission evaluator (gsec's AclPermissionEvaluator) and the role hierarchy.
createFullMappingByFactorValueCharacteristics(CellLevelCharacteristics, ExperimentalFactor) - Static method in class ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils: Create a full mapping of cell types from a cell type assignment to factor values in a cell type factor.
createGroup(String) - Method in interface ubic.gemma.core.security.SecurityService: If the group already exists, an exception will be thrown.
createGroup(String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
createGroup(String, List) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
createGroup(GroupsWebService.GroupCreateRequest) - Method in class ubic.gemma.rest.GroupsWebService: Create a new group.
createImage() - Method in interface ubic.gemma.core.visualization.Heatmap
createImage(int) - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
createImage(int) - Method in interface ubic.gemma.core.visualization.Heatmap: Render a heatmap image.
createImage(int) - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
createIndex(SingleCellDimension) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionUtils: Create an index of bioassays to their cell IDs and their position in the bioassays.
createInstance() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory
createInstance() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceBasedSecurityContextFactory
createInstance() - Method in class ubic.gemma.core.util.TextResourceToSetOfLinesFactoryBean
createMappingByFactorValueCharacteristics(CellLevelCharacteristics, ExperimentalFactor) - Static method in class ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils: Map the cell types from a cell type assignment to factor values in a cell type factor.
createMappingBySubSetCharacteristics(CellLevelCharacteristics, ExperimentalFactor, Map) - Static method in class ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils: Infer the mapping of cell type assignments to factor values using a subset structure.
createMask(boolean[]) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellMaskUtils: Create a mask from a boolean array.
createMatrix(List, List, List) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader
createMeanVariance(ExpressionExperiment, MeanVarianceRelation) - Method in interface ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper
createObject() - Method in class ubic.gemma.core.context.AbstractAsyncFactoryBean: Create a new bean as per AbstractAsyncFactoryBean.getObject().
createObject() - Method in class ubic.gemma.rest.util.OpenApiFactory
createObjectIdentity(String, Serializable, AclSid, boolean) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
createObjectIdentity(String, Serializable, AclSid, boolean) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
createOrUpdateAclSpecialCases(MutableAcl, Acl, Sid, Securable) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice: Subclasses can modify this to address special cases.
createOrUpdateAclSpecialCases(MutableAcl, Acl, Sid, Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
createPipeline(List) - Method in interface ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactory
createPipeline(List) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactoryImpl: Create a pipeline of single-cell data transformations.
createPreboarded(String, String, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService: Create a new preboarded for the given accession.
createPreboarded(String, String, String) - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl
createPreboarded(PreboardedWebService.CreatePreboardedRequest) - Method in class ubic.gemma.rest.PreboardedWebService: Create a new PreboardedExperiment for the supplied accession.
CreatePreboardedRequest() - Constructor for class ubic.gemma.rest.PreboardedWebService.CreatePreboardedRequest
createProcessedDataVectors(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Create processed vectors and optionally update ranks.
createProcessedDataVectors(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
createProcessedDataVectors(ExpressionExperiment, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Create processed vectors and optionally update ranks.
createProcessedDataVectors(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
createProcessedDataVectors(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Add processed data vectors
createProcessedDataVectors(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
createProcessedDataVectors(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
createProcessedDataVectors(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
createProcessedDataVectors(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Create a new set of processed vectors for an experiment.
createProcessedDataVectors(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
createProgressReporter(String, String) - Method in class ubic.gemma.cli.util.ConsoleProgressReporterFactory
createProgressReporter(String, String) - Method in class ubic.gemma.core.util.DefaultProgressReporterFactory
createProgressReporter(String, String) - Method in interface ubic.gemma.core.util.ProgressReporterFactory: Obtain a progress reporte for a specific log category.
createProtocolForConfig(DifferentialExpressionAnalysisConfig, Map) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
createPythonScriptArgs() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedAnnDataTransformation
createPythonScriptArgs() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedTransformation
createPythonScriptArgs() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSample
createPythonScriptArgs() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSortBySample
createReverseIndex(SingleCellDimension) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionUtils: Create a reverse index of cell IDs to their corresponding position in bioassays.
createRnaSeqBatchFactor(ExpressionExperiment, Map) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService: For RNA-seq, we based the batching on the available device/run/flowcell/lane information
createRnaSeqBatchFactor(ExpressionExperiment, Map) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl: For RNA-seq, we based the batching on the available device/run/flowcell/lane information
createRowKeys() - Method in class ubic.gemma.core.util.graphics.ColorMatrix: To be able to sort the rows by an arbitrary key.
createScriptArgs() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedTransformation
createScriptArgs() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractScriptBasedTransformation
createScriptArgs() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter
createSingleCellDataVectors(ExpressionExperiment, Iterable) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Create single-cell data vectors in batches to avoid OutOfMemoryError.
createSingleCellDataVectors(ExpressionExperiment, Iterable) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
createSingleCellDimension(ExpressionExperiment, SingleCellDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Create a single-cell dimension for a given experiment.
createSingleCellDimension(ExpressionExperiment, SingleCellDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
createSlicer(List) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtils: Create a slicer for single-cell data vectors.
createSlicer(List, Class, boolean) - Static method in class ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtils: Create a slicer function for bulk data vectors that can be applied on a Stream.
createSlicer(List, List, Set, Set) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtils: Create a slicer for single-cell data vectors whose cell IDs, CTAs, and CLCs are already pre-sliced.
createStatement(FactorValue, Statement) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Create a given statement and add it to the given factor value.
createStatement(FactorValue, Statement) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
createStream(SessionFactory, Function, boolean) - Static method in class ubic.gemma.persistence.util.QueryUtils: Safely create a Stream from either the current or a new Session.
createStreamMonitor(ExpressionExperiment, QuantitationType, String, int, long, Console) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils: Create a consumer for a Stream that will report progress of retrieving single-cell vectors.
createSubSets(ExpressionExperiment, SingleCellDimension, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellExperimentSubSetsCreationConfig) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetService: Subset biomaterials and bioassays by the given CellLevelCharacteristics.
createSubSets(ExpressionExperiment, SingleCellDimension, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellExperimentSubSetsCreationConfig) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceImpl
createSubSetsAndAggregate(ExpressionExperiment, QuantitationType, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateService: Create subsets and aggregate by any cell-level characteristics.
createSubSetsAndAggregate(ExpressionExperiment, QuantitationType, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl
createSubSetsAndAggregateByCellType(ExpressionExperiment, SingleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateService: Create subsets and aggregate by cell type.
createSubSetsAndAggregateByCellType(ExpressionExperiment, SingleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl
createSubSetsByCellType(ExpressionExperiment, SingleCellExperimentSubSetsCreationConfig) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetService: Subset a single-cell dataset by preferred cell type assignment the cell type factor and the
createSubSetsByCellType(ExpressionExperiment, SingleCellExperimentSubSetsCreationConfig) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceImpl
createTdbModel(Dataset, String, boolean, OntModelSpec, boolean) - Static method in class ubic.gemma.core.ontology.jena.OntologyLoader: Create an ontology model for a TDB.
createTemporaryFile(Path, SingleCellDataType) - Static method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationUtils: Obtain a temporary file for the output of a transformation.
createTemporaryFile(SingleCellDataType) - Method in interface ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactory
createTemporaryFile(SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactoryImpl: Obtain a temporary file for the output of a transformation.
createTerm2CoefficientNames(List, DoubleMatrix) - Static method in class ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtils
createTicket(TicketsWebService.CreateTicketRequest) - Method in class ubic.gemma.rest.TicketsWebService: Open a new ticket.
createTicketFromAccession(TicketsWebService.CreateTicketFromAccessionRequest) - Method in class ubic.gemma.rest.TicketsWebService: Open a ticket over an experiment named by accession, resolving the accession to the dataset(s) in one call.
CreateTicketFromAccessionRequest() - Constructor for class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
CreateTicketRequest() - Constructor for class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
createUser(String, String, String) - Method in interface ubic.gemma.core.security.authentication.UserManager
createUser(String, String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
createUser(UserDetails) - Method in interface ubic.gemma.core.security.authentication.UserManager
createUser(UserDetails) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
createUser(AdminWebService.CreateUserRequest) - Method in class ubic.gemma.rest.AdminWebService: Create a new active user with a server-generated one-time temporary password.
CreateUserRequest() - Constructor for class ubic.gemma.rest.AdminWebService.CreateUserRequest
CreateUserResponse() - Constructor for class ubic.gemma.rest.AdminWebService.CreateUserResponse
createVectorMatrix(Map, boolean) - Method in interface ubic.gemma.core.ontology.GoMetric
createVectorMatrix(Map, boolean) - Method in class ubic.gemma.core.ontology.GoMetricImpl
criteria - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeRequest: Subset of matcher names to apply (e.g.
criteriaApplied - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
CriteriaContext(CriteriaQuery, Root) - Constructor for class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao.CriteriaContext
CrossRefFetcher - Class in ubic.gemma.core.loader.crossref: Fetch bibliographic metadata for a DOI from the CrossRef REST API (api.crossref.org).
CrossRefFetcher() - Constructor for class ubic.gemma.core.loader.crossref.CrossRefFetcher
CSV - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoFormat
csvSplit(String) - Static method in class ubic.gemma.core.util.StringUtil: Split a single CSV-formatted line into fields.
CTS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
cumulate(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Stats: Convert an array into a cumulative array.
cumulateRight(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Stats: Convert an array into a cumulative array.
Curatable - Interface in ubic.gemma.model.common.auditAndSecurity.curation: Created by tesarst on 06/03/17.
CuratableDao<C> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Created by tesarst on 13/03/17.
Curate - Enum constant in enum class ubic.gemma.model.expression.experiment.WorkflowState
CURATED - Enum constant in enum class ubic.gemma.model.common.description.AnnotationRelationBasis: A curator already wrote it, as a Statement on an annotation: 10,040 datasets carry a GENO_0000222 has_genotype statement, 1,829 an RO_0002573 has modifier, 469 a TGEMO_00171 induced by.
CURATION - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: Manual curation of one or more EEs — annotate factor values, write factor descriptions, tag baseline relevance, etc.
CURATION_DETAILS_ALIAS - Static variable in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: HQL alias for Curatable.getCurationDetails().
CurationAgentHealthResponse() - Constructor for class ubic.gemma.rest.AdminWebService.CurationAgentHealthResponse
CurationBaseline() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationBaseline
CurationBasics() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationBasics
CurationCommitConflictException - Exception Class in ubic.gemma.rest.util: A curation commit refused as a 409, carrying which conflict it was.
CurationCommitConflictException(CurationCommitConflictException.Reason, String) - Constructor for exception class ubic.gemma.rest.util.CurationCommitConflictException
CurationCommitConflictException.Reason - Enum Class in ubic.gemma.rest.util: What the client should do about it.
CurationCommitConflictExceptionMapper - Class in ubic.gemma.rest.providers: Maps a CurationCommitConflictException to a 409 whose errors[0].reason is the stable code for which conflict it was, so a client routes on the code rather than on the wording of the message.
CurationCommitConflictExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.CurationCommitConflictExceptionMapper
CurationCommitRequest - Class in ubic.gemma.persistence.service.expression.experiment: Resolved, section-scoped inputs for one all-or-none curation commit (ExpressionExperimentService.commitCuration(ExpressionExperiment, CurationCommitRequest, boolean)).
CurationCommitRequest() - Constructor for class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
CurationCommitRequest.SampleCharacteristicAdd - Class in ubic.gemma.persistence.service.expression.experiment: A per-sample characteristic to create: clientRef, the resolved biomaterial id, and the tag.
CurationCommitRequest.TagAdd - Class in ubic.gemma.persistence.service.expression.experiment: A tag to create, paired with the document clientRef so the report can echo its new id.
CurationCommitResult - Class in ubic.gemma.persistence.service.expression.experiment: Per-section change tallies from one ExpressionExperimentService.commitCuration(ExpressionExperiment, CurationCommitRequest, boolean) call, mapped by the web layer to the wire CurationCommitReport.changes.
CurationCommitResult() - Constructor for class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
CurationDecision - Class in ubic.gemma.model.common.auditAndSecurity.curation: A curator's standing ruling that a change must NOT be made — or may be.
CurationDecision() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
CurationDecisionDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: DAO for CurationDecision rows -- standing rulings that a change must not be made to an experiment.
CurationDecisionDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Hibernate implementation of CurationDecisionDao.
CurationDecisionDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDaoImpl
CurationDecisionRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationDecisionRequest
CurationDecisionResponse() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
CurationDecisionScope - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: How wide a CurationDecision reaches — the difference between the refusal verbs the curation ledger actually uses.
CurationDecisionService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Standing rulings that a change must not be made to an experiment -- and the rarer ruling that one may be.
CurationDecisionServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Default CurationDecisionService.
CurationDecisionServiceImpl(CurationDecisionDao) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionServiceImpl
CurationDecisionType - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Which way a standing CurationDecision went.
CurationDetails - Class in ubic.gemma.model.common.auditAndSecurity.curation: Class encapsulating all the curation information for Curatable objects.
CurationDetails() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
CurationDetailsCommit() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
CurationDetailsEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
use TicketService.
CurationDetailsEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent: Deprecated.
CurationDetailsService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Deprecated.
this interface only exists as a compatibility shim while callers migrate off Curatable#getCurationDetails(). New code should query TicketService directly. The shim — and the underlying CurationDetails entity — will be retired once all callers move over.
CurationDetailsServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Default read-side implementation of CurationDetailsService.
CurationDetailsServiceImpl(TicketService) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImpl
CurationDetailsUpdateRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationDetailsUpdateRequest
CurationDetailsValueObject - Class in ubic.gemma.model.common.auditAndSecurity.curation: Value object exposing CurationDetails over the REST API.
CurationDetailsValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
CurationDetailsValueObject(CurationDetails) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
CurationDetailsValueObject(CurationDetails, Boolean) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject: As CurationDetailsValueObject(CurationDetails), plus the curation-lock state the caller already holds.
CurationDocument() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationDocument
CurationDraftDispositions - Class in ubic.gemma.model.common.auditAndSecurity.curation: Derive per-element CurationDraftDispositions.Disposition for a DRAFT AnnotationSet by diffing its payload against the PROPOSAL it was seeded from, and consulting AnnotationSet.getParkedElements().
CurationDraftDispositions.Disposition - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Result of a single-element diff.
CurationLock - Class in ubic.gemma.model.common.auditAndSecurity.curation: An advisory, steal-able claim on a dataset's curation.
CurationLock() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
CurationLockBulkRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationLockBulkRequest
CurationLockBulkResult() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationLockBulkResult
CurationLockedException(String, String) - Constructor for exception class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService.CurationLockedException
CurationLockResponse() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationLockResponse
CurationLockService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Advisory, steal-able claims on a dataset's curation.
CurationLockService.CurationLockedException - Exception Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Thrown when a lock is held by someone else and the caller did not ask to steal it.
CurationLockServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Default CurationLockService.
CurationLockServiceImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl
CurationNoteUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
curation notes will be migrated to ticket comments via TicketService.addComment(Ticket, Contact, String) once the curation-note ↔ ticket mapping lands (see CURATION_DETAILS_RETIREMENT.md). Until then this event is still emitted by DatasetsWebService.updateDatasetCurationDetails so the legacy curationNote field on CurationDetails stays populated.
CurationNoteUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent: Deprecated.
CurationPublications() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationPublications
CurationRunRef() - Constructor for class ubic.gemma.rest.DatasetsWebService.CurationRunRef
CurationStatusResponse() - Constructor for class ubic.gemma.rest.AdminWebService.CurationStatusResponse
CURATOR - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSource
CURATOR - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageJudgeKind: A person.
CURATOR - Enum constant in enum class ubic.gemma.model.common.description.PublicationAssociationSource: A human ruling.
CURATOR_GROUP_AUTHORITY - Static variable in class ubic.gemma.core.security.AuthorityConstants: Curators do everything an administrator does to DATA — edit designs, change a dataset's visibility, run analyses — and nothing an administrator does to the SERVER or to USER ACCOUNTS.
CURATOR_GROUP_NAME - Static variable in class ubic.gemma.core.security.AuthorityConstants
current(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService: The current holders of many datasets, keyed by dataset id, in ONE query.
current(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl
current(Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService: The current holder, or empty when the dataset is free.
current(Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl
CURRENT_USER_CONTEXT_KEY - Static variable in class ubic.gemma.cli.logging.log4j.UserDetailsThreadContextPopulator
CURRENT_VERSION - Static variable in class ubic.gemma.persistence.util.Cursor: Current cursor payload format version.
currentAssignee - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowQueueEntryResponse
currentPassword - Variable in class ubic.gemma.rest.RootWebService.ChangePasswordRequest: The user's current password, re-verified before the change is applied.
currentState - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowStateResponse
currentState - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowTransitionResponse
currentUserIsAdmin() - Method in class ubic.gemma.core.security.acl.BaseAclAdvice
currentUserIsAnonymous() - Method in class ubic.gemma.core.security.acl.BaseAclAdvice
currentUserIsRunningAsAdmin() - Method in class ubic.gemma.core.security.acl.BaseAclAdvice
Cursor - Class in ubic.gemma.persistence.util: Opaque cursor for keyset pagination of REST collections.
Cursor(int, String, Object[], Cursor.Direction) - Constructor for class ubic.gemma.persistence.util.Cursor: Build a cursor with an explicit payload format version.
Cursor(String, Object[], Cursor.Direction) - Constructor for class ubic.gemma.persistence.util.Cursor: Build a cursor with the current payload format version.
Cursor.Direction - Enum Class in ubic.gemma.persistence.util
CursorArg - Class in ubic.gemma.rest.util.args: Argument representing an opaque cursor for keyset (cursor) pagination.
CursorPage<O> - Class in ubic.gemma.persistence.util: A page of results returned by keyset (cursor) pagination.
CursorPage(List, Sort, Integer, String, String, Long) - Constructor for class ubic.gemma.persistence.util.CursorPage
CursorPaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util: Response wrapper for cursor-paginated results.
CursorPaginatedResponseDataObject(CursorPage, String[]) - Constructor for class ubic.gemma.rest.util.CursorPaginatedResponseDataObject
CursorPaginatedResponseDataObjectAuditEventValueObject(CursorPage, String[]) - Constructor for class ubic.gemma.rest.DatasetsWebService.CursorPaginatedResponseDataObjectAuditEventValueObject
CursorPaginatedResponseDataObjectBioAssayValueObject(CursorPage, String[]) - Constructor for class ubic.gemma.rest.DatasetsWebService.CursorPaginatedResponseDataObjectBioAssayValueObject
CursorPaginatedResponseDataObjectCompactAuditEventValueObject(CursorPage, String[]) - Constructor for class ubic.gemma.rest.DatasetsWebService.CursorPaginatedResponseDataObjectCompactAuditEventValueObject
CursorPaginatedResponseDataObjectTicketValueObject(CursorPage, String[]) - Constructor for class ubic.gemma.rest.DatasetsWebService.CursorPaginatedResponseDataObjectTicketValueObject
CustomModelResolver - Class in ubic.gemma.rest.swagger.resolver: Resolve Arg parameters' schema.
CustomModelResolver() - Constructor for class ubic.gemma.rest.swagger.resolver.CustomModelResolver
cv(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Stats: Compute the coefficient of variation of an array (standard deviation / mean).
CXG - Enum constant in enum class ubic.gemma.core.loader.expression.cellxgene.FileType
cytoplasmicRNA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
cytoplasmicRNA - Enum constant in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule

D

D - Enum constant in enum class ubic.gemma.model.analysis.expression.diff.Direction: Down
D - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Delete
daemonCount - Variable in class ubic.gemma.rest.AdminWebService.ThreadBlock
daoAuthenticationProvider(UserDetailsService, PasswordEncoder, String) - Method in class ubic.gemma.core.security.SecurityConfig: Custom DaoAuthenticationProvider that binds the username to the password encoder's ThreadLocal so GemmaLegacyAwarePasswordEncoder can recompute the legacy SHA-1(rawPassword + "{" + username + "}") hash.
DARK_RED - Static variable in class ubic.gemma.core.util.graphics.ColorMap
data - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeDryRunResponse: The candidates, in scan order.
DATA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoAmount: Only include data tables.
DATA_PROCESSING_REPORT - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType: This is reserved for a future use by #1529.
DataAddedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that a data type (for a specific QuantitationType, possibly new) was added.
DataAddedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent
DatabaseBackedGeneSetValueObject - Class in ubic.gemma.model.genome.gene
DatabaseBackedGeneSetValueObject() - Constructor for class ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject
DatabaseBackedGeneSetValueObject(GeneSet, Taxon, Long) - Constructor for class ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject: default constructor to satisfy java bean contract
DatabaseEntry - Class in ubic.gemma.model.common.description: A reference to a record in a database.
DatabaseEntry() - Constructor for class ubic.gemma.model.common.description.DatabaseEntry
DatabaseEntry.Factory - Class in ubic.gemma.model.common.description
DatabaseEntryArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for DatabaseEntry API.
DatabaseEntryArg(String, Class, T) - Constructor for class ubic.gemma.rest.util.args.DatabaseEntryArg
DatabaseEntryArgService - Class in ubic.gemma.rest.util.args
DatabaseEntryArgService(DatabaseEntryService) - Constructor for class ubic.gemma.rest.util.args.DatabaseEntryArgService
DatabaseEntryArrayArg - Class in ubic.gemma.rest.util.args
DatabaseEntryDao - Interface in ubic.gemma.persistence.service.common.description
DatabaseEntryDaoImpl - Class in ubic.gemma.persistence.service.common.description: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type DatabaseEntry.
DatabaseEntryDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImpl
DatabaseEntryIdArg - Class in ubic.gemma.rest.util.args: Long argument type for DatabaseEntry API, referencing the Taxon ID.
DatabaseEntryReadService - Interface in ubic.gemma.persistence.service.common.description: Read-only retrieval service for DatabaseEntry.
DatabaseEntryReadServiceImpl - Class in ubic.gemma.persistence.service.common.description: Implementation of DatabaseEntryReadService.
DatabaseEntryReadServiceImpl(DatabaseEntryDao) - Constructor for class ubic.gemma.persistence.service.common.description.DatabaseEntryReadServiceImpl
DatabaseEntryService - Interface in ubic.gemma.persistence.service.common.description
DatabaseEntryServiceImpl - Class in ubic.gemma.persistence.service.common.description: Spring Service base class for DatabaseEntryService, provides access to all services and entities referenced by this service.
DatabaseEntryServiceImpl(DatabaseEntryDao, DatabaseEntryReadService) - Constructor for class ubic.gemma.persistence.service.common.description.DatabaseEntryServiceImpl
DatabaseEntryStringArg - Class in ubic.gemma.rest.util.args: String argument type for DatabaseEntry API, Can also be null.
DatabaseEntryValueObject - Class in ubic.gemma.model.common.description: ValueObject for database entry
DatabaseEntryValueObject() - Constructor for class ubic.gemma.model.common.description.DatabaseEntryValueObject
DatabaseEntryValueObject(long) - Constructor for class ubic.gemma.model.common.description.DatabaseEntryValueObject
DatabaseEntryValueObject(DatabaseEntry) - Constructor for class ubic.gemma.model.common.description.DatabaseEntryValueObject
DatabaseSchemaPopulator - Class in ubic.gemma.persistence.initialization: Populates the database schema.
DatabaseSchemaPopulator(String) - Constructor for class ubic.gemma.persistence.initialization.DatabaseSchemaPopulator
DatabaseSchemaUpdatePopulator - Class in ubic.gemma.persistence.initialization: Populates an existing database with any incremental schema changes implied by the current Hibernate mapping.
DatabaseSchemaUpdatePopulator(String) - Constructor for class ubic.gemma.persistence.initialization.DatabaseSchemaUpdatePopulator
DatabaseSearchSource - Class in ubic.gemma.core.search.source: Search source for direct database results.
DatabaseSearchSource() - Constructor for class ubic.gemma.core.search.source.DatabaseSearchSource
DatabaseType - Enum Class in ubic.gemma.model.common.description
DataFileFetcher - Class in ubic.gemma.core.loader.expression.arrayExpress: ArrayExpress stores files in an FTP site as tarred-gzipped archives.
DataFileFetcher() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
DataFileOptionsUtils - Class in ubic.gemma.cli.options: Utilities to add and process options for data files (raw data, processed data, designs, etc.).
DataFileOptionsUtils() - Constructor for class ubic.gemma.cli.options.DataFileOptionsUtils
DataFileOptionValue - Class in ubic.gemma.cli.options: Shared option values for commands that write data files.
DataFileOptionValue(boolean, boolean, Path, Path, String, boolean) - Constructor for class ubic.gemma.cli.options.DataFileOptionValue: Creates a new DataFileOptionValue instance.
Dataframe<K> - Class in ubic.gemma.core.loader.util.anndata: Represents an AnnData dataframe.
Dataframe(H5Group, Class) - Constructor for class ubic.gemma.core.loader.util.anndata.Dataframe: Create a new dataframe from an H5 group.
Dataframe.Column<K,T> - Interface in ubic.gemma.core.loader.util.anndata
DataLoader - Interface in ubic.gemma.core.loader.expression: Base interface for loading expression data in Gemma.
DataLoaderConfig - Class in ubic.gemma.core.loader.expression
DataLoaderConfig(DataLoaderConfig.DataLoaderConfigBuilder) - Constructor for class ubic.gemma.core.loader.expression.DataLoaderConfig
DataLoaderConfig.DataLoaderConfigBuilder<C,B> - Class in ubic.gemma.core.loader.expression
DataLoaderConfigBuilder() - Constructor for class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder
DataLoaderConfigurer<T,C> - Interface in ubic.gemma.core.loader.expression: Configures a DataLoader from a DataLoaderConfig.
dataPath(Path) - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder: Load data from that specific path instead of looking up standard locations.
DataRemovedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that a data type (for a specific QuantitationType, possibly new) was removed.
DataRemovedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DataRemovedEvent
DataReplacedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Signifies that the data for the experiment was replaced (or filled in) after the experiment was loaded into the system.
DataReplacedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent
Dataset - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser.model
Dataset - Static variable in class ubic.gemma.core.ontology.jena.TGFVO
Dataset() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
DATASET - Enum constant in enum class ubic.gemma.cli.completion.CompletionType
DATASET - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoRecordType
DATASET_GROUP - Enum constant in enum class ubic.gemma.cli.completion.CompletionType
DATASET_TYPE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
DatasetArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for dataset (ExpressionExperiment) API.
DatasetArg(String, Class, T) - Constructor for class ubic.gemma.rest.util.args.DatasetArg
DatasetArgService - Class in ubic.gemma.rest.util.args
DatasetArgService(ExpressionExperimentService, SearchService, ArrayDesignService, BioAssayService, OutlierDetectionService, PublicationAssociationService) - Constructor for class ubic.gemma.rest.util.args.DatasetArgService
DatasetArgService.DesignChangeResult - Class in ubic.gemma.rest.util.args: Result of an applyDesignChange call.
DatasetArrayArg - Class in ubic.gemma.rest.util.args
DatasetAsset - Class in ubic.gemma.core.loader.expression.cellxgene.model
DatasetAsset() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
DatasetAssetDownloadMetadata - Class in ubic.gemma.core.loader.expression.cellxgene.model
DatasetAssetDownloadMetadata() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
DatasetBasicsResponse(Long, String, String) - Constructor for class ubic.gemma.rest.DatasetsWebService.DatasetBasicsResponse
DatasetBasicsUpdateRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.DatasetBasicsUpdateRequest
DatasetCombiner - Class in ubic.gemma.core.loader.expression.geo: Class to handle cases where there are multiple GEO dataset for a single actual experiment.
DatasetCombiner() - Constructor for class ubic.gemma.core.loader.expression.geo.DatasetCombiner
DatasetCombiner(boolean) - Constructor for class ubic.gemma.core.loader.expression.geo.DatasetCombiner
datasetConstraint(ExpressionExperiment) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Constraint results to be related to the given dataset.
DatasetDescription - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser.model
DatasetDescription() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
DatasetFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher: Retrieve GEO GDS files from the NCBI FTP server.
DatasetFetcher() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.DatasetFetcher
datasetId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
datasetId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
datasetId - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
datasetId - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowQueueEntryResponse
datasetId - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowStateResponse
datasetId - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowTransitionResponse
DatasetIdArg - Class in ubic.gemma.rest.util.args: Long argument type for dataset API, referencing the Dataset ID.
DatasetIdArg(long) - Constructor for class ubic.gemma.rest.util.args.DatasetIdArg
datasetIds - Variable in class ubic.gemma.rest.ExperimentSetsWebService.ExperimentSetMembersRequest
datasetIds - Variable in class ubic.gemma.rest.ExperimentSetsWebService.ExperimentSetRequest
DatasetImportRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
DatasetMetadata - Class in ubic.gemma.core.loader.expression.cellxgene.model
DatasetMetadata() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
DatasetMetadataFileValueObject(ExpressionExperimentMetaFileType, ExpressionExperiment) - Constructor for class ubic.gemma.rest.DatasetsWebService.DatasetMetadataFileValueObject
DatasetPermissionsValueObject(boolean, boolean) - Constructor for class ubic.gemma.rest.DatasetsWebService.DatasetPermissionsValueObject
DatasetPublicationValueObject - Class in ubic.gemma.model.common.description: A publication as it appears in the context of one dataset: the reference, plus the evidenced claim that ties it to (or rules it out for) that dataset.
DatasetPublicationValueObject() - Constructor for class ubic.gemma.model.common.description.DatasetPublicationValueObject
DatasetPublicationValueObject(BibliographicReference, PublicationAssociation) - Constructor for class ubic.gemma.model.common.description.DatasetPublicationValueObject
DatasetPublishedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted on POST /datasets/{id}/publish?reviewer=X, when a curator publishes a dataset under a named reviewer.
DatasetPublishedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DatasetPublishedEvent
DatasetSearchHitValueObject(ExpressionExperimentValueObject, Double) - Constructor for class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject
datasetShortName - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
DatasetShortNameChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Fired when a curator renames an ExpressionExperiment's shortName.
DatasetShortNameChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DatasetShortNameChangedEvent
DatasetStringArg - Class in ubic.gemma.rest.util.args: String argument type for dataset API, referencing the Dataset short name.
DatasetSummary - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser.model
DatasetSummary() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
DatasetsWebService - Class in ubic.gemma.rest: RESTful interface for datasets.
DatasetsWebService() - Constructor for class ubic.gemma.rest.DatasetsWebService
DatasetsWebService.AnnotationsUpdateRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.updateDatasetAnnotations(DatasetArg, DatasetsWebService.AnnotationsUpdateRequest).
DatasetsWebService.AnnotationTagInput - Class in ubic.gemma.rest: Write-shape for an annotation tag.
DatasetsWebService.AnnotationWithUsageStatisticsValueObject - Class in ubic.gemma.rest: This is an aggregated entity across value URI and value, thus the id and objectClass are omitted.
DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.BatchConfoundValueObject - Class in ubic.gemma.rest
DatasetsWebService.BatchEffectStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.BatchInformationValueObject - Class in ubic.gemma.rest
DatasetsWebService.BatchOutlierRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.batchMarkSampleOutliers(DatasetArg, DatasetsWebService.BatchOutlierRequest).
DatasetsWebService.BatchOutlierResponse - Class in ubic.gemma.rest
DatasetsWebService.Canonicalization - Class in ubic.gemma.rest: One accepted rewrite the grounding gate applied to a persisted annotation — a case/whitespace-only near-match canonicalized to the term's label, a blank label filled in from its URI, and/or a known Gemma-ontology term (e.g.
DatasetsWebService.CategoryWithUsageStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.CorrelationMatrixChoice - Enum Class in ubic.gemma.rest: Which of the two stored sample-correlation matrices DatasetsWebService.getDatasetSampleCorrelation(DatasetArg, DatasetsWebService.CorrelationMatrixChoice) should return.
DatasetsWebService.CurationBaseline - Class in ubic.gemma.rest
DatasetsWebService.CurationBasics - Class in ubic.gemma.rest
DatasetsWebService.CurationCommitReport - Class in ubic.gemma.rest: The server's reply — mirrors CAB's CurationCommitReport.
DatasetsWebService.CurationDecisionRequest - Class in ubic.gemma.rest: Body for DatasetsWebService.recordCurationDecision(DatasetArg, String, DatasetsWebService.CurationDecisionRequest).
DatasetsWebService.CurationDecisionResponse - Class in ubic.gemma.rest: Wire shape of one curation decision.
DatasetsWebService.CurationDetailsCommit - Class in ubic.gemma.rest: curationDetails section.
DatasetsWebService.CurationDetailsUpdateRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.updateDatasetCurationDetails(DatasetArg, DatasetsWebService.CurationDetailsUpdateRequest).
DatasetsWebService.CurationDocument - Class in ubic.gemma.rest: The whole desired curation state for one dataset (CAB's CurationDocument).
DatasetsWebService.CurationLockBulkRequest - Class in ubic.gemma.rest: Body for the bulk lock routes.
DatasetsWebService.CurationLockBulkResult - Class in ubic.gemma.rest: One dataset's outcome in a bulk lock request.
DatasetsWebService.CurationLockResponse - Class in ubic.gemma.rest: Wire shape of the curation lock.
DatasetsWebService.CurationPublications - Class in ubic.gemma.rest: Publications section — same identifier shape and set-replace semantics as PUT /publications.
DatasetsWebService.CurationRunRef - Class in ubic.gemma.rest: Which agent run is applying this commit.
DatasetsWebService.CurationSectionChange - Class in ubic.gemma.rest
DatasetsWebService.CursorPaginatedResponseDataObjectAuditEventValueObject - Class in ubic.gemma.rest: Cursor full-fidelity shape for DatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) (compact=false).
DatasetsWebService.CursorPaginatedResponseDataObjectBioAssayValueObject - Class in ubic.gemma.rest: Cursor-mode response shape for DatasetsWebService.getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean).
DatasetsWebService.CursorPaginatedResponseDataObjectCompactAuditEventValueObject - Class in ubic.gemma.rest: Cursor collapsed shape for DatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) (compact=true).
DatasetsWebService.CursorPaginatedResponseDataObjectTicketValueObject - Class in ubic.gemma.rest: Cursor shape for DatasetsWebService.getDatasetTickets(DatasetArg, CursorArg, LimitArg).
DatasetsWebService.DatasetBasicsResponse - Class in ubic.gemma.rest: Response body for DatasetsWebService.updateDatasetBasics(DatasetArg, DatasetsWebService.DatasetBasicsUpdateRequest) — the persisted name and description after the update.
DatasetsWebService.DatasetBasicsUpdateRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.updateDatasetBasics(DatasetArg, DatasetsWebService.DatasetBasicsUpdateRequest).
DatasetsWebService.DatasetImportRequest - Class in ubic.gemma.rest: Optional request body for DatasetsWebService.importDataset(DatasetsWebService.DatasetImportRequest).
DatasetsWebService.DatasetMetadataFileValueObject - Class in ubic.gemma.rest: Wire shape for DatasetsWebService.getDatasetMetadataFiles(DatasetArg): one entry per available metadata file.
DatasetsWebService.DatasetPermissionsValueObject - Class in ubic.gemma.rest: Lightweight view of a dataset's sharing state, returned by the permissions endpoint.
DatasetsWebService.DatasetSearchHitValueObject - Class in ubic.gemma.rest: Thin dataset projection for the typeahead /datasets/search endpoint.
DatasetsWebService.DatasetTicketsBulkRequest - Class in ubic.gemma.rest: Body for DatasetsWebService.getDatasetTicketsBulk(DatasetsWebService.DatasetTicketsBulkRequest).
DatasetsWebService.DesignCommit - Class in ubic.gemma.rest: The experimental-design section (CAB DesignCommit).
DatasetsWebService.DifferentialAnalysisRunRequest - Class in ubic.gemma.rest: Optional request body for DatasetsWebService.runDatasetDifferentialAnalysis(DatasetArg, DatasetsWebService.DifferentialAnalysisRunRequest).
DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject - Class in ubic.gemma.rest
DatasetsWebService.EntityRef - Class in ubic.gemma.rest: Identity half of every committable design entity: exactly one of gemmaId or clientRef.
DatasetsWebService.ExpressionExperimentSubSetGroupValueObject - Class in ubic.gemma.rest: A group of subsets, logically organized by a BioAssayDimension.
DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject - Class in ubic.gemma.rest
DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject - Class in ubic.gemma.rest
DatasetsWebService.ExpressionExperimentWithSearchResultValueObject - Class in ubic.gemma.rest
DatasetsWebService.FactorCommit - Class in ubic.gemma.rest: One experimental factor.
DatasetsWebService.FactorValueCommit - Class in ubic.gemma.rest: One factor value, with the samples it applies to (by GSM short name) and its statements.
DatasetsWebService.FactorValueNeedsAttentionRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.markFactorValueNeedsAttention(DatasetArg, Long, DatasetsWebService.FactorValueNeedsAttentionRequest) and DatasetsWebService.clearFactorValueNeedsAttention(DatasetArg, Long, String).
DatasetsWebService.FilteredAndInferredAndCursorPaginatedResponseDataObject<T> - Class in ubic.gemma.rest: Cursor-mode counterpart to DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject.
DatasetsWebService.FilteredAndInferredAndCursorPaginatedResponseDataObjectExpressionExperimentValueObject - Class in ubic.gemma.rest: Cursor shape for DatasetsWebService.getDatasetsByIds(DatasetArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) / DatasetsWebService.getBlacklistedDatasets(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg).
DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<T> - Class in ubic.gemma.rest
DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObjectExpressionExperimentValueObject - Class in ubic.gemma.rest: Legacy shape for DatasetsWebService.getDatasetsByIds(DatasetArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) / DatasetsWebService.getBlacklistedDatasets(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg).
DatasetsWebService.GeeqRecomputeRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.recomputeDatasetGeeqViaPost(DatasetArg, DatasetsWebService.GeeqRecomputeRequest).
DatasetsWebService.MeanVarianceValueObject - Class in ubic.gemma.rest: Wire shape for DatasetsWebService.getDatasetMeanVariance(DatasetArg): parallel mean / variance arrays.
DatasetsWebService.MeanVarianceValueObject.Fit - Class in ubic.gemma.rest
DatasetsWebService.MeasurementRef - Class in ubic.gemma.rest: A per-factor-value numeric measurement (continuous factors).
DatasetsWebService.OntologyTermRef - Class in ubic.gemma.rest: An ontology term reference — a human label plus an optional ontology URI.
DatasetsWebService.OntologyTermValueObject - Class in ubic.gemma.rest
DatasetsWebService.PcLoadingDirection - Enum Class in ubic.gemma.rest: Sort direction for DatasetsWebService.getDatasetSvdLoadings(DatasetArg, Integer, Integer, DatasetsWebService.PcLoadingDirection): both sorts by |loading| desc, positive filters to loading > 0 desc, negative filters to loading < 0 asc.
DatasetsWebService.PcLoadingsValueObject - Class in ubic.gemma.rest: Wire shape for DatasetsWebService.getDatasetSvdLoadings(DatasetArg, Integer, Integer, DatasetsWebService.PcLoadingDirection): the top-N probe loadings on a principal component plus the bioAssay scores on the same PC.
DatasetsWebService.PcLoadingsValueObject.Row - Class in ubic.gemma.rest
DatasetsWebService.PermissionsUpdateRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.updateDatasetPermissions(DatasetArg, DatasetsWebService.PermissionsUpdateRequest).
DatasetsWebService.PipelineStatusBulkRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.getDatasetPipelineStatusBulk(DatasetsWebService.PipelineStatusBulkRequest).
DatasetsWebService.PlatformSwitchRequest - Class in ubic.gemma.rest: Optional request body for DatasetsWebService.runDatasetSwitchPlatform(DatasetArg, DatasetsWebService.PlatformSwitchRequest).
DatasetsWebService.PublicationEntry - Class in ubic.gemma.rest: A single publication on the DatasetsWebService.updateDatasetPublications(DatasetArg, DatasetsWebService.PublicationsUpdateRequest) wire: which paper, and why.
DatasetsWebService.PublicationsUpdateRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.updateDatasetPublications(DatasetArg, DatasetsWebService.PublicationsUpdateRequest).
DatasetsWebService.QcMetricDefinitionValueObject - Class in ubic.gemma.rest: Wire shape for one metric column of DatasetsWebService.SequencingQcMetricsValueObject.
DatasetsWebService.QuantitationTypePatchRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.patchDatasetQuantitationType(DatasetArg, Long, DatasetsWebService.QuantitationTypePatchRequest).
DatasetsWebService.QuantitationTypePreferredRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.setDatasetQuantitationTypePreferred(DatasetArg, Long, DatasetsWebService.QuantitationTypePreferredRequest).
DatasetsWebService.QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObject<T> - Class in ubic.gemma.rest: Cursor-mode counterpart to DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject.
DatasetsWebService.QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObjectExperimentExpressionLevelsValueObject - Class in ubic.gemma.rest: Cursor shape for DatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean) / DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg, GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean).
DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<T> - Class in ubic.gemma.rest
DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject<T> - Class in ubic.gemma.rest
DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultByGeneValueObject - Class in ubic.gemma.rest
DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectExperimentExpressionLevelsValueObject - Class in ubic.gemma.rest: Legacy shape for DatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean) / DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg, GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean).
DatasetsWebService.QueriedAndFilteredAndInferredResponseDataObject<T> - Class in ubic.gemma.rest
DatasetsWebService.RenameDatasetRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.renameDatasetShortName(DatasetArg, DatasetsWebService.RenameDatasetRequest).
DatasetsWebService.RenameDatasetResponse - Class in ubic.gemma.rest: Response body for DatasetsWebService.renameDatasetShortName(DatasetArg, DatasetsWebService.RenameDatasetRequest).
DatasetsWebService.ResponseDataObjectCellTypeAssignmentValueObject - Class in ubic.gemma.rest
DatasetsWebService.ResponseDataObjectExpressionExperimentValueObject - Class in ubic.gemma.rest
DatasetsWebService.ResponseDataObjectListAuditEventValueObject - Class in ubic.gemma.rest: Legacy full-fidelity shape for DatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) (compact=false).
DatasetsWebService.ResponseDataObjectListBioAssayValueObject - Class in ubic.gemma.rest: Legacy-mode response shape for DatasetsWebService.getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean).
DatasetsWebService.ResponseDataObjectListCellLevelCharacteristicsValueObject - Class in ubic.gemma.rest
DatasetsWebService.ResponseDataObjectListCompactAuditEventValueObject - Class in ubic.gemma.rest: Legacy collapsed shape for DatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) (compact=true).
DatasetsWebService.ResponseDataObjectListTicketValueObject - Class in ubic.gemma.rest: Legacy shape for DatasetsWebService.getDatasetTickets(DatasetArg, CursorArg, LimitArg).
DatasetsWebService.ResponseDataObjectSingleCellDimensionValueObject - Class in ubic.gemma.rest
DatasetsWebService.RunQcMetricsValueObject - Class in ubic.gemma.rest: Wire shape for one sub-sample report row of DatasetsWebService.SampleQcMetricsValueObject.
DatasetsWebService.SampleCharacteristicCommit - Class in ubic.gemma.rest: One per-sample characteristic (CAB SampleCharacteristicCommit); the sample is a GSM short name.
DatasetsWebService.SampleCorrelationMatrixValueObject - Class in ubic.gemma.rest: Wire shape for DatasetsWebService.getDatasetSampleCorrelation(DatasetArg, DatasetsWebService.CorrelationMatrixChoice): a symmetric N×N Pearson correlation matrix with bioAssay ids + short names parallel to the rows/columns.
DatasetsWebService.SampleOutlierRequest - Class in ubic.gemma.rest: Request body for DatasetsWebService.markDatasetSampleOutlier(DatasetArg, Long, DatasetsWebService.SampleOutlierRequest).
DatasetsWebService.SampleQcMetricsValueObject - Class in ubic.gemma.rest: Wire shape for one bioAssay's row of DatasetsWebService.SequencingQcMetricsValueObject.
DatasetsWebService.Section<T> - Class in ubic.gemma.rest: A committable collection: authoritative items plus explicit deletedIds (the only way to remove).
DatasetsWebService.SequencingQcMetricsValueObject - Class in ubic.gemma.rest: Wire shape for DatasetsWebService.getDatasetQcMetrics(DatasetArg).
DatasetsWebService.SimpleSVDValueObject - Class in ubic.gemma.rest
DatasetsWebService.StaleDatasetValueObject - Class in ubic.gemma.rest: One row of DatasetsWebService.getStaleDatasets(OffsetArg, LimitArg): a dataset owing pipeline work, and what it owes.
DatasetsWebService.StatementCommit - Class in ubic.gemma.rest: One statement (subject / predicate / object triple with an optional category).
DatasetsWebService.TagCommit - Class in ubic.gemma.rest: One experiment-level tag (CAB TagCommit); a statement-shaped tag rides its statements.
DatasetsWebService.TaxonWithUsageStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.UsageStatistics - Interface in ubic.gemma.rest
DatasetTicketsBulkRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.DatasetTicketsBulkRequest
datasetType - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowQueueEntryResponse
datasetType - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowStateResponse
DatasetUpdateSummaryValueObject - Class in ubic.gemma.rest: One line of "what changed here recently" for a dataset: a short label, the event class it came from, when, and by whom.
DatasetUpdateSummaryValueObject() - Constructor for class ubic.gemma.rest.DatasetUpdateSummaryValueObject
DatasetVisualizationWebService - Class in ubic.gemma.rest: Dataset visualization endpoints.
DatasetVisualizationWebService() - Constructor for class ubic.gemma.rest.DatasetVisualizationWebService
dataSource(String, String, String, int, int) - Method in class ubic.gemma.core.config.DataSourceConfig: Production / dev datasource.
DataSourceConfig - Class in ubic.gemma.core.config: Renovations Phase 3: Java-config replacement for applicationContext-dataSource.xml.
DataSourceConfig() - Constructor for class ubic.gemma.core.config.DataSourceConfig
dataSourceInitializerStub() - Method in class ubic.gemma.core.config.DataSourceConfig: Dummy dataSourceInitializer stub.
DatatypeProperty - Interface in ubic.gemma.core.ontology.model
DataUpdater - Interface in ubic.gemma.core.loader.expression
DataUpdaterAuditService - Interface in ubic.gemma.core.loader.expression: Co-bean carrying the DataReplacedEvent emission written at the end of the data-replacement public methods on DataUpdaterImpl (addAffyDataFromAPTOutput, reprocessAffyDataFromCel, replaceData).
DataUpdaterAuditServiceImpl - Class in ubic.gemma.core.loader.expression: Implementation of DataUpdaterAuditService: a thin co-bean that exists so DataUpdaterAuditServiceImpl.recordDataReplaced(ExpressionExperiment, String) is invoked through a Spring proxy and the Audited aspect can intercept its return path and emit the DataReplacedEvent.
DataUpdaterAuditServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.DataUpdaterAuditServiceImpl
DataUpdaterImpl - Class in ubic.gemma.core.loader.expression: Update or fill in the data associated with an experiment.
DataUpdaterImpl() - Constructor for class ubic.gemma.core.loader.expression.DataUpdaterImpl
DataVector - Class in ubic.gemma.model.expression.bioAssayData: An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.
DataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVector
DataVectorDescriptive - Class in ubic.gemma.core.analysis.stats: Compute descriptive statistics for DataVector.
DataVectorDescriptive() - Constructor for class ubic.gemma.core.analysis.stats.DataVectorDescriptive
DataVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData: Base class for value objects of BulkExpressionDataVector.
DataVectorValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
DataVectorValueObject(Long) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
DataVectorValueObject(BulkExpressionDataVector, ExpressionExperimentValueObject, QuantitationTypeValueObject, BioAssayDimensionValueObject, ArrayDesignValueObject, Collection) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
DataVectorValueObject(DoubleVectorValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject: Copy constructor
dataWasBatchCorrected() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails: Indicate if batch correction was performed on the expression data.
DateUtil - Class in ubic.gemma.core.util: Date helpers.
DateUtil() - Constructor for class ubic.gemma.core.util.DateUtil
daxpy_j(int, double, double[], int, double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method multiplies a constant times a vector and adds the product to another vector --- dy[] = da*dx[] + dy[].
DbHealthIndicator - Class in ubic.gemma.rest.monitoring.health: Database health probe.
DbHealthIndicator(DataSource) - Constructor for class ubic.gemma.rest.monitoring.health.DbHealthIndicator
dbinom(double, double, double) - Static method in class ubic.gemma.core.util.math.SpecFunc: See dbinom_raw.
DbPoolResponse() - Constructor for class ubic.gemma.rest.AdminWebService.DbPoolResponse
dcopy_j(int, double[], int, double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method copies the vector dx[] to the vector dy[].
dcopyp_j(int, double[], double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method copies a portion of vector x[] to the corresponding portion of vector y[].
ddot_j(int, double[], int, double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method calculates the dot product of two vectors.
DE_EXCLUDE_URI - Static variable in class ubic.gemma.model.expression.experiment.FactorValueUtils: URI of TGEMO_00014 DE_Exclude, which marks samples to leave out of a differential expression analysis.
DE_INCLUDE_URI - Static variable in class ubic.gemma.model.expression.experiment.FactorValueUtils: URI of TGEMO_00013 DE_Include, which marks samples to keep in a differential expression analysis.
deBlatFormatChromosomeName(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Removes "chr" prefix from the chromosome name, if it is there.
debugMap(Map) - Static method in class ubic.gemma.core.loader.util.ParserAndLoaderTools: Print content of map if debug is set to true.
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCollectionFilteringProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationQuietReadProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationStreamFilteringProvider
decide(Authentication, Object, Collection, Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectMapReadProvider
decide(Investigation, CurationDecisionType, CurationDecisionScope, String, AnnotationSet, String, String, TriageJudgeKind) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionService: Record a decision.
decide(Investigation, CurationDecisionType, CurationDecisionScope, String, AnnotationSet, String, String, TriageJudgeKind) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionServiceImpl
decidedAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse
decidedAt - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
decidedBy - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse
decidedBy - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
decision - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionRequest
decision - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
decisionKey - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionRequest: WHAT was ruled on, in your own terms -- not which proposed item was in front of the curator.
decisionKey - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
decode(String) - Static method in class ubic.gemma.persistence.util.Cursor: Decode a base64url-encoded cursor string.
decodeBase64Float32(String, int, int) - Static method in class ubic.gemma.rest.HeatmapDataService: Decode a base64f32 string back into a double[][] of the given shape.
decodeCompressedArg(String) - Static method in class ubic.gemma.rest.util.ArgUtils: Decode a base64-encoded gzip-compressed argument.
decompress(InputStream) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
decompressToStream(InputStream) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
deepCopy(Object) - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
deepCopy(List) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
DEFAULT - Enum constant in enum class ubic.gemma.persistence.util.Sort.NullMode
DEFAULT - Enum constant in enum class ubic.gemma.rest.util.args.SortArg.Sort.NullMode
DEFAULT - Static variable in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig: Default preset for retrieving GEO records.
DEFAULT_ALLOW_PARS - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
DEFAULT_ALLOW_PREDICTED - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
DEFAULT_BARCODE_METADATA_FILE_SUFFIX - Static variable in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
DEFAULT_BARCODES_FILE_SUFFIX - Static variable in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
DEFAULT_BLAT_SCORE_THRESHOLD - Static variable in interface ubic.gemma.core.analysis.sequence.Blat: This value is basically a threshold fraction of aligned bases in the query.
DEFAULT_DISTINCT_VALUE_FRACTION - Static variable in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
DEFAULT_FEATURES_FILE_SUFFIX - Static variable in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
DEFAULT_GENES_FILE_SUFFIX - Static variable in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
DEFAULT_HIGH_EXPRESSION_CUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
DEFAULT_IDENTITY_THRESHOLD - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig: Sequence identity below which we throw hits away (expressed as a fraction)
DEFAULT_LIMIT - Static variable in class ubic.gemma.rest.CompletionsWebService: Default limit when the client does not supply one.
DEFAULT_LOW_EXPRESSION_CUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
DEFAULT_LOW_VARIANCE_CUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
DEFAULT_LOW_VARIANCE_CUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.LowVarianceFilter: Default low variance cut-off.
DEFAULT_MASK_OUTLIERS - Static variable in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
DEFAULT_MATRIX_FILE_SUFFIX - Static variable in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
DEFAULT_MAX_ENTRY_SIZE_IN_ARCHIVE_TO_SKIP - Static variable in interface ubic.gemma.core.loader.expression.geo.singleCell.ArchiveBasedSingleCellDetector
DEFAULT_MAX_NUMBER_OF_ENTRIES_TO_SKIP - Static variable in interface ubic.gemma.core.loader.expression.geo.singleCell.ArchiveBasedSingleCellDetector
DEFAULT_MAX_RESULTS_PER_RESULT_TYPE - Static variable in class ubic.gemma.model.common.search.SearchSettings: How many results per result type are allowed.
DEFAULT_MIN_PRESENT_COUNT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
DEFAULT_MIN_PRESENT_FRACTION - Static variable in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
DEFAULT_MIN_SHOULD_MATCH - Static variable in class ubic.gemma.core.ontology.search.OntologyQueries: Default share of a query's terms a document must carry to be a candidate.
DEFAULT_MINIMUM_EXON_OVERLAP_FRACTION - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig: Fraction of bases which must overlap with an annotated exon.
DEFAULT_MINIMUM_FRACTION_OF_UNIQUE_VALUES - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
DEFAULT_MINIMUM_FRACTION_OF_UNIQUE_VALUES - Static variable in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter
DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_GENE - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_GENE - Static variable in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter
DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_SAMPLE - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_SAMPLE - Static variable in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter
DEFAULT_MINIMUM_NUMBER_OF_SAMPLES_TO_APPLY_FILTER - Static variable in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter
DEFAULT_MINIMUM_NUMBER_OF_SAMPLES_TO_APPLY_REPETITIVE_VALUES_FILTER - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
DEFAULT_MINIMUM_VARIANCE - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
DEFAULT_MODE - Static variable in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter
DEFAULT_MODERATE_STATISTICS - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Default value for whether moderated test statistics should be used.
DEFAULT_NUMBER_OF_FETCH_THREADS - Static variable in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Default number of threads to use for fetching data.
DEFAULT_PERMISSIONS - Static variable in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationQuietReadProvider: Default permission set: READ or ADMINISTRATION (any one suffices).
DEFAULT_PYTHON_EXECUTABLE - Static variable in interface ubic.gemma.core.loader.expression.singleCell.transform.PythonBasedSingleCellDataTransformation
DEFAULT_REPETITIVE_VALUES_FILTER_MODE - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
DEFAULT_REQUEST_HEADER - Static variable in class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy
DEFAULT_SCORE_THRESHOLD - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig: BLAT score threshold below which we do not consider hits.
DEFAULT_SEP - Static variable in class ubic.gemma.core.util.matrix.MatrixWriter
DEFAULT_SIGNAL_TO_NOISE_THRESHOLD - Static variable in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
DEFAULT_THRESHOLD - Static variable in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
DEFAULT_TOP_LEFT - Static variable in class ubic.gemma.core.util.matrix.MatrixWriter
DEFAULT_TRIM_NONCANONICAL_CHROMOSOMES - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
DEFAULT_TTL_MINUTES - Static variable in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService: Default lease length.
defaultConfigLocation() - Static method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean: Convenience for tests that want the canonical Gemma mapping list without committing to a particular DataSource or property set: returns a ClassPathResource pointing at the production hibernate.cfg.xml.
DefaultHighlighter - Class in ubic.gemma.core.search: Default Highlighter implementation that returns the matched value verbatim under its field name.
DefaultHighlighter() - Constructor for class ubic.gemma.core.search.DefaultHighlighter
DefaultProgressReporterFactory - Class in ubic.gemma.core.util
DefaultProgressReporterFactory() - Constructor for class ubic.gemma.core.util.DefaultProgressReporterFactory
defaultSequencingMetadata(SequencingMetadata) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder: Default sequencing metadata to use.
DEFERRED_URIS - Static variable in interface ubic.gemma.core.ontology.ObsoleteTermCorrectionService: Terms that are mechanically correctable but that Paul has deferred (2026-08-19).
defineTask(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
DEFINITION_URI - Static variable in class ubic.gemma.core.ontology.OntologyUtils: The OBO definition annotation property, which UBERON, HP, MP and MONDO all use.
DelegatingAsyncTaskExecutor - Interface in ubic.gemma.core.util.concurrent
DelegatingExecutor - Interface in ubic.gemma.core.util.concurrent: An interface for Executor that delegate to another Executor.
DelegatingExecutorService - Interface in ubic.gemma.core.util.concurrent: An interface for ExecutorService that delegate to another ExecutorService.
DelegatingScheduledExecutorService - Interface in ubic.gemma.core.util.concurrent
DelegatingSchedulingTaskExecutor - Interface in ubic.gemma.core.util.concurrent
DelegatingSecurityContextAsyncTaskExecutor - Class in ubic.gemma.core.security.concurrent
DelegatingSecurityContextAsyncTaskExecutor(AsyncTaskExecutor) - Constructor for class ubic.gemma.core.security.concurrent.DelegatingSecurityContextAsyncTaskExecutor
DelegatingSecurityContextExecutorService - Class in ubic.gemma.core.security.concurrent
DelegatingSecurityContextExecutorService(ExecutorService) - Constructor for class ubic.gemma.core.security.concurrent.DelegatingSecurityContextExecutorService
DelegatingSecurityContextSchedulingTaskExecutor - Class in ubic.gemma.core.security.concurrent
DelegatingSecurityContextSchedulingTaskExecutor(SchedulingTaskExecutor) - Constructor for class ubic.gemma.core.security.concurrent.DelegatingSecurityContextSchedulingTaskExecutor
DelegatingSecurityContextTaskExecutor - Class in ubic.gemma.core.security.concurrent
DelegatingSecurityContextTaskExecutor(TaskExecutor) - Constructor for class ubic.gemma.core.security.concurrent.DelegatingSecurityContextTaskExecutor
DelegatingTaskExecutor - Interface in ubic.gemma.core.util.concurrent
DelegatingThreadContextAsyncTaskExecutor - Class in ubic.gemma.core.logging.log4j
DelegatingThreadContextAsyncTaskExecutor(AsyncTaskExecutor) - Constructor for class ubic.gemma.core.logging.log4j.DelegatingThreadContextAsyncTaskExecutor
DelegatingThreadContextCallable<T> - Class in ubic.gemma.core.logging.log4j
DelegatingThreadContextExecutor - Class in ubic.gemma.core.logging.log4j
DelegatingThreadContextExecutor(Executor) - Constructor for class ubic.gemma.core.logging.log4j.DelegatingThreadContextExecutor
DelegatingThreadContextExecutorService - Class in ubic.gemma.core.logging.log4j
DelegatingThreadContextExecutorService(ExecutorService) - Constructor for class ubic.gemma.core.logging.log4j.DelegatingThreadContextExecutorService
DelegatingThreadContextRunnable - Class in ubic.gemma.core.logging.log4j
DelegatingThreadContextScheduledExecutorService - Class in ubic.gemma.core.logging.log4j
DelegatingThreadContextScheduledExecutorService(ScheduledExecutorService) - Constructor for class ubic.gemma.core.logging.log4j.DelegatingThreadContextScheduledExecutorService
DelegatingThreadContextSchedulingTaskExecutor - Class in ubic.gemma.core.logging.log4j
DelegatingThreadContextSchedulingTaskExecutor(SchedulingTaskExecutor) - Constructor for class ubic.gemma.core.logging.log4j.DelegatingThreadContextSchedulingTaskExecutor
DelegatingThreadContextTaskExecutor - Class in ubic.gemma.core.logging.log4j
DelegatingThreadContextTaskExecutor(TaskExecutor) - Constructor for class ubic.gemma.core.logging.log4j.DelegatingThreadContextTaskExecutor
delete(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
delete(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
delete(Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: Delete the row with the given id.
delete(Long) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
delete(String) - Method in interface ubic.gemma.core.util.GemmaRestApiClient: Issue a DELETE against a given REST endpoint.
delete(String) - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
delete(AclObjectIdentity, boolean) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
delete(AclObjectIdentity, boolean) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
delete(AclSid) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
delete(AclSid) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
delete(User) - Method in interface ubic.gemma.core.security.authentication.BaseUserService: Remove a user from the persistent store.
delete(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
delete(UserGroup) - Method in interface ubic.gemma.core.security.authentication.BaseUserService: Remove a group from the persistent store
delete(UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
delete(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper: Delete the experiment set corresponding to the given VO.
delete(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
DELETE - Static variable in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Aliases, for readability.
deleteAce(int) - Method in class ubic.gemma.core.security.acl.domain.AclImpl
deleteAcl(ObjectIdentity, boolean) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
deleteAlignmentData(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
deleteAlignmentData(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
deleteAlignmentData(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: remove sequence alignment results associated with the bioSequences for this array design.
deleteAlignmentData(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
deleteAllAnalysisFiles(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete all analyses files for a given experiment.
deleteAllAnalysisFiles(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteAllAnnotatedFiles(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete all files that contain platform annotations for a given experiment.
deleteAllAnnotatedFiles(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteAllDataFiles(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete all data files for a given QT.
deleteAllDataFiles(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteAllFiles(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete any existing design, coexpression, data, or differential expression data files.
deleteAllFiles(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteAllProcessedDataFiles(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete all the processed files for a given experiment.
deleteAllProcessedDataFiles(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteAnalyses(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService: Delete any differential expression analyses associated with the experiment.
deleteAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
deleteAnalyses(ExpressionExperiment, Collection) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService: Delete the specified differential expression analyses associated with the experiment.
deleteAnalyses(ExpressionExperiment, Collection) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
deleteAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService: Deletes the given analysis.
deleteAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl: SUPPORTS overrides the class-level NEVER so a caller that is already in a transaction -- ExpressionExperimentService.applyDesignChange(ExpressionExperiment, ExperimentalDesignValueObject) cascading invalidated analyses -- can route through here instead of calling differentialExpressionAnalysisService.remove, which is database-only and leaves the archive and result-set TSV caches on the deployment volume.
deleteAnnotationSet(Long) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Delete an annotation set by id.
deleteBlacklistEntry(String) - Method in class ubic.gemma.rest.AdminWebService: Removes a blacklist entry by its accession.
deleteBySet(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDao: Delete every ruling on one set and report how many rows went.
deleteBySet(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDaoImpl
deleteCoexpressionDataFile(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete a coexpression data file if it exists.
deleteCoexpressionDataFile(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleted - Variable in class ubic.gemma.rest.AnnotationSetsWebService.ClearDispositionsResponse: How many rulings were deleted.
deletedAt - Variable in class ubic.gemma.rest.AdminWebService.UserValueObject: Non-null when the user has been soft-deleted.
deleteDatabaseEntities(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Security is handled within method
deleteDatabaseEntities(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
deleteDatabaseEntity(DatabaseBackedGeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Security is handled within method, when the set is loaded
deleteDatabaseEntity(DatabaseBackedGeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
deleteDataFile(ExpressionExperiment, boolean, ExpressionExperimentDataFileType) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete a processed data file if it exists.
deleteDataFile(ExpressionExperiment, boolean, ExpressionExperimentDataFileType) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteDataFile(ExpressionExperiment, QuantitationType, ExpressionExperimentDataFileType) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete a raw or single-cell data file if it exists.
deleteDataFile(ExpressionExperiment, QuantitationType, ExpressionExperimentDataFileType) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteDatasetProcessedData(DatasetArg, boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Delete the processed expression data vectors for a dataset (port of deleteProcessedData CLI).
deleteDatasetRawData(DatasetArg, QuantitationTypeArg, boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Delete the raw expression data vectors for a dataset (port of deleteRawData CLI).
deletedBy - Variable in class ubic.gemma.rest.AdminWebService.UserValueObject
deletedCount - Variable in class ubic.gemma.rest.AdminWebService.UsersListResponse: Total count of soft-deleted users (regardless of whether they're included in the list).
deleteDesignFile(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete the experimental design file for a given experiment.
deleteDesignFile(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteDifferentialExpressionResultSetTsvFile(Long) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete the cached TSV (if any) for a single differential-expression result set.
deleteDifferentialExpressionResultSetTsvFile(Long) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteDiffExArchiveFile(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete a diff.
deleteDiffExArchiveFile(DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
DeleteDiffExCli - Class in ubic.gemma.apps: Delete differential expression analsyes on a per-experiment basis.
DeleteDiffExCli() - Constructor for class ubic.gemma.apps.DeleteDiffExCli
deleteExistingFiles(ArrayDesign) - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
deleteExistingFiles(ArrayDesign) - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
DeleteExperimentsCli - Class in ubic.gemma.apps: Delete one or more experiments from the system.
DeleteExperimentsCli() - Constructor for class ubic.gemma.apps.DeleteExperimentsCli
deleteExperimentSet(Long) - Method in class ubic.gemma.rest.ExperimentSetsWebService
deleteFactorValues(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDeletion
deleteFactorValues(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDeletionImpl
deleteFiles(Collection) - Static method in class ubic.gemma.core.util.FileTools: Deletes the specified collection of files.
deleteGeneProductAlignmentAssociations(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
deleteGeneProductAlignmentAssociations(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
deleteGeneProductAlignmentAssociations(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
deleteGeneProductAlignmentAssociations(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
deleteGeneProductAnnotationAssociations(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
deleteGeneProductAnnotationAssociations(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
deleteGeneProductAnnotationAssociations(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
deleteGeneProductAnnotationAssociations(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
deleteGeneProductAssociations(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
deleteGeneProductAssociations(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
deleteGeneProductAssociations(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: deletes the gene product associations on the specified array design.
deleteGeneProductAssociations(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
deleteGroup(Long) - Method in class ubic.gemma.rest.GroupsWebService: Delete a group.
deleteGroup(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
deleteMetadataFile(ExpressionExperiment, ExpressionExperimentMetaFileType) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete a metadata file.
deleteMetadataFile(ExpressionExperiment, ExpressionExperimentMetaFileType) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteOldAnalyses(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.expression.AnalysisUtilService: Remove all analyses for the experiment (Differential, Coexpression and PCA).
deleteOldAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.expression.AnalysisUtilServiceImpl
deleteOldFiles(ArrayDesign) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService: Delete outdated annotation and associated experiment files.
deleteOldFiles(ArrayDesign) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
deleteProcessedData(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataDeleterService
deleteProcessedData(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataDeleterServiceImpl
deleteProcessedDataDesignFile(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
deleteProcessedDataDesignFile(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteRawData(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataDeleterService: Delete raw data vectors and associated data files.
deleteRawData(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.core.analysis.service.ExpressionDataDeleterServiceImpl
deleteSid(Sid) - Method in interface ubic.gemma.core.security.acl.domain.AclService: Remove an Sid and all associated ACEs.
deleteSid(Sid) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
deleteSingleCellData(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataDeleterService
deleteSingleCellData(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.core.analysis.service.ExpressionDataDeleterServiceImpl
deleteSingleCellDimension(ExpressionExperiment, SingleCellDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Delete the given single-cell dimension.
deleteSingleCellDimension(ExpressionExperiment, SingleCellDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
deleteStatistics(ExpressionExperiment, DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl: Remove old files which will otherwise be cruft.
deleteTicket(Long, String) - Method in class ubic.gemma.rest.TicketsWebService: Soft-close a ticket: transition to TicketState.CANCELLED and append a CANCELLED event.
deleteUser(String) - Method in interface ubic.gemma.core.security.authentication.UserManager
deleteUser(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
deleteUser(String) - Method in class ubic.gemma.rest.AdminWebService: Soft delete — marks the account as deleted, disables it, and preserves the row so dependent references (ACL sids, audit-event authorship FKs) don't dangle.
denotesADiseaseOrPhenotype(String) - Static method in enum class ubic.gemma.model.common.description.RelationTopicality: Whether a term URI names a disease or phenotype by virtue of the vocabulary it belongs to.
dense(double[][]) - Static method in class ubic.gemma.core.util.matrix.DoubleMatrixFactory
dense(int, int) - Static method in class ubic.gemma.core.util.matrix.DoubleMatrixFactory
dense(DoubleMatrix) - Static method in class ubic.gemma.core.util.matrix.DoubleMatrixFactory: Creates a matrix in which the underlying data is a copy; the row and column labels are not copied.
DenseDoubleMatrix<R,C> - Class in ubic.gemma.core.util.matrix: A dense matrix of doubles that knows about row and column names.
DenseDoubleMatrix(double[][]) - Constructor for class ubic.gemma.core.util.matrix.DenseDoubleMatrix
DenseDoubleMatrix(int, int) - Constructor for class ubic.gemma.core.util.matrix.DenseDoubleMatrix
DenseDoubleMatrix1D - Class in ubic.gemma.core.util.matrix: Use this class when fast iteration over the matrix is of primary interest.
DenseDoubleMatrix1D(double[]) - Constructor for class ubic.gemma.core.util.matrix.DenseDoubleMatrix1D
DenseDoubleMatrix1D(int) - Constructor for class ubic.gemma.core.util.matrix.DenseDoubleMatrix1D
DenseDoubleMatrix1D(int, double[], int, int) - Constructor for class ubic.gemma.core.util.matrix.DenseDoubleMatrix1D
DenseMatrix - Class in ubic.gemma.core.loader.util.anndata: Represents a dense AnnData matrix.
DenseMatrix(H5Dataset) - Constructor for class ubic.gemma.core.loader.util.anndata.DenseMatrix
deprecated(boolean) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder: Indicate if the property is deprecated.
DEPRECATED - Enum constant in enum class ubic.gemma.cli.util.CLI.CommandGroup
deprecateProperty(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer: Deprecate the given property.
derive(String, String, String) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions: Derive dispositions from the three payloads directly.
derive(AnnotationSet) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions: Derive dispositions for a draft, reading the proposal payload through the draft's parent.
DESC - Enum constant in enum class ubic.gemma.persistence.util.Sort.Direction
DESC - Enum constant in enum class ubic.gemma.rest.util.args.SortArg.Sort.Direction
Describable - Interface in ubic.gemma.model.common: Interface for entities that have a name and description.
DescribableComparator - Class in ubic.gemma.persistence.util
DescribableComparator() - Constructor for class ubic.gemma.persistence.util.DescribableComparator
DescribableUtils - Class in ubic.gemma.model.common: Utilities to manipulate Describable and collections thereof.
DescribableUtils() - Constructor for class ubic.gemma.model.common.DescribableUtils
describeFilterResult(DifferentialExpressionAnalysisFilterResult) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
describeFilterResult(ExpressionExperimentFilterResult) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
describeProperty(String, String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer: Provide a description for a given property.
description - Variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
description - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject
description - Variable in class ubic.gemma.rest.ExperimentSetsWebService.ExperimentSetRequest
description(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder
DESCRIPTION - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
descriptions(Collection) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder
DescriptiveWithMissing - Class in ubic.gemma.core.util.math: Mathematical functions for statistics that allow missing values without scotching the calculations.
design() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentWebUrl
DesignApplyOutcome - Class in ubic.gemma.model.expression.experiment: Outcome returned by the PUT /datasets/{id}/design apply path.
DesignApplyOutcome() - Constructor for class ubic.gemma.model.expression.experiment.DesignApplyOutcome
DesignApplyOutcome(boolean, ExperimentalDesignValueObject, DesignPreflightReport) - Constructor for class ubic.gemma.model.expression.experiment.DesignApplyOutcome
DesignChangeEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted by the PUT /datasets/{id}/design apply path when a proposed ExperimentalDesignValueObject is successfully written back as the experiment's new design.
DesignChangeEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DesignChangeEvent
DesignCommit() - Constructor for class ubic.gemma.rest.DatasetsWebService.DesignCommit
DesignCommitPlan - Class in ubic.gemma.persistence.service.expression.experiment: Side-channel the web-layer design mapper hands to ExpressionExperimentService.commitCuration(ExpressionExperiment, CurationCommitRequest, boolean) so the service can, after applying the proposed design, (1) resolve each new entity's clientRef to the database id it was assigned and (2) wire sample assignments that target freshly-created factor values.
DesignCommitPlan() - Constructor for class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
DesignCommitPlan.PendingAssignment - Class in ubic.gemma.persistence.service.expression.experiment: A sample assignment whose target factor value does not exist yet (identified by its clientRef).
DesignElementDataVector - Class in ubic.gemma.model.expression.bioAssayData: Data vector associated to a CompositeSequence.
DesignElementDataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
DesignElementDataVectorDao<T> - Interface in ubic.gemma.persistence.service.expression.bioAssayData
DesignElementMapper - Interface in ubic.gemma.core.loader.util.mapper: Maps gene identifiers to CompositeSequence.
DesignFileOptionValue - Class in ubic.gemma.cli.options: Options to write an experimental design file.
DesignFileOptionValue(boolean, boolean, Path, Path, boolean, boolean, boolean, boolean, String, boolean) - Constructor for class ubic.gemma.cli.options.DesignFileOptionValue
DesignFileOptionValue(DataFileOptionValue, boolean, boolean, boolean, boolean) - Constructor for class ubic.gemma.cli.options.DesignFileOptionValue
DesignMatrix - Class in ubic.gemma.core.util.math.linearmodels: Represents the A matrix in regression problems posed as Ax=b.
DesignMatrix(Object[], int, String) - Constructor for class ubic.gemma.core.util.math.linearmodels.DesignMatrix
DesignMatrix(ObjectMatrix, boolean) - Constructor for class ubic.gemma.core.util.math.linearmodels.DesignMatrix
DesignMatrix(ObjectMatrix) - Constructor for class ubic.gemma.core.util.math.linearmodels.DesignMatrix
DesignMatrix(ObjectMatrix, boolean, boolean) - Constructor for class ubic.gemma.core.util.math.linearmodels.DesignMatrix
DesignMatrix(StringMatrix) - Constructor for class ubic.gemma.core.util.math.linearmodels.DesignMatrix
DesignPreflightReport - Class in ubic.gemma.model.expression.experiment: Report returned by POST /datasets/{id}/designPreflight.
DesignPreflightReport() - Constructor for class ubic.gemma.model.expression.experiment.DesignPreflightReport
DesignPreflightReport.AnalysisRef - Class in ubic.gemma.model.expression.experiment
DesignPreflightReport.Blocker - Class in ubic.gemma.model.expression.experiment: One reason the proposed payload cannot be applied.
DesignPreflightReport.EntityRef - Class in ubic.gemma.model.expression.experiment
DesignPreflightReport.SubsetRef - Class in ubic.gemma.model.expression.experiment
DesignPreflightReport.Summary - Class in ubic.gemma.model.expression.experiment
destroy() - Method in class ubic.gemma.core.context.AbstractAsyncFactoryBean
destroy() - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
destroy() - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
destroy() - Method in class ubic.gemma.persistence.initialization.BootstrappedDataSourceFactory
destroy() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
destroyClient(URL, FTPClient) - Method in interface ubic.gemma.core.loader.util.ftp.FTPClientFactory: Destroy an FTP client that is known to be no-longer valid.
destroyClient(URL, FTPClient) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
destroyInstance(T) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory
destroyObject(OpenAPI) - Method in class ubic.gemma.rest.util.OpenApiFactory
destroyObject(T) - Method in class ubic.gemma.core.context.AbstractAsyncFactoryBean: Destroy a singleton instance.
detail() - Method in record class ubic.gemma.core.security.audit.payload.ReleaseDetailsUpdatePayload: Returns the value of the detail record component.
DETAILED - Static variable in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig: A preset configuration for retrieving detailed GEO records.
detect10x(String) - Static method in class ubic.gemma.core.loader.expression.singleCell.TenXCellRangerUtils: Detect if a description (i.e.
detect10x(String, Path) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurer
detect10x(String, Path) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer: Detect if a MEX dataset is using the 10x Chromium Sequencing platform.
detect10x(String, Path) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer
detect10xChemistry(String) - Static method in class ubic.gemma.core.loader.expression.singleCell.TenXCellRangerUtils: We essentially rely on the presence of specific production number of reagent kits in the extraction protocol section.
detect10xChemistry(String, Path) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurer
detect10xChemistry(String, Path) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer: Detect the chemistry used by a 10x dataset.
detect10xChemistry(String, Path) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer
detect10xFiltered(String) - Static method in class ubic.gemma.core.loader.expression.singleCell.TenXCellRangerUtils: Detect if a description (i.e.
detect10xFromMexFile(Path) - Static method in class ubic.gemma.core.loader.expression.singleCell.TenXCellRangerUtils
detect10xGenome(String, Path) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurer
detect10xGenome(String, Path) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer: Detect the genome used by a 10x dataset.
detect10xGenome(String, Path) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer
detect10xUnfiltered(String) - Static method in class ubic.gemma.core.loader.expression.singleCell.TenXCellRangerUtils: Detect if a description (i.e.
DetectQuantitationTypeCli - Class in ubic.gemma.apps
DetectQuantitationTypeCli() - Constructor for class ubic.gemma.apps.DetectQuantitationTypeCli
detectSuspiciousValues(ExpressionDataDoubleMatrix, QuantitationType) - Static method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtils: Detect suspicious values for a given quantitation type.
detectUnfiltered(String, Path) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurer
detectUnfiltered(String, Path) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer: Detect if a MEX dataset is unfiltered.
detectUnfiltered(String, Path) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer
determineAnalysisType(BioAssaySet, Collection, ExperimentalFactor, boolean) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Determines the analysis to execute based on the experimental factors, factor values, and block design.
determineAnalysisType(BioAssaySet, Collection, ExperimentalFactor, boolean, Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: A variant that decides from a given set of samples rather than every sample in the experiment.
determineAnalysisType(BioAssaySet, DifferentialExpressionAnalysisConfig) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
determineAnalysisType(BioAssaySet, DifferentialExpressionAnalysisConfig, Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: A variant that decides from a given set of samples rather than every sample in the experiment.
determinedBy - Static variable in class ubic.gemma.core.ontology.jena.RO
DEV - Static variable in class ubic.gemma.core.context.EnvironmentProfiles: Mutually-exclusive environment profiles.
DEVELOPMENT_STAGE - Static variable in class ubic.gemma.model.common.description.Categories
developmentStage - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
dhyper(int, int, int, int) - Static method in class ubic.gemma.core.util.math.SpecFunc: Ported from R (Catherine Loader)
diagnose() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition
diagnosticsOnly() - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
diagonal(DoubleMatrix2D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil: Extract the diagonal from a matrix.
DifferentialAnalysisRunRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.DifferentialAnalysisRunRequest
DifferentialExpressionAnalysis - Class in ubic.gemma.model.analysis.expression.diff: An analysis of changes in expression levels across experimental conditions
DifferentialExpressionAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
DifferentialExpressionAnalysis.Factory - Class in ubic.gemma.model.analysis.expression.diff
DifferentialExpressionAnalysisCli - Class in ubic.gemma.apps: A command line interface to the DifferentialExpressionAnalysis.
DifferentialExpressionAnalysisCli() - Constructor for class ubic.gemma.apps.DifferentialExpressionAnalysisCli
DifferentialExpressionAnalysisConfig - Class in ubic.gemma.core.analysis.expression.diff: Holds the settings used for differential expression analysis, and defines some defaults.
DifferentialExpressionAnalysisConfig() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
DifferentialExpressionAnalysisConfig(DifferentialExpressionAnalysisConfig) - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Copy constructor.
DifferentialExpressionAnalysisDao - Interface in ubic.gemma.persistence.service.analysis.expression.diff
DifferentialExpressionAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates the experiment was the subject of a differential expression analysis.
DifferentialExpressionAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionAnalysisEvent
DifferentialExpressionAnalysisFilter - Class in ubic.gemma.core.analysis.expression.diff: Filter used for performing DEA.
DifferentialExpressionAnalysisFilter(DifferentialExpressionAnalysisConfig) - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode - Enum Class in ubic.gemma.core.analysis.expression.diff
DifferentialExpressionAnalysisFilterResult - Class in ubic.gemma.core.analysis.expression.diff: Holds the result of data filtering for differential expression analysis.
DifferentialExpressionAnalysisFilterResult() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
DifferentialExpressionAnalysisHelperService - Interface in ubic.gemma.core.analysis.expression.diff: Service methods to do database-related work for differential expression analysis
DifferentialExpressionAnalysisHelperServiceImpl - Class in ubic.gemma.core.analysis.expression.diff: Transactional methods for dealing with differential expression analyses.
DifferentialExpressionAnalysisHelperServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceImpl
DifferentialExpressionAnalysisPayload - Record Class in ubic.gemma.core.security.audit.payload: Structured payload for the DifferentialExpressionAnalysisEvent written at the end of DifferentialExpressionAnalyzerServiceImpl#persistAnalysis.
DifferentialExpressionAnalysisPayload(String) - Constructor for record class ubic.gemma.core.security.audit.payload.DifferentialExpressionAnalysisPayload: Creates an instance of a DifferentialExpressionAnalysisPayload record class.
DifferentialExpressionAnalysisReadService - Interface in ubic.gemma.persistence.service.analysis.expression.diff: Read-only retrieval service for DifferentialExpressionAnalysis.
DifferentialExpressionAnalysisReadServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff: Implementation of DifferentialExpressionAnalysisReadService.
DifferentialExpressionAnalysisReadServiceImpl(DifferentialExpressionAnalysisDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
DifferentialExpressionAnalysisRemoveTaskCommand - Class in ubic.gemma.core.tasks.analysis.diffex: Specialized command object for removing analysis results.
DifferentialExpressionAnalysisRemoveTaskCommand(ExpressionExperiment, DifferentialExpressionAnalysis) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand
DifferentialExpressionAnalysisResult - Class in ubic.gemma.model.analysis.expression.diff: Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one factor.
DifferentialExpressionAnalysisResult() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
DifferentialExpressionAnalysisResult.Factory - Class in ubic.gemma.model.analysis.expression.diff
DifferentialExpressionAnalysisResultByGeneValueObject(DifferentialExpressionAnalysisResult, Long, Long, Baseline) - Constructor for class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
DifferentialExpressionAnalysisResultComparator - Class in ubic.gemma.persistence.util
DifferentialExpressionAnalysisResultComparator() - Constructor for class ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator
DifferentialExpressionAnalysisResultComparator.Factory - Class in ubic.gemma.persistence.util
DifferentialExpressionAnalysisResultListFileService - Interface in ubic.gemma.core.analysis.service: File service for arbitrary list of DifferentialExpressionAnalysisResult.
DifferentialExpressionAnalysisResultListFileServiceImpl - Class in ubic.gemma.core.analysis.service
DifferentialExpressionAnalysisResultListFileServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileServiceImpl
DifferentialExpressionAnalysisResultSetValueObject - Class in ubic.gemma.model.analysis.expression.diff: Wraps an ExpressionAnalysisResultSet and expose it to the public API.
DifferentialExpressionAnalysisResultSetValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
DifferentialExpressionAnalysisResultSetValueObject(Long) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject: Create a simple analysis results set VO with limited data.
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet, boolean, Map, boolean) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject: Create an expression analysis result set VO with all its associated results.
DifferentialExpressionAnalysisResultSetVisualizationValueObject - Class in ubic.gemma.core.tasks.visualization: This class contains data for a column in metaheatmap visualization.
DifferentialExpressionAnalysisResultSetVisualizationValueObject() - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
DifferentialExpressionAnalysisResultSetVisualizationValueObject(int[]) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
DifferentialExpressionAnalysisResultValueObject - Class in ubic.gemma.model.analysis.expression.diff: Unlike DiffExResultSetSummaryValueObject, this value object is meant for the public API.
DifferentialExpressionAnalysisResultValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
DifferentialExpressionAnalysisResultValueObject(DifferentialExpressionAnalysisResult, boolean) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
DifferentialExpressionAnalysisResultValueObject(DifferentialExpressionAnalysisResult, boolean, Set, boolean) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
DifferentialExpressionAnalysisService - Interface in ubic.gemma.persistence.service.analysis.expression.diff: Service interface for DifferentialExpressionAnalysis.
DifferentialExpressionAnalysisServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
DifferentialExpressionAnalysisServiceImpl(DifferentialExpressionAnalysisDao, DifferentialExpressionAnalysisReadService) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
DifferentialExpressionAnalysisTask - Interface in ubic.gemma.core.tasks.analysis.diffex
DifferentialExpressionAnalysisTaskCommand - Class in ubic.gemma.core.tasks.analysis.diffex: A command object to be used by spaces.
DifferentialExpressionAnalysisTaskCommand(boolean, ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment, DifferentialExpressionAnalysis) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
DifferentialExpressionAnalysisTaskImpl - Class in ubic.gemma.core.tasks.analysis.diffex: A differential expression analysis spaces task
DifferentialExpressionAnalysisTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskImpl
DifferentialExpressionAnalysisUtil - Class in ubic.gemma.core.analysis.expression.diff: A helper class for the differential expression analyzers.
DifferentialExpressionAnalysisUtil() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil
DifferentialExpressionAnalysisValueObject - Class in ubic.gemma.model.analysis.expression.diff: Summary of a differential expression analysis
DifferentialExpressionAnalysisValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
DifferentialExpressionAnalysisValueObject(DifferentialExpressionAnalysis) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject: Does not populate the resultSets.
DifferentialExpressionAnalysisWriterCli - Class in ubic.gemma.apps: Writes differential expression analysis files to disk.
DifferentialExpressionAnalysisWriterCli() - Constructor for class ubic.gemma.apps.DifferentialExpressionAnalysisWriterCli
DifferentialExpressionAnalyzerAuditService - Interface in ubic.gemma.core.analysis.expression.diff: Co-bean facade for the DifferentialExpressionAnalysisEvent audit emission carried out at the end of DifferentialExpressionAnalyzerServiceImpl.persistAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig).
DifferentialExpressionAnalyzerAuditServiceImpl - Class in ubic.gemma.core.analysis.expression.diff: Implementation of DifferentialExpressionAnalyzerAuditService.
DifferentialExpressionAnalyzerAuditServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerAuditServiceImpl
DifferentialExpressionAnalyzerService - Interface in ubic.gemma.core.analysis.expression.diff
DifferentialExpressionAnalyzerServiceImpl - Class in ubic.gemma.core.analysis.expression.diff: Differential expression service to run the differential expression analysis (and persist the results using the appropriate data access objects).
DifferentialExpressionAnalyzerServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
DifferentialExpressionFileUtils - Class in ubic.gemma.core.analysis.expression.diff
DifferentialExpressionFileUtils() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionFileUtils
DifferentialExpressionGenesConditionsValueObject - Class in ubic.gemma.core.tasks.visualization: Represents a complete set of data for a differential expression query over a set of genes x conditions (resultSets x contrasts).
DifferentialExpressionGenesConditionsValueObject() - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
DifferentialExpressionGenesConditionsValueObject.Cell - Class in ubic.gemma.core.tasks.visualization
DifferentialExpressionGenesConditionsValueObject.Condition - Class in ubic.gemma.core.tasks.visualization: Represents one column in the differential expression view; one contrast in a resultset in an experiment.
DifferentialExpressionGenesConditionsValueObject.DiffExGene - Class in ubic.gemma.core.tasks.visualization
DifferentialExpressionMetaAnalysisValueObject - Class in ubic.gemma.core.analysis.expression.diff: A value object with meta analysis results.
DifferentialExpressionMetaAnalysisValueObject() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
DifferentialExpressionResultCache - Interface in ubic.gemma.persistence.service.analysis.expression.diff: Cache for differential expression results.
DifferentialExpressionResultCacheImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff: Cache for data from differential expression result queries.
DifferentialExpressionResultCacheImpl() - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
DifferentialExpressionResultDao - Interface in ubic.gemma.persistence.service.analysis.expression.diff
DifferentialExpressionResultDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff: This is a key class for queries to retrieve differential expression results (as well as standard CRUD aspects of working with DifferentialExpressionResults).
DifferentialExpressionResultDaoImpl(SessionFactory, DifferentialExpressionResultCache) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
DifferentialExpressionResultReadService - Interface in ubic.gemma.persistence.service.analysis.expression.diff: Read-only retrieval service for DifferentialExpressionAnalysisResult.
DifferentialExpressionResultReadServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff: Implementation of DifferentialExpressionResultReadService.
DifferentialExpressionResultReadServiceImpl(DifferentialExpressionResultDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
DifferentialExpressionResultService - Interface in ubic.gemma.persistence.service.analysis.expression.diff: Main entry point to retrieve differential expression data.
DifferentialExpressionResultServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff: Facade for DifferentialExpressionResultService.
DifferentialExpressionResultServiceImpl(DifferentialExpressionResultDao, DifferentialExpressionResultReadService) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
DifferentialExpressionSearchTask - Interface in ubic.gemma.core.tasks.visualization: Created with IntelliJ IDEA.
DifferentialExpressionSearchTaskCommand - Class in ubic.gemma.core.tasks.visualization: Created with IntelliJ IDEA.
DifferentialExpressionSearchTaskCommand(Collection, Collection, String, String) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
DifferentialExpressionSearchTaskImpl - Class in ubic.gemma.core.tasks.visualization: Encapsulates the search for differential expression results, for a set of genes and experiments (which can be grouped)
DifferentialExpressionSearchTaskImpl() - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskImpl
DifferentialExpressionSuitabilityEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Used to indicate the suitability status of an ExpressionExperiment for differential expression analysis.
DifferentialExpressionSuitabilityEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionSuitabilityEvent
DifferentialExpressionValueObject - Class in ubic.gemma.model.analysis.expression.diff: Represents the results for one probe.
DifferentialExpressionValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
DifferentialExpressionValueObject(Long) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
DifferentialExpressionValueObject(DifferentialExpressionAnalysisResult) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
DiffExAnalysisResultSetWriter - Class in ubic.gemma.core.analysis.service: Writer for DifferentialExpressionAnalysis.
DiffExAnalysisResultSetWriter(EntityUrlBuilder, BuildInfo) - Constructor for class ubic.gemma.core.analysis.service.DiffExAnalysisResultSetWriter
DiffExAnalyzer - Interface in ubic.gemma.core.analysis.expression.diff
DiffExAnalyzerUtils - Class in ubic.gemma.core.analysis.expression.diff
DiffExAnalyzerUtils() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
DiffExGene(long, String, String) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
DiffExGeneWarmupService - Class in ubic.gemma.core.analysis.expression.diff: Periodic warm-up of the DEA "find results by gene" path.
DiffExGeneWarmupService() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExGeneWarmupService
DiffExMetaAnalyzerService - Interface in ubic.gemma.core.analysis.expression.diff: Used to perform meta-analyses of complete data sets (actually result sets), select the top genes, and potentially store the results.
DiffExMetaAnalyzerServiceImpl - Class in ubic.gemma.core.analysis.expression.diff
DiffExMetaAnalyzerServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceImpl
DiffExMetaAnalyzerTask - Interface in ubic.gemma.core.tasks.analysis.diffex
DiffExMetaAnalyzerTaskCommand - Class in ubic.gemma.core.tasks.analysis.diffex: A command object to be used by spaces.
DiffExMetaAnalyzerTaskCommand(Collection) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
DiffExMetaAnalyzerTaskCommand(Collection, String, String, boolean) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
DiffExMetaAnalyzerTaskImpl - Class in ubic.gemma.core.tasks.analysis.diffex: A differential expression meta-analysis space task
DiffExMetaAnalyzerTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskImpl
DiffExpressionSelectedFactorCommand - Class in ubic.gemma.core.analysis.expression.diff: A command object with a selected factor and associated experiment.
DiffExpressionSelectedFactorCommand() - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
DiffExpressionSelectedFactorCommand(Long, Long) - Constructor for class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
DiffExprGeneSearchResult - Class in ubic.gemma.model.analysis.expression.diff: Value object for differential expression result for one result - corresponds to the DifferentialExpressionAnalysisResults for one gene in one ResultSet (combined for multiple probes), but represents only the "selected" analysisResult.
DiffExprGeneSearchResult(Long, Long) - Constructor for class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
DiffExResultSetSummaryValueObject - Class in ubic.gemma.model.analysis.expression.diff: Summary of a result set.
DiffExResultSetSummaryValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet) - Constructor for class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet, ResultSetCountsValueObject) - Constructor for class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Variant constructor that uses a pre-aggregated counts snapshot (cached) for the hit-list fields instead of walking ExpressionAnalysisResultSet.getHitListSizes().
DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet, ResultSetCountsValueObject, DiffExResultSetSummaryValueObject.Prefetch) - Constructor for class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Variant constructor that also accepts a DiffExResultSetSummaryValueObject.Prefetch snapshot of the result-set's experimentalFactors + baselineGroup associations gathered up-front by a batched HQL fetch in the caller.
DiffExResultSetSummaryValueObject.Prefetch - Class in ubic.gemma.model.analysis.expression.diff: Pre-aggregated experimentalFactors + baselineGroup for a single ExpressionAnalysisResultSet, sourced from a batched join-fetch query so the VO ctor avoids three sequential lazy initializations.
DIRECT - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSource: Directly access GEO via www.ncbi.nlm.nih.gov/geo.
Direction - Enum Class in ubic.gemma.model.analysis.expression.diff: Represents the direction of a change e.g.
disableEmail() - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
disableEmail() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl: For use in tests.
DisallowedWorkflowTransitionException - Exception Class in ubic.gemma.persistence.service.expression.experiment: Thrown when WorkflowService.advance(Investigation, WorkflowState, String, Long) is asked for a transition the state machine forbids (e.g.
DisallowedWorkflowTransitionException(WorkflowState, WorkflowState, Set) - Constructor for exception class ubic.gemma.persistence.service.expression.experiment.DisallowedWorkflowTransitionException
disassemble(Object) - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
disassemble(List) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
discardEmptyCells(Boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Discard (or keep) empty cells.
DISCLOSURE - Enum constant in enum class ubic.gemma.model.annotations.WithheldFromApi.Reason: Not per-caller, but still should not leave the building: internal filesystem paths, raw instrument headers, submitter-local identifiers, internal free-text notes.
disconnect(FTPClient) - Method in class ubic.gemma.core.util.NetDatasourceUtil
discontinuedIdForSymbol(String, Integer) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
Discovery - Enum constant in enum class ubic.gemma.model.expression.experiment.WorkflowState
DISEASE - Static variable in class ubic.gemma.model.common.description.Categories
diseaseState - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
disjunction() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
disjunction() - Method in class ubic.gemma.rest.util.args.FilterArgParser
disjunction(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
DISJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
DISJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
DISJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
DISJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
DisjunctionContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
DiskSpaceHealthIndicator - Class in ubic.gemma.rest.monitoring.health: Disk-space health probe.
DiskSpaceHealthIndicator() - Constructor for class ubic.gemma.rest.monitoring.health.DiskSpaceHealthIndicator
DISMISSED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.FindingDisposition: The curator disagrees; the finding is wrong or does not matter.
displayMax - Variable in class ubic.gemma.core.util.graphics.ColorMatrix
displayMin - Variable in class ubic.gemma.core.util.graphics.ColorMatrix: Min and max values to display, which might not be the actual min and max values in the matrix.
displayName(Contact) - Static method in class ubic.gemma.model.common.auditAndSecurity.ContactUtils: The best available human-readable name for a contact: its name, else the account's userName.
disposition - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionRequest
disposition - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse
DispositionRequest() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.DispositionRequest
DispositionResponse() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse
dispositions - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse: The STANDING ruling on each finding — most recent per targetId, not the full append-only sequence; GET /annotation-sets/{id}/dispositions?history=true is where a ruling that moved is visible.
dissociateFromSeries(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset: This is used when we break a series up into two, along organism lines.
Distance - Class in ubic.gemma.core.util.math: Alternative distance and similarity metrics for vectors.
Distance() - Constructor for class ubic.gemma.core.util.math.Distance
DISTANCE - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementKind
distinctRunIds - Variable in class ubic.gemma.rest.AdminWebService.AgentRunsBlock: Distinct runIds seen on AnnotationSet rows with role=PROPOSAL in the last 7 days.
DL - Enum constant in enum class ubic.gemma.core.ontology.providers.OntologyService.LanguageLevel: OWL-DL
DNA - Enum constant in enum class ubic.gemma.model.genome.biosequence.PolymerType
DNA - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType: Generic DNA sequence of any other type not representable by another value
DNASE_HYPERSENSITIVITY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
dnrm2_j(int, double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method calculates the Euclidean norm of the vector stored in dx[] with storage increment incx.
dnrm2p_j(int, double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method calculates the Euclidean norm of a portion of a vector x[].
doAll() - Method in class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskCommand
doAll() - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
doArrayDesign(Object, Map) - Method in class ubic.gemma.persistence.persister.ArrayDesignPersister: Persister-shrink S2c typed dispatch: returns null if the entity is not an ArrayDesign.
doAuthenticatedWork() - Method in class ubic.gemma.apps.AclLinterCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.BibRefUpdaterCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.BlacklistCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.CellXGeneDataAdderCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.CompleteCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.DeleteExperimentsCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.ExperimentalDesignViewCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
doAuthenticatedWork() - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI: Main entry point to service class which reads a gene file and persists the genes in that file.
doAuthenticatedWork() - Method in class ubic.gemma.apps.FactorValueOntologyWriterCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.FindObsoleteTermsCli: Deprecated.
doAuthenticatedWork() - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator
doAuthenticatedWork() - Method in class ubic.gemma.apps.GeoGrabberCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.LoadExpressionDataCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.MergeDuplicateBibRefsCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.MultifunctionalityCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI
doAuthenticatedWork() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI
doAuthenticatedWork() - Method in class ubic.gemma.apps.ProtocolAdderCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.ProtocolDeleterCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.ProtocolListCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.PubMedLoaderCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.PubMedSearcher
doAuthenticatedWork() - Method in class ubic.gemma.apps.SingleCellDataLoaderCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.TaxonLoaderCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.UpdateExternalRelationsCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.UpdateGene2CsCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.UpdateOntologyRelationsCli
doAuthenticatedWork() - Method in class ubic.gemma.apps.UpdatePubMedCli
doAuthenticatedWork() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI
doCommon(T, Map) - Method in class ubic.gemma.persistence.persister.CommonPersister: Persister-shrink S2 typed dispatch: handles the User / Characteristic arms formerly carried by the doPersist override.
documentCount - Variable in class ubic.gemma.rest.AdminWebService.IndexStatusValueObject: Document count from a matchAll fetchTotalHitCount; -1 on query failure.
doDelete - Variable in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
DoesNotNeedAttentionEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
resolve the open GENERIC / BATCH_INFO_NEEDED ticket(s) targeting the entity via TicketService.transition(Ticket, TicketState, Contact, String) (target state TicketState.RESOLVED). See CurationDetailsEvent for the full migration map.
DoesNotNeedAttentionEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent: Deprecated.
dof(DoubleArrayList, IntArrayList) - Static method in class ubic.gemma.core.util.math.KruskalWallis
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.rest.security.BearerTokenAuthenticationFilter
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.rest.servlet.CorsFilter
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.rest.servlet.RequestIdMdcFilter
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilter
doGenome(T, Map) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persister-shrink S2 typed dispatch: handles the Gene / GeneProduct / BioSequence / Taxon / BioSequence2GeneProduct / SequenceSimilaritySearchResult / Chromosome arms formerly carried by the doPersist override.
doGenomeUpdate(T, Map) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persister-shrink S2 typed dispatch for persist-or-update.
DOI - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
doLoadValueObject(O) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao: Load a value object for a given entity.
doLoadValueObject(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
doLoadValueObject(ExpressionExperimentSet) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
doLoadValueObject(BlacklistedEntity) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
doLoadValueObject(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
doLoadValueObject(Characteristic) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
doLoadValueObject(DatabaseEntry) - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImpl
doLoadValueObject(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
doLoadValueObject(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl: Loads a single value objects for the given array design.
doLoadValueObject(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
doLoadValueObject(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl
doLoadValueObject(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
doLoadValueObject(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
doLoadValueObject(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl
doLoadValueObject(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
doLoadValueObject(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
doLoadValueObject(Geeq) - Method in class ubic.gemma.persistence.service.expression.experiment.GeeqDaoImpl
doLoadValueObject(BioSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
doLoadValueObject(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
doLoadValueObject(GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
doLoadValueObject(BlatResult) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl
doLoadValueObject(Taxon) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
doLoadValueObjects(Collection) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao: Load all the value objects for the given entities.
doLoadValueObjects(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
DONE - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetStatus
DONE - Enum constant in enum class ubic.gemma.model.pipeline.JobState
doNicely(EntrezUtils.EntrezCall, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Coordinate calls to the Entrez API so that we always respect the recommended usage.
doPersist(Collection, Map) - Method in class ubic.gemma.persistence.persister.CommonPersister
doPersist(Set, Map) - Method in class ubic.gemma.persistence.persister.CommonPersister
doPersist(T, Map) - Method in class ubic.gemma.persistence.persister.ArrayDesignPersister: Polymorphic dispatch entry point reached by RelationshipPersister via the still-extant inheritance chain.
doPersist(T, Map) - Method in class ubic.gemma.persistence.persister.CommonPersister: Polymorphic dispatch entry point on the persister chain.
doPersist(T, Map) - Method in class ubic.gemma.persistence.persister.GenomePersister: Polymorphic dispatch entry point reached by ArrayDesignPersister via the still-extant inheritance chain.
doPersist(T, Map) - Method in class ubic.gemma.persistence.persister.RelationshipPersister: Polymorphic dispatch entry point reached by PersisterHelperImpl via its (still-extant) extends RelationshipPersister.
doPersistOrUpdate(T, Map) - Method in class ubic.gemma.persistence.persister.ArrayDesignPersister: Polymorphic persist-or-update dispatch entry point reached by the chain.
doPersistOrUpdate(T, Map) - Method in class ubic.gemma.persistence.persister.CommonPersister
doPersistOrUpdate(T, Map) - Method in class ubic.gemma.persistence.persister.GenomePersister: Polymorphic dispatch entry point for persist-or-update reached by the chain.
doPersistOrUpdate(T, Map) - Method in class ubic.gemma.persistence.persister.RelationshipPersister: Polymorphic persist-or-update dispatch entry point.
doRelationship(T, Map) - Method in class ubic.gemma.persistence.persister.RelationshipPersister: Typed dispatch surface for the S2e dispatcher: returns null when the entity is neither Gene2GOAssociation nor ExpressionExperimentSet.
doReportProgress(double, long, long, boolean) - Method in class ubic.gemma.cli.util.ConsoleProgressReporter
doReportProgress(double, long, long, boolean) - Method in class ubic.gemma.core.util.AbstractProgressReporter
doReportProgress(double, long, long, boolean) - Method in class ubic.gemma.core.util.LoggingProgressReporter
doReportUnknownProgress(long, boolean) - Method in class ubic.gemma.cli.util.ConsoleProgressReporter
doReportUnknownProgress(long, boolean) - Method in class ubic.gemma.core.util.AbstractProgressReporter
doReportUnknownProgress(long, boolean) - Method in class ubic.gemma.core.util.LoggingProgressReporter
dose - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
doSubmittedTasksMaintenance() - Method in class ubic.gemma.core.job.SubmittedTasksMaintenance: Check if a task has been running or queued for too long, and cancel it if necessary.
doTask(Callable, long, String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
doTask(Callable, long, String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
DOUBLE - Enum constant in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType
double2float(double[]) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
double2int(double[]) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
double2long(double[]) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
doubleArrayToBytes(double[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
doubleArrayToBytes(double[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
DoubleMatrix<R,C> - Class in ubic.gemma.core.util.matrix: Abstract base class for 2D matrices of double values with named columns and rows.
DoubleMatrix() - Constructor for class ubic.gemma.core.util.matrix.DoubleMatrix
DoubleMatrixFactory - Class in ubic.gemma.core.util.matrix: Use this factory to create matrices of type selected at runtime (String parameterization only)
DoubleMatrixFactory() - Constructor for class ubic.gemma.core.util.matrix.DoubleMatrixFactory
DoubleMatrixReader - Class in ubic.gemma.core.util.matrix: Reader for DoubleMatrix.
DoubleMatrixReader() - Constructor for class ubic.gemma.core.util.matrix.DoubleMatrixReader
doubleMatrixToBytes(double[][]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
doubleMatrixToBytes(double[][]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
doubleStandardize(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixStats: Iteratively standardize the columns and rows of the matrix.
DoubleVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData: Value object for a BulkExpressionDataVector containing doubles.
DoubleVectorValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
DoubleVectorValueObject(BulkExpressionDataVector, ExpressionExperimentValueObject, QuantitationTypeValueObject, BioAssayDimensionValueObject, ArrayDesignValueObject, Collection) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
DoubleVectorValueObject(BulkExpressionDataVector, ExpressionExperimentValueObject, QuantitationTypeValueObject, BioAssayDimensionValueObject, ArrayDesignValueObject, Collection, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: Create a vector where we expect to have to create one or more gaps to match other vectors, defined by dimToMatch.
DoubleVectorValueObject(DoubleVectorValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: Copy constructor.
DoubleVectorValueObjectUtils - Class in ubic.gemma.model.expression.bioAssayData: Utilities for converting DoubleVectorValueObject to BulkExpressionDataVector instances.
DoubleVectorValueObjectUtils() - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObjectUtils
down(String) - Static method in class ubic.gemma.rest.monitoring.health.HealthResult
down(Map) - Static method in class ubic.gemma.rest.monitoring.health.HealthResult
DOWN - Enum constant in enum class ubic.gemma.rest.monitoring.health.HealthResult.Status
DOWN - Static variable in enum class ubic.gemma.model.analysis.expression.diff.Direction: Aliases for readability.
download(URL, Path, boolean) - Method in class ubic.gemma.core.util.SimpleDownloader: Download a file from a URL to a local destination.
downloadAllSingleCellDataInCellXGene(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
downloadAllSingleCellDataInCellXGene(GeoSeries, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
downloadAsync(URL, Path, boolean) - Method in class ubic.gemma.core.util.SimpleDownloader: Download a file from a URL to a local destination asynchronously.
downloadDatasetAsset(String, String, FileType) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher
downloadInParallel(List, boolean) - Method in class ubic.gemma.core.util.SimpleDownloader: Download a file from a URL to a local destination asynchronously.
downloadSingleCellData(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector
downloadSingleCellData(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
downloadSingleCellData(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector: Retrieve single-cell data for the given GEO sample to disk.
downloadSingleCellData(GeoSample) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Download single-cell data for the given GEO sample.
downloadSingleCellData(GeoSample, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
downloadSingleCellData(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector: Download single-cell data for the given GEO series.
downloadSingleCellData(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Download single-cell data from a GEO series to disk.
downloadSingleCellData(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
downloadSingleCellData(GeoSeries) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Download single-cell data for the given GEO series.
downloadSingleCellData(GeoSeries, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector: Download a specific supplementary file at the series-level.
downloadSingleCellData(GeoSeries, GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Download a sample in the context of a series.
downloadSingleCellData(GeoSeries, GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector: Download a GEO sample within the context of its series.
downloadSingleCellData(GeoSeries, GeoSample) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SeriesAwareSingleCellDetector
downloadSingleCellData(GeoSeries, GeoSample, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
downloadSingleCellData(GeoSeries, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
downloadSingleCellData(GeoSeries, SingleCellDataType, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Download a specific supplementary file for the given data type.
downloadSingleCellDataInCellXGene(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
downloadSingleCellDataInCellXGene(GeoSeries, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Download single-cell data from CELLxGENE that is linked to a GEO series.
downloadSingleCellDataInCellXGene(GeoSeries, String, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Download a specific dataset from CELLxGENE that is linked to a GEO series.
downloadSingleCellDataInCellXGene(GeoSeries, String, String, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Download a specific dataset from CELLxGENE that is linked to a GEO series.
doWork() - Method in class ubic.gemma.apps.AffyProbeCollapseCli
doWork() - Method in class ubic.gemma.apps.CellXGeneDataDownloaderCli
doWork() - Method in class ubic.gemma.apps.CellXGeneGrabberCli
doWork() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli
doWork() - Method in class ubic.gemma.apps.GeoSingleCellDataDownloaderCli
doWork() - Method in class ubic.gemma.apps.IndexGemmaCLI
doWork() - Method in class ubic.gemma.apps.InitializeDatabaseCli
doWork() - Method in class ubic.gemma.apps.ListExpressionDataFIleLocksCli
doWork() - Method in class ubic.gemma.apps.SingleCellDataTransformCli
doWork() - Method in class ubic.gemma.apps.UcscCellBrowserGrabberCli
doWork() - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli
doWork() - Method in class ubic.gemma.apps.UpdateDatabaseCli
doWork() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI
doWork() - Method in class ubic.gemma.cli.util.AbstractCLI: Command line implementation.
dqrdc_j(double[][], int, int, double[], int[], int) - Static method in class ubic.gemma.core.util.math.linalg.Dqrsl: This method decomposes an n by p matrix X into a product, QR, of an orthogonal n by n matrix Q and an upper triangular n by p matrix R.
Dqrsl - Class in ubic.gemma.core.util.math.linalg: This class contains the LINPACK DQRDC (QR decomposition) and DQRSL (QR solve) routines.
Dqrsl() - Constructor for class ubic.gemma.core.util.math.linalg.Dqrsl
dqrsl_j(double[][], int, int, double[], double[], double[], double[], double[], double[], double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Dqrsl: This method "applies the output of DQRDC to compute coordinate transformations, projections, and least squares solutions." For details, see the comments in the code.
DRAFT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetRole
drawColumnNames(Graphics, boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay: Draws column names vertically (turned 90 degrees counter-clockwise)
drawMatrix(ColorMatrix, Graphics, boolean, boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay: Gets called from #paintComponent and #saveImage.
drawRowNames(Graphics, boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay: Draws row names (horizontally)
drawScaleBar(Graphics, Dimension, double, double) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
drawVerticalString(Graphics, String, Font, int, int) - Static method in class ubic.gemma.core.util.graphics.text.Util: Draws a string vertically, turned 90 degrees counter-clockwise.
DRIFTED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.ExternalIssueSyncState: External issue and local ticket disagree (reconciliation needed).
dropColumn(DoubleMatrix2D, int) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
dropColumns(DoubleMatrix2D, Collection) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
dropSamplesNotAnalyzed(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Remove the samples that are not analyzed (see DiffExAnalyzerUtils.isAnalyzed(BioMaterial)) from a data matrix.
drotg_j(double[]) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method constructs a Givens plane rotation.
dryRun - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeRequest: If true, evaluate matches but do not persist any PreboardedExperiment rows.
dryRun - Variable in class ubic.gemma.rest.AdminWebService.ObsoleteTermCorrectionSubmission
DryRunResult(List, String, Date, List, Integer) - Constructor for class ubic.gemma.core.geoscrape.GeoScrapeService.DryRunResult: Deprecated.
dscal_j(int, double, double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method scales a vector by a constant.
dscalp_j(int, double, double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method scales a portion of a vector by a constant.
dswap_j(int, double[], int, double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method interchanges two vectors.
dualChannel - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
dualChannelGenomic - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
DUALMODE - Enum constant in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType: Indicates this platform can be used in either a one- or two- channel mode.
DUMMY - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType: A placeholder element used for annotation associations for RNA-seq
dummyMailSender() - Method in class ubic.gemma.core.config.DataSourceConfig
DummyMailSender - Class in ubic.gemma.core.util: Mock mail sender for testing.
DummyMailSender() - Constructor for class ubic.gemma.core.util.DummyMailSender
DUPLICATE_PROBE_NAME_MUNGE_SEPARATOR - Static variable in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl: When we encounter two probes with the same name, we add this string along with a unique identifier to the end of the name.
durbinWatson(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Durbin-Watson computation.

E

E - Enum constant in enum class ubic.gemma.model.analysis.expression.diff.Direction: Either direction (up or down).
ebayes(LeastSquaresFit) - Static method in class ubic.gemma.core.util.math.linearmodels.ModeratedTstat: Does essentially the same thing as limma::ebayes
EbayesFailureException - Exception Class in ubic.gemma.core.analysis.expression.diff: Occurs when empirical bayes estimation fails.
EbayesFailureException(DifferentialExpressionAnalysisConfig, Throwable) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.EbayesFailureException
ebayesUpdate(double, double, DoubleMatrix1D) - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: Provide results of limma eBayes algorithm.
edit() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentWebUrl
editableBy(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Retrieve a list of users allowed to edit a given securable.
editableBy(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
editDistance(String, String) - Static method in class ubic.gemma.core.util.math.StringDistance: The edit distance counts the differences between two strings, where we would count a difference not only when strings have different characters but also when one has a character whereas the other does not.
EDITED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions.Disposition: Draft has the key but with different content.
EE2AD_QUERY_SPACE - Static variable in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Query space used by the EXPRESSION_EXPERIMENT2ARRAY_DESIGN table.
Ee2AdUpdateJob - Class in ubic.gemma.core.scheduler
Ee2AdUpdateJob() - Constructor for class ubic.gemma.core.scheduler.Ee2AdUpdateJob
ee2adUpdateJobDetail(TableMaintenanceUtil, SecurityContext) - Method in class ubic.gemma.core.config.SchedulerConfig
ee2adUpdateTrigger(JobDetail) - Method in class ubic.gemma.core.config.SchedulerConfig: Every working day at 19:30.
EE2C_QUERY_SPACE - Static variable in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Query space used by the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
EE2CAclQueryUtils - Class in ubic.gemma.persistence.util: This class provides a fast-path to AclQueryUtils that uses the denormalized mask for anonymous users.
EE2CAclQueryUtils() - Constructor for class ubic.gemma.persistence.util.EE2CAclQueryUtils
ee2cExperimentalDesignUpdateJobDetail(TableMaintenanceUtil, SecurityContext) - Method in class ubic.gemma.core.config.SchedulerConfig
ee2cExperimentalDesignUpdateTrigger(JobDetail) - Method in class ubic.gemma.core.config.SchedulerConfig: Every working day at 19:20.
ee2cExperimentUpdateJobDetail(TableMaintenanceUtil, SecurityContext) - Method in class ubic.gemma.core.config.SchedulerConfig
ee2cExperimentUpdateTrigger(JobDetail) - Method in class ubic.gemma.core.config.SchedulerConfig: Every working day at 19:00.
ee2cSampleUpdateJobDetail(TableMaintenanceUtil, SecurityContext) - Method in class ubic.gemma.core.config.SchedulerConfig
ee2cSampleUpdateTrigger(JobDetail) - Method in class ubic.gemma.core.config.SchedulerConfig: Every working day at 19:10.
Ee2cUpdateJob - Class in ubic.gemma.core.scheduler
Ee2cUpdateJob() - Constructor for class ubic.gemma.core.scheduler.Ee2cUpdateJob
eeId - Variable in class ubic.gemma.rest.PreboardedWebService.PromoteRequest
eeId - Variable in class ubic.gemma.rest.PreboardedWebService.PromoteResponse
eeService - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
EeWriteService - Interface in ubic.gemma.persistence.service.expression.experiment: Write service for ExpressionExperiment graphs.
EeWriteServiceImpl - Class in ubic.gemma.persistence.persister: Strangler-fig replacement for the EE-graph write path historically owned by ExpressionPersister (now removed; the polymorphic EE dispatch arms have been folded into PersisterHelperImpl.doPersist(Collection, Map)).
EeWriteServiceImpl() - Constructor for class ubic.gemma.persistence.persister.EeWriteServiceImpl
EFETCH - Static variable in class ubic.gemma.core.loader.entrez.EntrezUtils
effective(Collection) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage: The most recent ruling among judgements, or empty when nobody has ruled.
effectiveFor(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService: The ruling that counts — the most recent — or empty when nobody has ruled.
effectiveFor(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
effectiveForIds(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService: Batched AnnotationSetTriageService.effectiveFor(AnnotationSet).
effectiveForIds(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
effectiveForInvestigationIds(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService: The effective ruling for each of several datasets, keyed by dataset id — newest ruling across every annotation set the dataset owns.
effectiveForInvestigationIds(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
effects(DoubleMatrix1D) - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition: Compute effects matrix Q'y (as in Rb = Q'y).
effects(DoubleMatrix2D) - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition: Compute effects matrix Q'y (as in Rb = Q'y)
ehcache(CacheManager) - Method in class ubic.gemma.persistence.cache.EhcacheConfig: Spring's facade over the JCache CacheManager.
EhcacheConfig - Class in ubic.gemma.persistence.cache: Spring application-cache configuration backed by Ehcache 3 (jakarta classifier) via JCache (JSR-107).
EhcacheConfig() - Constructor for class ubic.gemma.persistence.cache.EhcacheConfig
Eigenvalue - Class in ubic.gemma.model.analysis.expression.pca
Eigenvalue() - Constructor for class ubic.gemma.model.analysis.expression.pca.Eigenvalue
Eigenvalue.Factory - Class in ubic.gemma.model.analysis.expression.pca
Eigenvector - Class in ubic.gemma.model.analysis.expression.pca: A right singular vector (a.k.a.
Eigenvector() - Constructor for class ubic.gemma.model.analysis.expression.pca.Eigenvector: No-arg constructor added to satisfy javabean contract
Eigenvector.Factory - Class in ubic.gemma.model.analysis.expression.pca
EITHER - Static variable in enum class ubic.gemma.model.analysis.expression.diff.Direction: Aliases for readability.
ELINK - Static variable in class ubic.gemma.core.loader.entrez.EntrezUtils
email - Variable in class ubic.gemma.rest.AdminWebService.CreateUserRequest
email - Variable in class ubic.gemma.rest.AdminWebService.UserValueObject
EmailNotificationContext - Class in ubic.gemma.core.job.notification: author: anton date: 10/02/13
EmailNotificationContext(String, String, String) - Constructor for class ubic.gemma.core.job.notification.EmailNotificationContext
empty() - Static method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex
empty() - Static method in class ubic.gemma.persistence.util.Filters: Create an empty filter.
EMPTY - Static variable in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata
EmptyBulkExpressionDataMatrix - Class in ubic.gemma.core.datastructure.matrix: An empty bulk expression data matrix.
EmptyBulkExpressionDataMatrix(ExpressionExperiment, BioAssayDimension, QuantitationType) - Constructor for class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
EmptyExpressionMatrix - Class in ubic.gemma.core.datastructure.matrix: Used to make a 'dummy matrix' that has the column information populated.
EmptyExpressionMatrix(ExpressionExperiment, Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
EmptyExpressionMatrix(ExpressionExperiment, BioAssayDimension) - Constructor for class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
Empty is not the same as unknown - Section in ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder.locatePubMedIds(String)
EmptySingleCellExpressionDataMatrix - Class in ubic.gemma.core.datastructure.matrix
EmptySingleCellExpressionDataMatrix(ExpressionExperiment, SingleCellDimension, QuantitationType) - Constructor for class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
enabled - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject
enabled - Variable in class ubic.gemma.rest.AdminWebService.UpdateUserRequest
enabled - Variable in class ubic.gemma.rest.AdminWebService.UserValueObject
enabledCount - Variable in class ubic.gemma.rest.AdminWebService.OntologiesResponse
enabledCount - Variable in class ubic.gemma.rest.AdminWebService.UsersListResponse
encode() - Method in class ubic.gemma.persistence.util.Cursor: Encode this cursor as a base64url-encoded JSON string (no padding).
encode(CharSequence) - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder
ends - Static variable in class ubic.gemma.core.ontology.jena.RO
english(Set) - Static method in class ubic.gemma.core.ontology.search.OntologyAnalyzers: An EnglishAnalyzer with the given stem-exclusion set, plus separator-insensitive folding of designation-shaped runs at BOTH index and query time.
Ensembl2NcbiValueObject - Class in ubic.gemma.core.loader.util.biomart: Value object that represents a file record line from BioMart as configured with query parameters.
Ensembl2NcbiValueObject() - Constructor for class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
EnsemblIdDesignElementMapper - Class in ubic.gemma.core.loader.util.mapper: Match design elements using Ensembl IDs.
EnsemblIdDesignElementMapper(Map) - Constructor for class ubic.gemma.core.loader.util.mapper.EnsemblIdDesignElementMapper
ensureInitialized(OntologyService) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean) if necessary.
ensureInitialized(OntologyService, OntologyService.InferenceMode, OntologyService.LanguageLevel, boolean, boolean) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean), but first setting how we load it.
ensureInitializedLite(OntologyService) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean), but setting the language level to LITE, inferencing to NONE, processImports to false, and enable search to false, if the ontology isn't already loaded.
ensureInSession(Collection) - Method in class ubic.gemma.persistence.service.AbstractService: Deprecated.
avoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate session
ensureInSession(O) - Method in class ubic.gemma.persistence.service.AbstractService: Deprecated.
avoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate session
ensureLog2Scale(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionUtils
ensureLog2Scale(ExpressionDataDoubleMatrix, boolean) - Static method in class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionUtils: Ensures that the given matrix is on a Log2 scale.
enterClause(FilterArgParser.ClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.clause().
enterClause(FilterArgParser.ClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.clause().
enterCollection(FilterArgParser.CollectionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.collection().
enterCollection(FilterArgParser.CollectionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.collection().
enterCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.collectionOperator().
enterCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.collectionOperator().
enterDisjunction(FilterArgParser.DisjunctionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.disjunction().
enterDisjunction(FilterArgParser.DisjunctionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.disjunction().
enteredAt - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowHistoryEntry
enteredCurrentStateAt - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
enteredCurrentStateAt - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
enteredCurrentStateAt - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowQueueEntryResponse
enteredCurrentStateAt - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowStateResponse
enteredCurrentStateAt - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowTransitionResponse
enterEveryRule(ParserRuleContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
enterFilter(FilterArgParser.FilterContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.filter().
enterFilter(FilterArgParser.FilterContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.filter().
enterOperator(FilterArgParser.OperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.operator().
enterOperator(FilterArgParser.OperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.operator().
enterPredicate(FilterArgParser.PredicateContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.predicate().
enterPredicate(FilterArgParser.PredicateContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.predicate().
enterQuantifier(FilterArgParser.QuantifierContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.quantifier().
enterQuantifier(FilterArgParser.QuantifierContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.quantifier().
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.QuantifierContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
enterScalar(FilterArgParser.ScalarContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.scalar().
enterScalar(FilterArgParser.ScalarContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.scalar().
enterSubClause(FilterArgParser.SubClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.subClause().
enterSubClause(FilterArgParser.SubClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.subClause().
entity - Variable in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl
entity(Class, Long) - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrlChooser
entity(T) - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrlChooser
entity(ArrayDesign) - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrlChooser
entity(ExpressionExperiment) - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrlChooser
EntityArgService<T,S> - Interface in ubic.gemma.rest.util.args: Bridges Arg operating on entities with their corresponding FilteringService.
entityArgValueOf(Class, String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService: Invoke either a static valueOf method or a suitable constructor to instantiate the argument.
entityLocator - Variable in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
entityLocator - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
EntityLocator - Interface in ubic.gemma.cli.util: Locate various entities using identifiers supplied by the CLI.
EntityLocatorImpl - Class in ubic.gemma.cli.util
EntityLocatorImpl() - Constructor for class ubic.gemma.cli.util.EntityLocatorImpl
EntityMapper<T> - Interface in ubic.gemma.core.loader.util.mapper: Map external identifiers to Gemma entities.
EntityMapper.MappingStatistics - Class in ubic.gemma.core.loader.util.mapper: Mapping statistics computed from a given set of entities and identifiers.
EntityMapper.StatefulEntityMapper<T> - Interface in ubic.gemma.core.loader.util.mapper: A stateful entity mapper keeps an internal state for a set of candidates to optimize the mapping process.
EntityMapperUtils - Class in ubic.gemma.core.loader.util.mapper
EntityMapperUtils() - Constructor for class ubic.gemma.core.loader.util.mapper.EntityMapperUtils
entityName - Variable in class ubic.gemma.rest.AdminWebService.IndexStatusValueObject: JPA entity name (e.g.
EntityNotFoundException - Exception Class in ubic.gemma.rest.util
EntityNotFoundException(String) - Constructor for exception class ubic.gemma.rest.util.EntityNotFoundException
EntityOptionsUtils - Class in ubic.gemma.cli.util: Utilities for adding options to the CLI that can subsequently be retrieved with EntityLocator.
EntityOptionsUtils() - Constructor for class ubic.gemma.cli.util.EntityOptionsUtils
entityPath - Variable in class ubic.gemma.persistence.util.EntityUrlBuilder.WebEntityUrl
EntityRef() - Constructor for class ubic.gemma.rest.DatasetsWebService.EntityRef
EntityRef(Long, String) - Constructor for class ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef
EntityTaskCommand<T> - Class in ubic.gemma.core.tasks: A simple task command that contains an entity ID and class.
EntityTaskCommand(Class, Long) - Constructor for class ubic.gemma.core.tasks.EntityTaskCommand
entityType - Variable in class ubic.gemma.persistence.util.EntityUrlBuilder.SomeEntitiesUrl
entityUrlBuilder - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
entityUrlBuilder(String) - Method in class ubic.gemma.core.config.ServiceBeansConfig: Marked Primary because gsec's XML also defines an entityUrlBuilder bean (with a different host-url source); the legacy XML used primary="true" so that Gemma's host-url-configured builder wins over gsec's at injection sites that ask for the type without qualifier.
EntityUrlBuilder - Class in ubic.gemma.persistence.util: This builder allows for generating URLs for entities in Gemma Web and REST.
EntityUrlBuilder(String) - Constructor for class ubic.gemma.persistence.util.EntityUrlBuilder
EntityUrlBuilder.AllEntitiesUrl<T> - Class in ubic.gemma.persistence.util
EntityUrlBuilder.AllRestEntitiesUrl<T> - Class in ubic.gemma.persistence.util
EntityUrlBuilder.AllWebEntitiesUrl<T> - Class in ubic.gemma.persistence.util
EntityUrlBuilder.ArrayDesignUrl - Class in ubic.gemma.persistence.util
EntityUrlBuilder.ArrayDesignWebUrl - Class in ubic.gemma.persistence.util
EntityUrlBuilder.EntityUrl<T> - Class in ubic.gemma.persistence.util: Represents a URL for an Identifiable entity.
EntityUrlBuilder.EntityUrlChooser - Class in ubic.gemma.persistence.util: Allows for choosing a specific entity.
EntityUrlBuilder.ExperimentalDesignWebUrl - Class in ubic.gemma.persistence.util
EntityUrlBuilder.ExpressionExperimentUrl - Class in ubic.gemma.persistence.util
EntityUrlBuilder.ExpressionExperimentWebUrl - Class in ubic.gemma.persistence.util
EntityUrlBuilder.ExternalEntityUrl<T> - Class in ubic.gemma.persistence.util
EntityUrlBuilder.OntologyEntityUrl<T> - Class in ubic.gemma.persistence.util
EntityUrlBuilder.RestEntityUrl<T> - Class in ubic.gemma.persistence.util: Generate a URL for Gemma REST.
EntityUrlBuilder.SomeEntitiesUrl<T> - Class in ubic.gemma.persistence.util
EntityUrlBuilder.SomeRestEntitiesUrl<T> - Class in ubic.gemma.persistence.util
EntityUrlBuilder.SomeWebEntitiesUrl<T> - Class in ubic.gemma.persistence.util
EntityUrlBuilder.WebEntityUrl - Class in ubic.gemma.persistence.util: Generate a URL for Gemma Web.
EntityUrlChooser(String) - Constructor for class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrlChooser
EntrezException - Exception Class in ubic.gemma.core.loader.entrez: Exception raised when an Entrez reply contains an ERROR tag.
EntrezException(String, List) - Constructor for exception class ubic.gemma.core.loader.entrez.EntrezException
EntrezQuery - Class in ubic.gemma.core.loader.entrez: Represents an Entrez search query.
EntrezQuery(String, String, int) - Constructor for class ubic.gemma.core.loader.entrez.EntrezQuery
EntrezRetmode - Enum Class in ubic.gemma.core.loader.entrez: Possible values for the Entrez retmode parameter.
EntrezUtils - Class in ubic.gemma.core.loader.entrez: Low-level utilities for generating Entrez URLs.
EntrezUtils() - Constructor for class ubic.gemma.core.loader.entrez.EntrezUtils
EntrezUtils.EntrezCall<T> - Interface in ubic.gemma.core.loader.entrez
EntrezXmlUtils - Class in ubic.gemma.core.loader.entrez: Utilities for manipulating Entrez XML responses.
EntrezXmlUtils() - Constructor for class ubic.gemma.core.loader.entrez.EntrezXmlUtils
entries - Variable in class ubic.gemma.rest.AdminWebService.BlacklistListResponse
entries() - Method in class ubic.gemma.core.util.math.distribution.Histogram: The number of entries in the histogram (the number of times fill has been called).
ENTRY_TYPE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
ENUM - Enum constant in enum class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaFieldType
ENUM - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
EnumArray - Class in ubic.gemma.core.loader.util.anndata: An array backend by a H5 enum dataset.
EnumArray(H5Dataset) - Constructor for class ubic.gemma.core.loader.util.anndata.EnumArray
EnumConverter<T> - Class in ubic.gemma.cli.util: Convert Enum to string.
EnumeratedByCommandConverter<T,E> - Interface in ubic.gemma.cli.util: This interface is implemented by Converter that can use an external command to get possible values.
EnumeratedByCommandStringConverter - Class in ubic.gemma.cli.util
EnumeratedConverter<T,E> - Interface in ubic.gemma.cli.util: This interface is implemented by converters that can enumerate their possible values.
EnumeratedStringConverter - Class in ubic.gemma.cli.util: A string converter that can only convert from a finite set of possible values.
environmentalHistory - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
EnvironmentProfiles - Class in ubic.gemma.core.context: Spring profile name constants used in the Gemma context.
EnvironmentProfiles() - Constructor for class ubic.gemma.core.context.EnvironmentProfiles
EOF() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
eq - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
EQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
EQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
EQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
EQUAL - Enum constant in enum class ubic.gemma.model.util.ModelUtils.EqualityOutcome
equalize() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD: Implements the method described in the SPELL paper, alternative interpretation as related by Q.
equals(T, T) - Static method in class ubic.gemma.persistence.util.IdentifiableUtils: Compare two identifiables of the same type without risking initializing them.
equals(Object) - Method in class ubic.gemma.cli.batch.BatchTaskProcessingResult
equals(Object) - Method in class ubic.gemma.cli.completion.CompletionSource.Completion
equals(Object) - Method in class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator.CommandMeta
equals(Object) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
equals(Object) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.RunMetrics
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat
equals(Object) - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat
equals(Object) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket
equals(Object) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig
equals(Object) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
equals(Object) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
equals(Object) - Method in class ubic.gemma.core.datastructure.sparse.SparseArrayList
equals(Object) - Method in class ubic.gemma.core.datastructure.sparse.SparseRangeArrayList
equals(Object) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
equals(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
equals(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
equals(Object) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
equals(Object) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
equals(Object) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
equals(Object) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
equals(Object) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig
equals(Object) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic
equals(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleContactMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
equals(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraBase
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackageSet
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExternalId
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFiles
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPlatform
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPool
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
equals(Object) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
equals(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
equals(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
equals(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
equals(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
equals(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
equals(Object) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
equals(Object) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
equals(Object) - Method in class ubic.gemma.core.loader.util.mapper.EntityMapper.MappingStatistics
equals(Object) - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound
equals(Object) - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.Annotation
equals(Object) - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
equals(Object) - Method in record class ubic.gemma.core.ontology.lexical.LexicalOntologyIndex.Hit: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.ontology.lexical.LexicalTerm: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata.Taxon: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ubic.gemma.core.ontology.model.OntologyXref
equals(Object) - Method in class ubic.gemma.core.ontology.ols.OlsTerm
equals(Object) - Method in class ubic.gemma.core.ontology.search.OntologySearchResult
equals(Object) - Method in class ubic.gemma.core.ontology.simple.AbstractOntologyResourceSimple
equals(Object) - Method in class ubic.gemma.core.ontology.simple.OntologyStatementSimple
equals(Object) - Method in class ubic.gemma.core.pipeline.JobSnapshot
equals(Object) - Method in class ubic.gemma.core.pipeline.SchedulerHandle
equals(Object) - Method in class ubic.gemma.core.pipeline.SubmitRequest
equals(Object) - Method in class ubic.gemma.core.search.SearchContext
equals(Object) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
equals(Object) - Method in class ubic.gemma.core.security.acl.domain.AclEntry
equals(Object) - Method in class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
equals(Object) - Method in class ubic.gemma.core.security.acl.domain.AclImpl
equals(Object) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
equals(Object) - Method in class ubic.gemma.core.security.acl.domain.AclPrincipalSid
equals(Object) - Method in record class ubic.gemma.core.security.audit.AuditEventPayload.None: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.DifferentialExpressionAnalysisPayload: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.ReleaseDetailsUpdatePayload: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.SampleRemovalPayload: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ubic.gemma.core.security.audit.payload.SingleCellSubSetsCreatedPayload: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterService.LintResult
equals(Object) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
equals(Object) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
equals(Object) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
equals(Object) - Method in class ubic.gemma.core.util.locking.FileLockInfo
equals(Object) - Method in record class ubic.gemma.core.util.runtime.CpuInfo: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ubic.gemma.core.util.runtime.FileLockInfo
equals(Object) - Method in record class ubic.gemma.core.util.runtime.MemInfo: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ubic.gemma.core.util.SimpleDownloader.URLAndDestination
equals(Object) - Method in class ubic.gemma.core.util.SimpleRetryContext
equals(Object) - Method in class ubic.gemma.core.util.SimpleRetryPolicy
equals(Object) - Method in class ubic.gemma.model.analysis.AnalysisResultSet: Returns true if the argument is an AnalysisResultSet instance and all identifiers for this entity equal the identifiers of the argument entity.
equals(Object) - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject
equals(Object) - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis
equals(Object) - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix: Returns true if the argument is an SampleCoexpressionMatrix instance and all identifiers for this entity equal the identifiers of the argument entity.
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.Baseline
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.Contrast
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult: Returns true if the argument is an GeneDifferentialExpressionMetaAnalysisResult instance and all identifiers for this entity equal the identifiers of the argument entity.
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
equals(Object) - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
equals(Object) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
equals(Object) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
equals(Object) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
equals(Object) - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
equals(Object) - Method in class ubic.gemma.model.analysis.ProtocolValueObject
equals(Object) - Method in class ubic.gemma.model.association.Gene2GeneAssociation
equals(Object) - Method in class ubic.gemma.model.association.Gene2GOAssociation
equals(Object) - Method in class ubic.gemma.model.association.ReferenceAssociation
equals(Object) - Method in class ubic.gemma.model.blacklist.BlacklistedExperiment
equals(Object) - Method in class ubic.gemma.model.blacklist.BlacklistedPlatform
equals(Object) - Method in class ubic.gemma.model.common.AbstractDescribable: Important note: The name should be compared in a case-insensitive manner.
equals(Object) - Method in class ubic.gemma.model.common.AbstractIdentifiable: Important note: Two objects with the same class and non-null ID must be considered equal.
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.Contact
equals(Object) - Method in record class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject.LastEventTriple: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition: By id once both sides have one, otherwise by (set, targetId, decidedBy, decidedAt).
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage: By id once both sides have one, otherwise by the business key.
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision: By id once both sides have one, otherwise by (investigation, scope, key, decidedBy, decidedAt).
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails: Compares the objects type and IDs.
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.User
equals(Object) - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup
equals(Object) - Method in class ubic.gemma.model.common.BaseValueObject
equals(Object) - Method in class ubic.gemma.model.common.description.AnnotationRelation
equals(Object) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
equals(Object) - Method in class ubic.gemma.model.common.description.BibliographicReference
equals(Object) - Method in class ubic.gemma.model.common.description.BibRefAnnotation: Returns true if the argument is an BibRefAnnotation instance and all identifiers for this entity equal the identifiers of the argument entity.
equals(Object) - Method in class ubic.gemma.model.common.description.Category
equals(Object) - Method in class ubic.gemma.model.common.description.Characteristic
equals(Object) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
equals(Object) - Method in class ubic.gemma.model.common.description.CitationValueObject
equals(Object) - Method in class ubic.gemma.model.common.description.DatabaseEntry
equals(Object) - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
equals(Object) - Method in class ubic.gemma.model.common.description.ExternalDatabase
equals(Object) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
equals(Object) - Method in class ubic.gemma.model.common.description.PublicationAssociation
equals(Object) - Method in class ubic.gemma.model.common.description.Value
equals(Object) - Method in class ubic.gemma.model.common.IdentifiableValueObject
equals(Object) - Method in class ubic.gemma.model.common.measurement.Measurement
equals(Object) - Method in class ubic.gemma.model.common.measurement.Unit
equals(Object) - Method in class ubic.gemma.model.common.protocol.Protocol
equals(Object) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
equals(Object) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
equals(Object) - Method in class ubic.gemma.model.common.search.SearchResult
equals(Object) - Method in class ubic.gemma.model.common.search.SearchResultValueObject
equals(Object) - Method in class ubic.gemma.model.common.search.SearchSettings
equals(Object) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
equals(Object) - Method in class ubic.gemma.model.expression.arrayDesign.AlternateName
equals(Object) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
equals(Object) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject
equals(Object) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
equals(Object) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
equals(Object) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject
equals(Object) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
equals(Object) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
equals(Object) - Method in class ubic.gemma.model.expression.biomaterial.Compound
equals(Object) - Method in class ubic.gemma.model.expression.biomaterial.Treatment
equals(Object) - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
equals(Object) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
equals(Object) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject
equals(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef
equals(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
equals(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef
equals(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef
equals(Object) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
equals(Object) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
equals(Object) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
equals(Object) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
equals(Object) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
equals(Object) - Method in record class ubic.gemma.model.expression.experiment.ExpressionExperimentIdAndShortName: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject
equals(Object) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
equals(Object) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
equals(Object) - Method in class ubic.gemma.model.expression.experiment.FactorValue
equals(Object) - Method in class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
equals(Object) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
equals(Object) - Method in class ubic.gemma.model.expression.experiment.Geeq
equals(Object) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
equals(Object) - Method in class ubic.gemma.model.expression.experiment.PreboardedExperiment
equals(Object) - Method in class ubic.gemma.model.expression.experiment.Statement
equals(Object) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
equals(Object) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
equals(Object) - Method in class ubic.gemma.model.genome.Chromosome
equals(Object) - Method in class ubic.gemma.model.genome.Gene
equals(Object) - Method in class ubic.gemma.model.genome.gene.GeneAlias
equals(Object) - Method in class ubic.gemma.model.genome.gene.GeneProduct
equals(Object) - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject
equals(Object) - Method in class ubic.gemma.model.genome.gene.GeneSet
equals(Object) - Method in class ubic.gemma.model.genome.gene.GeneSetMember
equals(Object) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
equals(Object) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
equals(Object) - Method in class ubic.gemma.model.genome.gene.GOGroupValueObject
equals(Object) - Method in class ubic.gemma.model.genome.gene.Multifunctionality
equals(Object) - Method in class ubic.gemma.model.genome.PhysicalLocation
equals(Object) - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
equals(Object) - Method in class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
equals(Object) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
equals(Object) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
equals(Object) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
equals(Object) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
equals(Object) - Method in class ubic.gemma.model.genome.Taxon
equals(Object) - Method in class ubic.gemma.model.pipeline.PipelineJob
equals(Object) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
equals(Object) - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
equals(Object) - Method in class ubic.gemma.model.util.UninitializedCollection
equals(Object) - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLock
equals(Object) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
equals(Object) - Method in record class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao.BioSequenceLite: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
equals(Object) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm
equals(Object) - Method in class ubic.gemma.persistence.util.Cursor
equals(Object) - Method in class ubic.gemma.persistence.util.FactorValueVector
equals(Object) - Method in class ubic.gemma.persistence.util.Filter
equals(Object) - Method in class ubic.gemma.persistence.util.Filters
equals(Object) - Method in class ubic.gemma.persistence.util.Sort
equals(Object) - Method in class ubic.gemma.persistence.util.Subquery.Alias
equals(Object) - Method in class ubic.gemma.persistence.util.Subquery
equals(Object) - Method in class ubic.gemma.rest.AdminWebService.ReindexAcceptedResponse
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationCategoryValueObject
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.LexicalTermMetadataValueObject
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSimpleValueObject
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSynonymValueObject
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonConstraintValueObject
equals(Object) - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonValueObject
equals(Object) - Method in class ubic.gemma.rest.AuthWebService.LoginResponse
equals(Object) - Method in class ubic.gemma.rest.CompletionsWebService.CompletionValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.BatchEffectStatisticsValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetMetadataFileValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.EntityRef
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject.Fit
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermRef
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject.Row
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.RunQcMetricsValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.Section
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.SequencingQcMetricsValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.SimpleSVDValueObject
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
equals(Object) - Method in class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject
equals(Object) - Method in class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject
equals(Object) - Method in class ubic.gemma.rest.GeneWebService.GeneDifferentialExpressionGroupValueObject
equals(Object) - Method in class ubic.gemma.rest.GoTermsWebService.GoTermGeneCountValueObject
equals(Object) - Method in class ubic.gemma.rest.monitoring.HealthWebService.ComponentValueObject
equals(Object) - Method in class ubic.gemma.rest.monitoring.HealthWebService.HealthValueObject
equals(Object) - Method in class ubic.gemma.rest.monitoring.InfoWebService.BuildBlock
equals(Object) - Method in class ubic.gemma.rest.monitoring.InfoWebService.InfoValueObject
equals(Object) - Method in class ubic.gemma.rest.monitoring.InfoWebService.JavaBlock
equals(Object) - Method in class ubic.gemma.rest.monitoring.InfoWebService.OsBlock
equals(Object) - Method in class ubic.gemma.rest.monitoring.InfoWebService.UptimeBlock
equals(Object) - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject
equals(Object) - Method in class ubic.gemma.rest.RootWebService.UserValueObject
equals(Object) - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
equals(Object) - Method in class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
equals(Object) - Method in class ubic.gemma.rest.util.args.SortArg.Sort
equals(Object) - Method in class ubic.gemma.rest.util.BuildInfoValueObject
equals(Object) - Method in class ubic.gemma.rest.util.ResponseErrorObject
equals(Object) - Method in class ubic.gemma.rest.util.Sendfile
equals(Object) - Method in class ubic.gemma.rest.util.SortValueObject
equals(Object) - Method in class ubic.gemma.rest.util.WellComposedError
equals(Object) - Method in class ubic.gemma.rest.util.WellComposedErrorBody
equals(Object) - Method in class ubic.gemma.rest.util.WellComposedWarning
equals(Object, Object) - Static method in class ubic.gemma.model.util.ModelUtils: Compare two object without initializing them.
equals(Object, Object) - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
equals(String, String, String, String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Compare a pair of ontology terms.
equals(List, List) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
equalsByName(Describable, Describable) - Static method in class ubic.gemma.model.common.DescribableUtils: Check if two Describable objects are considered equals by their names.
error - Variable in class ubic.gemma.rest.AdminWebService.CurationAgentHealthResponse: Populated when the probe threw (timeout, connection refused, malformed URL, etc.).
error - Variable in class ubic.gemma.rest.AdminWebService.IndexStatusValueObject: Populated only when documentCount == -1.
error - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject: Set if inspection threw; the rest of the row will be partially populated.
error(Throwable) - Method in class ubic.gemma.cli.pipeline.PipelineJobReporter: Terminal failure.
error(WellComposedErrorBody) - Method in class ubic.gemma.rest.util.ResponseErrorObject.ResponseErrorObjectBuilder: Error beign reported.
errorMessage - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
errors(List) - Method in class ubic.gemma.rest.util.WellComposedErrorBody.WellComposedErrorBodyBuilder
escape(String) - Method in class ubic.gemma.core.ontology.search.JenaTextOntologySearchService
escape(String) - Method in interface ubic.gemma.core.ontology.search.OntologySearchService: Escape Lucene metacharacters in a free-text query.
escape(String) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Escape all reserved Lucene characters in the given query.
escapeLike(String) - Static method in class ubic.gemma.persistence.util.QueryUtils
escapeLike(String, char) - Static method in class ubic.gemma.persistence.util.QueryUtils: Escape the SQL LIKE wildcards in s using an explicit escape character.
escapeMarkdown(String) - Static method in class ubic.gemma.core.util.MarkdownUtils: Escape special Markdown characters in a string.
ESEARCH - Static variable in class ubic.gemma.core.loader.entrez.EntrezUtils
EST - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
EST - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType
ESUMMARY - Static variable in class ubic.gemma.core.loader.entrez.EntrezUtils
euclDistance(DoubleArrayList, DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Distance: Calculate the Euclidean distance between two vectors.
EutilFetch - Class in ubic.gemma.core.loader.entrez: High-level API for interacting with NCBI Entrez utilities.
EutilFetch() - Constructor for class ubic.gemma.core.loader.entrez.EutilFetch
evaluate(XPathExpression, Node) - Static method in class ubic.gemma.core.util.XMLUtils: Evaluate an XPath expression that produces a NodeList.
evaluate(GeoRecord) - Method in class ubic.gemma.core.geoscrape.BrainKeywordMatcher
evaluate(GeoRecord) - Method in interface ubic.gemma.core.geoscrape.GeoRecordMatcher: Decide whether this matcher flags the given record.
evaluate(GeoRecord) - Method in class ubic.gemma.core.geoscrape.SingleCellBrainMatcher
evaluate(GeoRecord) - Method in class ubic.gemma.core.geoscrape.TfPerturbationMatcher
evaluateToString(XPathExpression, Node) - Static method in class ubic.gemma.core.util.XMLUtils: Evaluate an XPath expression that produces a NodeList.
EVALUATION - Enum constant in enum class ubic.gemma.model.expression.experiment.AgentCurationKind: A scored assessment of curation that already exists — an agent grading annotations against a reference, or comparing two runs, rather than suggesting a change (AgentCurationKind.PROPOSAL) or reporting defects to act on (AgentCurationKind.AUDIT).
evictAfterRebuild(GemmaRestApiClient, Log) - Static method in class ubic.gemma.cli.util.RestCacheEviction: Evict the after-rebuild regions on the configured gemma-rest host.
evictAnnotationRelationQueryCache() - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Evict the query cache for the ANNOTATION_RELATION table.
evictAnnotationRelationQueryCache() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
evictBioAssaysCache(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
evictBioAssaysCache(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
evictCharacteristicsCache(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
evictCharacteristicsCache(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
evictEe2AdQueryCache() - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Evict the query cache for the EXPRESSION_EXPERIMENT2_ARRAY_DESIGN table.
evictEe2AdQueryCache() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
evictEe2CQueryCache() - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Evict the query cache for the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
evictEe2CQueryCache() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
evictFromCache(Long) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: Invalidate the cached 'report' for the experiment with the given id.
evictFromCache(Long) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
evictFromCache(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
evictFromCache(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
evictGene2CsQueryCache() - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Evict the query cache for the GENE2CS table.
evictGene2CsQueryCache() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
evictIf(Cache, Predicate) - Static method in class ubic.gemma.persistence.cache.CacheUtils: Evict entries from the cache where the key matches a given predicate.
evictions - Variable in class ubic.gemma.rest.AdminWebService.CacheStatRow
evictOtherPartsCache(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
evictOtherPartsCache(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
evictQuantitationTypesCache(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
evictQuantitationTypesCache(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
evidence(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
EXACT - Enum constant in enum class ubic.gemma.core.ontology.model.OntologyXref.Strength: Asserted equivalent — OBO MONDO:equivalentTo, or SKOS exactMatch.
EXACT - Enum constant in enum class ubic.gemma.model.common.search.SearchSettings.SearchMode: Very fast search mode, designed for exact matching of identifiers, etc.
EXACT_IDENTIFIER - Enum constant in enum class ubic.gemma.model.common.search.SearchMatchType: Matched a canonical identifier — numeric primary key, accession, NCBI/Ensembl gene id, dataset/platform short name.
EXACT_SYMBOL - Enum constant in enum class ubic.gemma.model.common.search.SearchMatchType: Exact match on an official gene symbol.
EXACT_SYNONYM - Enum constant in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia: Query normalises to one of the term's exact-OBO synonyms exactly.
exampleExperimentId(Long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
ExampleUsageValueObject(String, String, String, String, String, String, String, String, String, String, String, String, Long) - Constructor for class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
exception() - Element in annotation interface ubic.gemma.core.security.audit.AuditedOnError: Optional exception-class filter.
EXCLUDE_SAMPLE_IDENTIFIERS_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
ExcludeArg<T> - Class in ubic.gemma.rest.util.args
excludedExperimentIds(Collection) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery: Hold experiments out of the evidence.
excludedSubjectCategoryUris(Collection) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery: Subject categories to leave out, for a caller that wants everything except one kind of implying term.
excludedWordsFromStemming() - Method in class ubic.gemma.core.ontology.OntologyConfig
excludeSampleIdentifiers - Variable in class ubic.gemma.cli.options.ExpressionDataFileOptionValue
execute(Runnable) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextExecutor
execute(Runnable) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextTaskExecutor
execute(Runnable) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutor
execute(Runnable, long) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextAsyncTaskExecutor
execute(SimpleRetryCallable, Object) - Method in class ubic.gemma.core.util.SimpleRetry: Execute the given callable with a retry strategy.
executeAs(JobExecutionContext) - Method in class ubic.gemma.core.scheduler.BatchInfoRepopulationJob
executeAs(JobExecutionContext) - Method in class ubic.gemma.core.scheduler.Ee2AdUpdateJob
executeAs(JobExecutionContext) - Method in class ubic.gemma.core.scheduler.Ee2cUpdateJob
executeAs(JobExecutionContext) - Method in class ubic.gemma.core.scheduler.SecureQuartzJobBean
executeCommand(CLIContext) - Method in class ubic.gemma.cli.util.AbstractCLI: Execute the given command given CLI arguments.
executeCommand(CLIContext) - Method in interface ubic.gemma.cli.util.CLI: Execute the given command given CLI arguments.
executeInternal(JobExecutionContext) - Method in class ubic.gemma.core.scheduler.SecureQuartzJobBean
executeUpdateByBatch(Query, String, Collection, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
Executors - Class in ubic.gemma.core.util.concurrent: Extends Executors to ensure that security context logging works as expected.
Executors() - Constructor for class ubic.gemma.core.util.concurrent.Executors
existingFactorKey(Long) - Static method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan: Parent-key helpers keep the "F:" / "C:" convention in one place.
exists - Variable in class ubic.gemma.rest.AdminWebService.IndexStatusValueObject: True if the on-disk index directory exists; null if indexPath is null.
exists(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location: Check if a given path exists relative to this location.
existsAndHasExpectedSize(Path, String, long, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector: Check if a file at a given destination exists and has the size of a remote file.
existsAndHasExpectedSize(Path, String, long, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleH5FileInSeriesSingleCellDetector: Check if a file at a given destination exists and has the size of a remote file.
existsByExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDao
existsByExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImpl
existsByExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadService
existsByExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadServiceImpl
existsByExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
existsByExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl
existsByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
existsByShortName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
existsByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
existsByShortName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
existsByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Check if a dataset with a given short name.
existsByShortName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
EXISTS rewrite (Session 2 of the ACL EXISTS refactor) - Section in class ubic.gemma.persistence.util.AclQueryUtils
exitClause(FilterArgParser.ClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.clause().
exitClause(FilterArgParser.ClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.clause().
exitCollection(FilterArgParser.CollectionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.collection().
exitCollection(FilterArgParser.CollectionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.collection().
exitCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.collectionOperator().
exitCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.collectionOperator().
exitDisjunction(FilterArgParser.DisjunctionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.disjunction().
exitDisjunction(FilterArgParser.DisjunctionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.disjunction().
exitEveryRule(ParserRuleContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
exitFilter(FilterArgParser.FilterContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.filter().
exitFilter(FilterArgParser.FilterContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.filter().
exitOperator(FilterArgParser.OperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.operator().
exitOperator(FilterArgParser.OperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.operator().
exitPredicate(FilterArgParser.PredicateContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.predicate().
exitPredicate(FilterArgParser.PredicateContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.predicate().
exitQuantifier(FilterArgParser.QuantifierContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.quantifier().
exitQuantifier(FilterArgParser.QuantifierContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.quantifier().
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.QuantifierContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
exitScalar(FilterArgParser.ScalarContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.scalar().
exitScalar(FilterArgParser.ScalarContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.scalar().
exitSubClause(FilterArgParser.SubClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.subClause().
exitSubClause(FilterArgParser.SubClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.subClause().
EXP - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
expander - Variable in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
EXPERIMENT - Enum constant in enum class ubic.gemma.cli.util.CLI.CommandGroup
EXPERIMENT_LEVEL - Enum constant in enum class ubic.gemma.model.common.description.RelationTopicality: The relation records how one experiment was run: a dose, a duration, a developmental stage, a sample's sex.
EXPERIMENTAL_FACTOR - Enum constant in enum class ubic.gemma.cli.completion.CompletionType
EXPERIMENTAL_FACTOR_OR_INTERACTION_FOR_DEA - Enum constant in enum class ubic.gemma.cli.completion.CompletionType: Complete experimental factors and interactions suitable for DEA.
ExperimentalDesign - Class in ubic.gemma.model.expression.experiment: Hibernate Search 7 mapping: indexed root and embedded contributor to ExpressionExperiment.getExperimentalDesign().
ExperimentalDesign() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesign
ExperimentalDesign.Factory - Class in ubic.gemma.model.expression.experiment
ExperimentalDesignDao - Interface in ubic.gemma.persistence.service.expression.experiment
ExperimentalDesignDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExperimentalDesignDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl
ExperimentalDesignImportCli - Class in ubic.gemma.apps
ExperimentalDesignImportCli() - Constructor for class ubic.gemma.apps.ExperimentalDesignImportCli
ExperimentalDesignImporter - Interface in ubic.gemma.core.loader.expression.simple: Parse a description of ExperimentalFactors from a file, and associate it with a given ExpressionExperiment.
ExperimentalDesignImporterImpl - Class in ubic.gemma.core.loader.expression.simple: See interface for docs.
ExperimentalDesignImporterImpl() - Constructor for class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl
ExperimentalDesignReadService - Interface in ubic.gemma.persistence.service.expression.experiment: Read-only retrieval service for ExperimentalDesign.
ExperimentalDesignReadServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of ExperimentalDesignReadService.
ExperimentalDesignReadServiceImpl(ExperimentalDesignDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignReadServiceImpl
ExperimentalDesignService - Interface in ubic.gemma.persistence.service.expression.experiment
ExperimentalDesignServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Spring Service base class for ubic.gemma.model.expression.experiment.ExperimentalDesignService, provides access to all services and entities referenced by this service.
ExperimentalDesignServiceImpl(ExperimentalDesignDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignServiceImpl
ExperimentalDesignUpdatedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Describes an event that involved a change of assignment of factor value to bio material, or other changes in the experimental design.
ExperimentalDesignUpdatedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent
ExperimentalDesignUtils - Class in ubic.gemma.model.expression.experiment
ExperimentalDesignUtils() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesignUtils
ExperimentalDesignValueObject - Class in ubic.gemma.model.expression.experiment: Full structural representation of an ExperimentalDesign: factors, their factor values (with statements carrying stable database IDs), and the assignment of biomaterials to factor values.
ExperimentalDesignValueObject() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
ExperimentalDesignValueObject(ExperimentalDesign, Collection) - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject: Build the design VO from an ExperimentalDesign and the BioAssays of the owning experiment.
ExperimentalDesignValueObject.BioMaterialFactorValueAssignment - Class in ubic.gemma.model.expression.experiment: Assignment of a single BioMaterial (sample) to its assigned FactorValues.
ExperimentalDesignValueObject.ExperimentalFactorEntry - Class in ubic.gemma.model.expression.experiment: One ExperimentalFactor, with its factor values inlined.
ExperimentalDesignViewCli - Class in ubic.gemma.apps
ExperimentalDesignViewCli() - Constructor for class ubic.gemma.apps.ExperimentalDesignViewCli
ExperimentalDesignVisualizationService - Interface in ubic.gemma.core.visualization
ExperimentalDesignVisualizationServiceImpl - Class in ubic.gemma.core.visualization: Tools for visualizing experimental designs.
ExperimentalDesignVisualizationServiceImpl() - Constructor for class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl
ExperimentalDesignWriter - Class in ubic.gemma.core.datastructure.matrix.io: Output compatible with ExperimentalDesignImporterImpl.
ExperimentalDesignWriter(EntityUrlBuilder, BuildInfo, boolean) - Constructor for class ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriter
ExperimentalDesignWriterCLI - Class in ubic.gemma.apps: Writes out the experimental design for a given experiment.
ExperimentalDesignWriterCLI() - Constructor for class ubic.gemma.apps.ExperimentalDesignWriterCLI
ExperimentalFactor - Class in ubic.gemma.model.expression.experiment: ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
ExperimentalFactor() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalFactor: No-arg constructor added to satisfy javabean contract
ExperimentalFactor.Factory - Class in ubic.gemma.model.expression.experiment
ExperimentalFactorDao - Interface in ubic.gemma.persistence.service.expression.experiment
ExperimentalFactorDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExperimentalFactorDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl
ExperimentalFactorEntry() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
ExperimentalFactorEntry(ExperimentalFactor) - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
experimentalFactorOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
ExperimentalFactorOntologyService - Class in ubic.gemma.core.ontology.providers: Experimental Factor Ontology
ExperimentalFactorOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.ExperimentalFactorOntologyService
ExperimentalFactorReadService - Interface in ubic.gemma.persistence.service.expression.experiment: Read-only retrieval service for ExperimentalFactor.
ExperimentalFactorReadServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of ExperimentalFactorReadService.
ExperimentalFactorReadServiceImpl(ExperimentalFactorDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorReadServiceImpl
ExperimentalFactorService - Interface in ubic.gemma.persistence.service.expression.experiment
ExperimentalFactorServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExperimentalFactorServiceImpl(ExperimentalFactorDao, DifferentialExpressionAnalysisService, BioMaterialService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl
ExperimentalFactorValueObject - Class in ubic.gemma.model.expression.experiment
ExperimentalFactorValueObject() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject: Required when using the class as a spring bean.
ExperimentalFactorValueObject(Long) - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
ExperimentalFactorValueObject(ExperimentalFactor) - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
ExperimentalFactorValueObject(ExperimentalFactor, boolean) - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
experimentCount - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.PriorCurationUsage
ExperimentExpressionLevelsValueObject - Class in ubic.gemma.model.expression.bioAssayData
ExperimentExpressionLevelsValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject
ExperimentExpressionLevelsValueObject(long, Map, boolean, String) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject
ExperimentExpressionLevelsValueObject(long, Map, boolean, String, Map) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject: Variant that carries per-gene differential-expression statistics for the contrast represented by the result-set used to build the response.
ExperimentExpressionLevelsValueObject.GeneDiffExStats - Class in ubic.gemma.model.expression.bioAssayData: Per-gene differential-expression statistics carried alongside expression levels for the /datasets/{dataset}/expressions/differential endpoint.
ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject - Class in ubic.gemma.model.expression.bioAssayData
ExperimentExpressionLevelsValueObject.VectorElementValueObject - Class in ubic.gemma.model.expression.bioAssayData
ExperimentFactorUtils - Class in ubic.gemma.model.expression.experiment
ExperimentFactorUtils() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentFactorUtils
ExperimentIdentity(String, Long, boolean, Set) - Constructor for class ubic.gemma.core.loader.expression.geo.GeoSourceMetadataBuilder.ExperimentIdentity
experimentIds - Variable in class ubic.gemma.rest.AdminPipelineWebService.SubmitBatchRequest
ExperimentSetMembersRequest() - Constructor for class ubic.gemma.rest.ExperimentSetsWebService.ExperimentSetMembersRequest
ExperimentSetRequest() - Constructor for class ubic.gemma.rest.ExperimentSetsWebService.ExperimentSetRequest
ExperimentSetsWebService - Class in ubic.gemma.rest: Experiment sets — named, ACL'd collections of datasets ("dataset groups" in the old DWR surface).
ExperimentSetsWebService(ExpressionExperimentSetService, ExpressionExperimentSetValueObjectHelper) - Constructor for class ubic.gemma.rest.ExperimentSetsWebService
ExperimentSetsWebService.ExperimentSetMembersRequest - Class in ubic.gemma.rest: Membership replacement body.
ExperimentSetsWebService.ExperimentSetRequest - Class in ubic.gemma.rest: Create / rename body.
experimentTags(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig.GeoUpdateConfigBuilder
experimentType - Variable in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
expiresAt - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockResponse
ExpLevelConsolidationArg - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be one of the expression level consolidation options.
EXPRESSION - Enum constant in enum class ubic.gemma.model.common.description.DatabaseType
EXPRESSION_EXPERIMENT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetType
EXPRESSION_PROFILING_BY_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
EXPRESSION_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
EXPRESSION_PROFILING_BY_MPSS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
EXPRESSION_PROFILING_BY_RT_PRC - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
EXPRESSION_PROFILING_BY_SAGE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
EXPRESSION_PROFILING_BY_SNP_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
EXPRESSION_PROFILING_BY_TILING_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
ExpressionAnalysis - Class in ubic.gemma.model.analysis.expression: An analysis of one or more ExpressionExperiments
ExpressionAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.ExpressionAnalysis
ExpressionAnalysisResultSet - Class in ubic.gemma.model.analysis.expression.diff: A group of results for an ExpressionExperiment.
ExpressionAnalysisResultSet() - Constructor for class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
ExpressionAnalysisResultSet.Factory - Class in ubic.gemma.model.analysis.expression.diff
ExpressionAnalysisResultSetArg - Class in ubic.gemma.rest.util.args: Represents an expression analysis result set identifier.
ExpressionAnalysisResultSetArgService - Class in ubic.gemma.rest.util.args
ExpressionAnalysisResultSetArgService(ExpressionAnalysisResultSetService) - Constructor for class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgService
ExpressionAnalysisResultSetDao - Interface in ubic.gemma.persistence.service.analysis.expression.diff
ExpressionAnalysisResultSetDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
ExpressionAnalysisResultSetDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
ExpressionAnalysisResultSetFileService - Interface in ubic.gemma.core.analysis.service
ExpressionAnalysisResultSetFileServiceImpl - Class in ubic.gemma.core.analysis.service
ExpressionAnalysisResultSetFileServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileServiceImpl
ExpressionAnalysisResultSetService - Interface in ubic.gemma.persistence.service.analysis.expression.diff: 🔒 The loaders below are ACL-guarded.
ExpressionAnalysisResultSetServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
ExpressionAnalysisResultSetServiceImpl(ExpressionAnalysisResultSetDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
ExpressionDataBooleanMatrix - Class in ubic.gemma.core.datastructure.matrix: Matrix of booleans mapped from an ExpressionExperiment.
ExpressionDataBooleanMatrix(ExpressionExperiment, Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
ExpressionDataBooleanMatrix(ExpressionExperiment, Collection, List) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
ExpressionDataCorrMatCli - Class in ubic.gemma.apps: Create correlation visualizations for expression experiments
ExpressionDataCorrMatCli() - Constructor for class ubic.gemma.apps.ExpressionDataCorrMatCli
ExpressionDataDeleterService - Interface in ubic.gemma.core.analysis.service: A high-level service for deleting data and their associated files.
ExpressionDataDeleterServiceImpl - Class in ubic.gemma.core.analysis.service
ExpressionDataDeleterServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.ExpressionDataDeleterServiceImpl
ExpressionDataDoubleMatrix - Class in ubic.gemma.core.datastructure.matrix: A data structure that holds a reference to the data for a given expression experiment.
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix, int[][]) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
ExpressionDataDoubleMatrix(ExpressionExperiment, Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
ExpressionDataDoubleMatrix(ExpressionExperiment, Collection, Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
ExpressionDataDoubleMatrix(ExpressionExperiment, Collection, QuantitationType) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
ExpressionDataDoubleMatrix(ExpressionExperiment, DoubleMatrix, QuantitationType) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Create a matrix given a 'raw' matrix that uses the same samples as the experiment.
ExpressionDataFileOptionValue - Class in ubic.gemma.cli.options: Options to write an expression data file.
ExpressionDataFileOptionValue(boolean, boolean, Path, Path, boolean, boolean, boolean, ScaleType, String, boolean) - Constructor for class ubic.gemma.cli.options.ExpressionDataFileOptionValue
ExpressionDataFileOptionValue(DataFileOptionValue, boolean, boolean, boolean, ScaleType) - Constructor for class ubic.gemma.cli.options.ExpressionDataFileOptionValue
ExpressionDataFileService - Interface in ubic.gemma.core.analysis.service
ExpressionDataFileServiceImpl - Class in ubic.gemma.core.analysis.service: Supports the creation and location of 'flat file' versions of data in the system, for download by users.
ExpressionDataFileServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
expressionDataFileTaskExecutor(VirtualThreadExecutorMetrics) - Method in class ubic.gemma.core.config.ServiceBeansConfig: Executor for generating data files (CEL / count matrices / TSVs).
expressionDataFileTaskExecutorMetrics() - Method in class ubic.gemma.core.config.ServiceBeansConfig: Micrometer binder for the ServiceBeansConfig.expressionDataFileTaskExecutor(VirtualThreadExecutorMetrics) VT executor.
ExpressionDataFileUtils - Class in ubic.gemma.core.analysis.service: Generate filenames for various types of data files.
ExpressionDataFileUtils() - Constructor for class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
ExpressionDataFilter<T> - Interface in ubic.gemma.core.analysis.preprocess.filter: Base interface for expression data filters.
ExpressionDataFilterUtils - Class in ubic.gemma.core.analysis.preprocess.filter
ExpressionDataFilterUtils() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilterUtils
ExpressionDataHeatmap - Class in ubic.gemma.core.visualization: Expression data heatmap for experiments and subsets.
ExpressionDataIntegerMatrix - Class in ubic.gemma.core.datastructure.matrix: Warning, not fully tested.
ExpressionDataIntegerMatrix(ExpressionExperiment, Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
ExpressionDataMatrix<T> - Interface in ubic.gemma.core.datastructure.matrix: Represents a matrix of data from an ExpressionExperiment.
ExpressionDataMatrixColumnSort - Class in ubic.gemma.core.datastructure.matrix: Methods to organize ExpressionDataMatrices by column (or at least provide the ordering).
ExpressionDataMatrixColumnSort() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
ExpressionDataMatrixRowElement - Class in ubic.gemma.core.datastructure.matrix: Encapsulates information about the row 'label' for a ExpressionDataMatrix.
ExpressionDataMatrixRowElement(ExpressionDataMatrix, int) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
ExpressionDataMatrixRowElement(ExpressionDataMatrixRowElement) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
ExpressionDataMatrixService - Interface in ubic.gemma.core.analysis.service: Tools for easily getting data matrices for analysis in a consistent way.
ExpressionDataMatrixServiceImpl - Class in ubic.gemma.core.analysis.service: Tools for easily getting data matrices for analysis in a consistent way.
ExpressionDataMatrixServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
ExpressionDataMatrixWriter<T,VT> - Interface in ubic.gemma.core.datastructure.matrix.io: Base interface for writing ExpressionDataMatrix.
ExpressionDataMatrixWriterCLI - Class in ubic.gemma.apps: Prints preferred data matrix to a file.
ExpressionDataMatrixWriterCLI() - Constructor for class ubic.gemma.apps.ExpressionDataMatrixWriterCLI
ExpressionDataPrimitiveDoubleMatrix - Interface in ubic.gemma.core.datastructure.matrix: Interface for matrices that can provide unboxed doubles.
ExpressionDataPrimitiveIntMatrix - Interface in ubic.gemma.core.datastructure.matrix
ExpressionDataStringMatrix - Class in ubic.gemma.core.datastructure.matrix
ExpressionDataStringMatrix(ExpressionExperiment, Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
ExpressionDataSVD - Class in ubic.gemma.core.analysis.preprocess.svd: Perform SVD on an expression data matrix, E = U S V'.
ExpressionDataSVD(ExpressionDataDoubleMatrix) - Constructor for class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD: Does normalization.
ExpressionDataSVD(ExpressionDataDoubleMatrix, boolean) - Constructor for class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
ExpressionDataWriterUtils - Class in ubic.gemma.core.datastructure.matrix.io: Utilities for writing expression data files.
ExpressionDataWriterUtils() - Constructor for class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils
ExpressionExperiment - Class in ubic.gemma.model.expression.experiment: Hibernate Search 7 indexed root.
ExpressionExperiment() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperiment
ExpressionExperiment.Factory - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: An event involving an ExpressionExperiment
ExpressionExperimentAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentAnalysisEvent
ExpressionExperimentBatchCorrectionService - Interface in ubic.gemma.core.analysis.preprocess.batcheffects
ExpressionExperimentBatchCorrectionServiceImpl - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Methods for correcting batch effects.
ExpressionExperimentBatchCorrectionServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
ExpressionExperimentBatchInformationService - Interface in ubic.gemma.core.analysis.preprocess.batcheffects: Provides status of batch information for datasets.
ExpressionExperimentBatchInformationServiceImpl - Class in ubic.gemma.core.analysis.preprocess.batcheffects
ExpressionExperimentBatchInformationServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
ExpressionExperimentBibRefFinder - Class in ubic.gemma.core.loader.entrez.pubmed
ExpressionExperimentBibRefFinder(String) - Constructor for class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder
ExpressionExperimentBibRefFinder(GeoBrowser, String) - Constructor for class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder: Inject the GEO client, so that resolution can be tested without reaching Entrez.
ExpressionExperimentDao - Interface in ubic.gemma.persistence.service.expression.experiment: Created by tesarst on 13/03/17.
ExpressionExperimentDao.Identifiers - Class in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
ExpressionExperimentDataFileType - Enum Class in ubic.gemma.core.analysis.service
ExpressionExperimentDataUpdaterCli - Class in ubic.gemma.apps: Update GEO data for an experiment.
ExpressionExperimentDataUpdaterCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli
ExpressionExperimentDataVectorService - Interface in ubic.gemma.persistence.service.expression.experiment: Raw + processed data vector CRUD operations for ExpressionExperiment.
ExpressionExperimentDataVectorServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of ExpressionExperimentDataVectorService.
ExpressionExperimentDataVectorServiceImpl(ExpressionExperimentDao, BioAssayDimensionService, QuantitationTypeService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
ExpressionExperimentDetailsValueObject - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentDetailsValueObject() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Required when using the class as a spring bean.
ExpressionExperimentDetailsValueObject(ExpressionExperiment) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
ExpressionExperimentDetailsValueObject(ExpressionExperiment, boolean) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Variant that skips reading the three last*Event associations off CurationDetails when skipEvents=true.
ExpressionExperimentDetailsValueObject(ExpressionExperiment, AclObjectIdentity, AclSid) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
ExpressionExperimentDetailsValueObject(ExpressionExperimentValueObject) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
ExpressionExperimentFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Default filter used for various analyses of expression experiments.
ExpressionExperimentFilter(ExpressionExperimentFilterConfig) - Constructor for class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
ExpressionExperimentFilterConfig - Class in ubic.gemma.core.analysis.preprocess.filter: Holds settings for filtering with ExpressionExperimentFilter.
ExpressionExperimentFilterConfig() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
ExpressionExperimentFilterResult - Class in ubic.gemma.core.analysis.preprocess.filter: Hold the results of filtering with ExpressionExperimentFilter.
ExpressionExperimentFilterResult() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
ExpressionExperimentGeoService - Interface in ubic.gemma.persistence.service.expression.experiment: This service provides access to GEO metadata for any given Gemma dataset.
ExpressionExperimentGeoServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentGeoServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentGeoServiceImpl
ExpressionExperimentIdAndShortName - Record Class in ubic.gemma.model.expression.experiment: A minimalistic projection of an ExpressionExperiment.
ExpressionExperimentIdAndShortName(Long, String) - Constructor for record class ubic.gemma.model.expression.experiment.ExpressionExperimentIdAndShortName: Creates an instance of a ExpressionExperimentIdAndShortName record class.
ExpressionExperimentLoadTask - Interface in ubic.gemma.core.tasks.analysis.expression
ExpressionExperimentLoadTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
ExpressionExperimentLoadTaskCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
ExpressionExperimentLoadTaskCommand(boolean, boolean, String, boolean, boolean, String) - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
ExpressionExperimentLoadTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression
ExpressionExperimentLoadTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskImpl
ExpressionExperimentManipulatingCLI - Class in ubic.gemma.apps: Base class for CLIs that needs one or more expression experiment as an input.
ExpressionExperimentManipulatingCLI() - Constructor for class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
ExpressionExperimentMetadataChangelogEntryAdderCli - Class in ubic.gemma.apps: CLI tool for adding manual entries to the changelog file of an experiment.
ExpressionExperimentMetadataChangelogEntryAdderCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli
ExpressionExperimentMetadataChangelogViewerCli - Class in ubic.gemma.apps: CLI tool for viewing the changelog file of an experiment.
ExpressionExperimentMetadataChangelogViewerCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentMetadataChangelogViewerCli
ExpressionExperimentMetadataFileAdderCli - Class in ubic.gemma.apps: Add a metadata file to an experiment and record an entry in the changelog file.
ExpressionExperimentMetadataFileAdderCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli
ExpressionExperimentMetaFileType - Enum Class in ubic.gemma.persistence.service.expression.experiment: Types of metadata files that can be attached to an ExpressionExperiment.
ExpressionExperimentPlatformSwitchCli - Class in ubic.gemma.apps: Switch the array design used to the merged one.
ExpressionExperimentPlatformSwitchCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli
ExpressionExperimentPlatformSwitchEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: The event that this experiment has had its array design switched (typically to a 'merged' one.
ExpressionExperimentPlatformSwitchEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentPlatformSwitchEvent
ExpressionExperimentPlatformSwitchService - Class in ubic.gemma.core.loader.expression: Switch an expression experiment from one array design to another.
ExpressionExperimentPlatformSwitchService() - Constructor for class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService
ExpressionExperimentPlatformSwitchTask - Interface in ubic.gemma.core.tasks.analysis.expression
ExpressionExperimentPlatformSwitchTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression: Async-task wrapper around ExpressionExperimentPlatformSwitchService.switchExperimentToArrayDesign(ExpressionExperiment, ArrayDesign).
ExpressionExperimentPlatformSwitchTaskCommand(ExpressionExperiment, ArrayDesign) - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskCommand
ExpressionExperimentPlatformSwitchTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression
ExpressionExperimentPlatformSwitchTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskImpl
ExpressionExperimentPrePersistService - Interface in ubic.gemma.persistence.service.expression.experiment: Sets up the array designs before saving an experiment.
ExpressionExperimentPrePersistServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Sets up the array designs, put the designelements in the data vectors.
ExpressionExperimentPrePersistServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistServiceImpl
ExpressionExperimentPrimaryPubCli - Class in ubic.gemma.apps: Update the primary publication for experiments.
ExpressionExperimentPrimaryPubCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli
ExpressionExperimentReadService - Interface in ubic.gemma.persistence.service.expression.experiment: Thin read-only retrieval service for ExpressionExperiment.
ExpressionExperimentReadServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of ExpressionExperimentReadService.
ExpressionExperimentReadServiceImpl(ExpressionExperimentDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
ExpressionExperimentReferenceValueObject - Class in ubic.gemma.model.expression.experiment: Compact dataset identity — enough to name a dataset and link to it.
ExpressionExperimentReferenceValueObject() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject
ExpressionExperimentReferenceValueObject(Long, String, String) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject: Creates a new ExpressionExperimentReferenceValueObject instance.
ExpressionExperimentReportService - Interface in ubic.gemma.core.analysis.report: Methods for reading and creating reports on ExpressinExperiments.
ExpressionExperimentReportServiceImpl - Class in ubic.gemma.core.analysis.report: Handles creation, serialization and/or marshaling of reports about expression experiments.
ExpressionExperimentReportServiceImpl() - Constructor for class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
ExpressionExperimentReportTask - Interface in ubic.gemma.core.tasks.maintenance: Handles delegation of report generation (to the space, or run locally)
ExpressionExperimentReportTaskCommand - Class in ubic.gemma.core.tasks.maintenance
ExpressionExperimentReportTaskCommand(Boolean) - Constructor for class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
ExpressionExperimentReportTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
ExpressionExperimentReportTaskImpl - Class in ubic.gemma.core.tasks.maintenance
ExpressionExperimentReportTaskImpl() - Constructor for class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskImpl
expressionExperimentReportTrigger(ExpressionExperimentReportService, SecurityContext) - Method in class ubic.gemma.core.config.SchedulerConfig: Every first of the month at 00:15.
expressionExperimentSearch(String) - Static method in class ubic.gemma.model.common.search.SearchSettings: Convenience method to get pre-configured settings.
expressionExperimentSearch(String, Taxon) - Static method in class ubic.gemma.model.common.search.SearchSettings: Convenience method to get pre-configured settings.
ExpressionExperimentSearchService - Interface in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentSearchServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Handles searching for experiments and experiment sets
ExpressionExperimentSearchServiceImpl(ExpressionExperimentSetService, DifferentialExpressionAnalysisService, SecurityService, SearchService, TaxonService, ExpressionExperimentService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl
ExpressionExperimentService - Interface in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm - Class in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentServiceImpl(ExpressionExperimentDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
ExpressionExperimentSet - Class in ubic.gemma.model.analysis.expression: A grouping of expression studies.
ExpressionExperimentSet() - Constructor for class ubic.gemma.model.analysis.expression.ExpressionExperimentSet: No-arg constructor added to satisfy javabean contract
ExpressionExperimentSet.Factory - Class in ubic.gemma.model.analysis.expression
ExpressionExperimentSetDao - Interface in ubic.gemma.persistence.service.analysis.expression
ExpressionExperimentSetDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression
ExpressionExperimentSetDaoImpl(SessionFactory, ExpressionExperimentDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
ExpressionExperimentSetService - Interface in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentSetServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Spring Service base class for ubic.gemma.model.analysis.expression.ExpressionExperimentSetService, provides access to all services and entities referenced by this service.
ExpressionExperimentSetServiceImpl(ExpressionExperimentSetDao, ExpressionExperimentReadService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
ExpressionExperimentSetValueObject - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentSetValueObject() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject: Required when using the class as a spring bean.
ExpressionExperimentSetValueObject(Long) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
ExpressionExperimentSetValueObjectHelper - Interface in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentSetValueObjectHelperImpl - Class in ubic.gemma.persistence.service.expression.experiment: This class will handle population of ExpressionExperimentSetValueObjects.
ExpressionExperimentSetValueObjectHelperImpl(ExpressionExperimentSetService, ExpressionExperimentService, TaxonService, SecurityService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
ExpressionExperimentSubSet - Class in ubic.gemma.model.expression.experiment: A subset of assays (or derived assays) from an ExpressionExperiment.
ExpressionExperimentSubSet() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet: No-arg constructor added to satisfy javabean contract
ExpressionExperimentSubSet.Factory - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentSubSetDao - Interface in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentSubSetDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.
ExpressionExperimentSubSetDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl
ExpressionExperimentSubSetGroupValueObject(BioAssayDimension, List, List, List) - Constructor for class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetGroupValueObject
ExpressionExperimentSubSetReadService - Interface in ubic.gemma.persistence.service.expression.experiment: Read-only retrieval service for ExpressionExperimentSubSet objects in the context of a parent ExpressionExperiment.
ExpressionExperimentSubSetReadServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of ExpressionExperimentSubSetReadService.
ExpressionExperimentSubSetReadServiceImpl(ExpressionExperimentDao, ExpressionExperimentSubSetDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
ExpressionExperimentSubSetService - Interface in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentSubSetServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentSubSetServiceImpl(ExpressionExperimentSubSetDao, ExpressionExperimentSubSetReadService, DifferentialExpressionAnalysisService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
ExpressionExperimentSubSetUtils - Class in ubic.gemma.model.expression.experiment: Utility methods for ExpressionExperimentSubSet.
ExpressionExperimentSubSetUtils() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSetUtils
ExpressionExperimentSubsetValueObject - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentSubsetValueObject() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet, Map, Map, boolean, boolean, boolean) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
ExpressionExperimentSubsetWithFactorValuesObject(ExpressionExperimentSubSet, Set, Map, boolean, Map) - Constructor for class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject
ExpressionExperimentSubSetWithGroupsValueObject(ExpressionExperimentSubSet, List) - Constructor for class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject
ExpressionExperimentUpdateFromGEOEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that we have updated an expression experiment's information from GEO, after it was already loaded in Gemma.
ExpressionExperimentUpdateFromGEOEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentUpdateFromGEOEvent
ExpressionExperimentValueObject - Class in ubic.gemma.model.expression.experiment
ExpressionExperimentValueObject() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Required when using the class as a spring bean.
ExpressionExperimentValueObject(Long) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
ExpressionExperimentValueObject(ExpressionExperiment) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
ExpressionExperimentValueObject(ExpressionExperimentIdAndShortName) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
ExpressionExperimentValueObject(ExpressionExperiment, boolean, boolean) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Creates a new value object out of given Expression Experiment.
ExpressionExperimentValueObject(ExpressionExperiment, boolean, boolean, boolean) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Variant that skips reading the three last*Event associations off CurationDetails when skipEvents=true.
ExpressionExperimentValueObject(ExpressionExperiment, AclObjectIdentity, AclSid) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Creates a new ExpressionExperiment value object with additional information about ownership.
ExpressionExperimentValueObject(ExpressionExperimentValueObject) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
ExpressionExperimentVectorMergeEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that the "Vector merging" has been done on the associated experiment.
ExpressionExperimentVectorMergeEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentVectorMergeEvent
ExpressionExperimentVectorsManipulatingCli<T> - Class in ubic.gemma.apps: Base class for CLI tools that manipulate expression experiment vectors.
ExpressionExperimentVectorsManipulatingCli(Class) - Constructor for class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject) - Constructor for class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject, SearchResult, String, boolean) - Constructor for class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
ExpressionExperimentWriteAuditService - Interface in ubic.gemma.persistence.service.expression.experiment: Co-bean for ExpressionExperimentWriteServiceImpl: a thin layer that exists so the preferred-QuantitationType change-audit methods are invoked through a Spring proxy, allowing the AuditedAspect to intercept the return path.
ExpressionExperimentWriteAuditServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Co-bean implementation of ExpressionExperimentWriteAuditService.
ExpressionExperimentWriteAuditServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteAuditServiceImpl
ExpressionExperimentWriteService - Interface in ubic.gemma.persistence.service.expression.experiment: Thin write/mutation service for ExpressionExperiment.
ExpressionExperimentWriteServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of ExpressionExperimentWriteService.
ExpressionExperimentWriteServiceImpl(ExpressionExperimentDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl
ExpressionMetadataChangelogFileService - Interface in ubic.gemma.core.analysis.service: Service for reading and appending to changelog files.
ExpressionMetadataChangelogFileServiceImpl - Class in ubic.gemma.core.analysis.service
ExpressionMetadataChangelogFileServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileServiceImpl
extendAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService: Like redo, but we don't save the results, we just add the full set of results to the analysis given.
extendAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
ExtendedRuntime - Class in ubic.gemma.core.util.runtime
ExtendedRuntime() - Constructor for class ubic.gemma.core.util.runtime.ExtendedRuntime
external() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl: Generate an external URL.
EXTERNAL - Enum constant in enum class ubic.gemma.model.common.description.AnnotationRelationBasis: A third-party resource asserts it: MGI's Disease Ontology report, Cellosaurus's disease-list / derived-from-site-list.
EXTERNAL_DATABASE - Enum constant in enum class ubic.gemma.cli.completion.CompletionType
EXTERNAL_IMPORT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSource
EXTERNAL_IMPORT - Enum constant in enum class ubic.gemma.model.common.description.PublicationAssociationSource: The upstream record's own link from a non-GEO loader (CELLxGENE collection DOI, ArrayExpress, the simple-metadata loader).
ExternalDatabase - Class in ubic.gemma.model.common.description
ExternalDatabase() - Constructor for class ubic.gemma.model.common.description.ExternalDatabase
ExternalDatabase.Factory - Class in ubic.gemma.model.common.description
ExternalDatabaseAdderCli - Class in ubic.gemma.apps: Add a new external database, but requires editing the code to do so.
ExternalDatabaseAdderCli() - Constructor for class ubic.gemma.apps.ExternalDatabaseAdderCli
ExternalDatabaseDao - Interface in ubic.gemma.persistence.service.common.description
ExternalDatabaseDaoImpl - Class in ubic.gemma.persistence.service.common.description
ExternalDatabaseDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl
ExternalDatabaseOverviewCli - Class in ubic.gemma.apps
ExternalDatabaseOverviewCli() - Constructor for class ubic.gemma.apps.ExternalDatabaseOverviewCli
ExternalDatabaseReadService - Interface in ubic.gemma.persistence.service.common.description: Read-only retrieval service for ExternalDatabase.
ExternalDatabaseReadServiceImpl - Class in ubic.gemma.persistence.service.common.description: Implementation of ExternalDatabaseReadService.
ExternalDatabaseReadServiceImpl(ExternalDatabaseDao) - Constructor for class ubic.gemma.persistence.service.common.description.ExternalDatabaseReadServiceImpl
ExternalDatabaseReleaseAuditService - Interface in ubic.gemma.persistence.service.common.description: Co-bean carrying the @Audited hook for ReleaseDetailsUpdateEvent writes.
ExternalDatabaseReleaseAuditServiceImpl - Class in ubic.gemma.persistence.service.common.description: Implementation of ExternalDatabaseReleaseAuditService.
ExternalDatabaseReleaseAuditServiceImpl() - Constructor for class ubic.gemma.persistence.service.common.description.ExternalDatabaseReleaseAuditServiceImpl
ExternalDatabases - Class in ubic.gemma.model.common.description: Enumerates various globally available ExternalDatabase by name.
ExternalDatabases() - Constructor for class ubic.gemma.model.common.description.ExternalDatabases
ExternalDatabaseService - Interface in ubic.gemma.persistence.service.common.description
ExternalDatabaseServiceImpl - Class in ubic.gemma.persistence.service.common.description
ExternalDatabaseServiceImpl(ExternalDatabaseDao) - Constructor for class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
ExternalDatabaseUpdaterCli - Class in ubic.gemma.apps
ExternalDatabaseUpdaterCli() - Constructor for class ubic.gemma.apps.ExternalDatabaseUpdaterCli
ExternalDatabaseUtils - Class in ubic.gemma.core.loader.util: Utilities for working with various external databases.
ExternalDatabaseUtils() - Constructor for class ubic.gemma.core.loader.util.ExternalDatabaseUtils
ExternalDatabaseValueObject - Class in ubic.gemma.model.common.description
ExternalDatabaseValueObject() - Constructor for class ubic.gemma.model.common.description.ExternalDatabaseValueObject
ExternalDatabaseValueObject(Long, String, boolean) - Constructor for class ubic.gemma.model.common.description.ExternalDatabaseValueObject
ExternalDatabaseValueObject(ExternalDatabase) - Constructor for class ubic.gemma.model.common.description.ExternalDatabaseValueObject
ExternalFileGeneLoaderCLI - Class in ubic.gemma.apps: CLI for loading genes from a non NCBI files.
ExternalFileGeneLoaderCLI() - Constructor for class ubic.gemma.apps.ExternalFileGeneLoaderCLI
ExternalFileGeneLoaderService - Interface in ubic.gemma.core.loader.genome.gene
ExternalFileGeneLoaderServiceImpl - Class in ubic.gemma.core.loader.genome.gene: Class to provide functionality to load genes from a tab delimited file.
ExternalFileGeneLoaderServiceImpl() - Constructor for class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl
ExternalIdentificationValueObject(String, String, String, String, String, String, String, String) - Constructor for class ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject
ExternalIssueSyncState - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Sync state of a Ticket's optional GitHub-issue mirror (Decision 7 of AUDIT_AS_WORKFLOW_RECCE.md).
extract(File, Collection, File) - Method in class ubic.gemma.core.ontology.providers.OntologySlimExtractor: Extract a STAR module of source around seedUris, writing the resulting OWL to slimOut as RDF/XML.
extract(File, Collection, Collection, File) - Method in class ubic.gemma.core.ontology.providers.OntologySlimExtractor: As OntologySlimExtractor.extract(File, Collection, File), but additionally seeds every class that bears one of roleUris (or a descendant of one) via RO:0000087 has_role.
extract(InputStream) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractor
extract(InputStream) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractor
extract(InputStream) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractor
extract(InputStream) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ScanDateExtractor
extract(InputStream) - Static method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractor
extractBearerToken(String) - Static method in class ubic.gemma.rest.security.BearerTokenAuthenticationFilter: Extract the bare opaque token from an Authorization header value, or null if the header is missing / not a Bearer scheme / has an empty token.
ExtractedMolecule - Enum Class in ubic.gemma.model.expression.bioAssay: What was extracted from the sample and assayed — GEO's !Sample_molecule_chN.
extractFetchIds(Document) - Static method in class ubic.gemma.core.loader.entrez.EntrezXmlUtils: Extract IDs from an EFetch call.
extractGenePix(BufferedReader) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor: This method should be generic for GenePix/GPR/ATR file formats.
extractLinkIds(Document, String, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezXmlUtils: Extract IDs from an ELink call.
extractMultipleChildren(Node, String) - Static method in class ubic.gemma.core.util.XMLUtils
extractOneChild(Node, String) - Static method in class ubic.gemma.core.util.XMLUtils
extractOneChildText(Node, String) - Static method in class ubic.gemma.core.util.XMLUtils
extractPublisher(BibliographicReference, Node) - Static method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
extractSearchIds(Document) - Static method in class ubic.gemma.core.loader.entrez.EntrezXmlUtils: Extract IDs from an ESearch call.
extractTagData(Document, String) - Static method in class ubic.gemma.core.util.XMLUtils
extractTerms(SearchSettings, Consumer) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Extract terms, regardless of their logical organization.
extractTermsDnf(SearchSettings, boolean, Consumer) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Extract a DNF (Disjunctive Normal Form) from the terms of a query.
extractTermsDnf(SearchSettings, Consumer) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils

F

F - Enum constant in enum class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
FACTOR_RNAME_PREFIX - Static variable in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
FACTOR_VALUE - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetType: A single FactorValue.
FACTOR_VALUE_BASELINE_SUFFIX - Static variable in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
FACTOR_VALUE_RNAME_PREFIX - Static variable in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
FactorAssociatedAnalysisResultSet<R> - Class in ubic.gemma.model.analysis.expression
FactorAssociatedAnalysisResultSet() - Constructor for class ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet
FactorCommit() - Constructor for class ubic.gemma.rest.DatasetsWebService.FactorCommit
factorCount - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
factorCount - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
FactorEntry() - Constructor for class ubic.gemma.rest.HeatmapDataValueObject.FactorEntry
FactorEntry(ExperimentalFactorValueObject, LinkedHashMap) - Constructor for class ubic.gemma.rest.HeatmapDataValueObject.FactorEntry
FactorType - Enum Class in ubic.gemma.model.expression.experiment
FactorValue - Class in ubic.gemma.model.expression.experiment: The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
FactorValue() - Constructor for class ubic.gemma.model.expression.experiment.FactorValue
FactorValue.Factory - Class in ubic.gemma.model.expression.experiment
FactorValueArg<A> - Class in ubic.gemma.rest.util.args: Represents an API arguments that maps to a FactorValue by its ID or name.
FactorValueArg(String, Class, A) - Constructor for class ubic.gemma.rest.util.args.FactorValueArg
FactorValueBasicValueObject - Class in ubic.gemma.model.expression.experiment: Each factorvalue can be associated with multiple characteristics (or with a measurement).
FactorValueBasicValueObject() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject: Required when using the class as a spring bean.
FactorValueBasicValueObject(Long) - Constructor for class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
FactorValueBasicValueObject(FactorValue) - Constructor for class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
FactorValueBasicValueObjectSerializer - Class in ubic.gemma.rest.serializers
FactorValueBasicValueObjectSerializer() - Constructor for class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer
FactorValueCategoryStat() - Constructor for class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat
FactorValueCategoryStat(String, String, long, long) - Constructor for class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat
FactorValueCommit() - Constructor for class ubic.gemma.rest.DatasetsWebService.FactorValueCommit
FactorValueComparator - Class in ubic.gemma.persistence.util
FactorValueComparator() - Constructor for class ubic.gemma.persistence.util.FactorValueComparator
FactorValueDao - Interface in ubic.gemma.persistence.service.expression.experiment
FactorValueDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.experiment.FactorValue.
FactorValueDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
FactorValueDeletion - Interface in ubic.gemma.persistence.service.expression.experiment: This interface needed to be extracted for factor value deletions in order to be able to make the methods transactional
FactorValueDeletionImpl - Class in ubic.gemma.persistence.service.expression.experiment: Handles deletions of a factor values.
FactorValueDeletionImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueDeletionImpl
FactorValueIdArg - Class in ubic.gemma.rest.util.args: Maps a long identifier to a FactorValue.
FactorValueIdArg(long) - Constructor for class ubic.gemma.rest.util.args.FactorValueIdArg
FactorValueNeedsAttentionEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that a factor value needs attention.
FactorValueNeedsAttentionEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FactorValueNeedsAttentionEvent
FactorValueNeedsAttentionRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.FactorValueNeedsAttentionRequest
FactorValueNeedsAttentionService - Interface in ubic.gemma.persistence.service.expression.experiment: Service to manipulate the "needs attention" flag on FactorValues.
FactorValueNeedsAttentionServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Ticket-backed implementation of FactorValueNeedsAttentionService.
FactorValueNeedsAttentionServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceImpl
FactorValueOntologyService - Interface in ubic.gemma.core.ontology: Ontology service for factor values and their annotations.
FactorValueOntologyServiceImpl - Class in ubic.gemma.core.ontology
FactorValueOntologyServiceImpl(FactorValueService, EntityUrlBuilder) - Constructor for class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl
FactorValueOntologyUtils - Class in ubic.gemma.core.ontology
FactorValueOntologyUtils() - Constructor for class ubic.gemma.core.ontology.FactorValueOntologyUtils
FactorValueOntologyUtils.Annotation - Class in ubic.gemma.core.ontology
FactorValueOntologyUtils.AnnotationIds - Class in ubic.gemma.core.ontology
FactorValueOntologyUtils.StatementVisitor<U,E> - Interface in ubic.gemma.core.ontology
FactorValueOntologyWriterCli - Class in ubic.gemma.apps
FactorValueOntologyWriterCli() - Constructor for class ubic.gemma.apps.FactorValueOntologyWriterCli
FactorValueReadService - Interface in ubic.gemma.persistence.service.expression.experiment: Read-only retrieval service for FactorValue.
FactorValueReadServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of FactorValueReadService.
FactorValueReadServiceImpl(FactorValueDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
FactorValueService - Interface in ubic.gemma.persistence.service.expression.experiment
FactorValueServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Spring Service base class for FactorValueService, provides access to all services and entities referenced by this service.
FactorValueServiceImpl(FactorValueDao, StatementDao, FactorValueReadService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
FactorValueUtils - Class in ubic.gemma.model.expression.experiment
FactorValueUtils() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueUtils
FactorValueValueArg - Class in ubic.gemma.rest.util.args: Deprecated.
FactorValueValueArg(String) - Constructor for class ubic.gemma.rest.util.args.FactorValueValueArg: Deprecated.
FactorValueValueObject - Class in ubic.gemma.model.expression.experiment: Deprecated.
aim towards using the FactorValueBasicValueObject. This one is confusing. Once usage of this type has been completely phased out, revise the BioMaterialValueObject and relevant DAOs and Services.
FactorValueValueObject() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.

Required when using the class as a spring bean.
FactorValueValueObject(Long) - Constructor for class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
FactorValueValueObject(FactorValue) - Constructor for class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
FactorValueValueObject(FactorValue, boolean) - Constructor for class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.

Create a FactorValue VO.
FactorValueValueObject(FactorValue, Statement) - Constructor for class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.

Create a FactorValue VO focusing on a specific statement.
FactorValueValueObjectSerializer - Class in ubic.gemma.rest.serializers: Deprecated.
FactorValueValueObjectSerializer() - Constructor for class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer: Deprecated.
FactorValueVector - Class in ubic.gemma.persistence.util
FactorValueVector(Collection, Collection) - Constructor for class ubic.gemma.persistence.util.FactorValueVector
Factory() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.Reporter.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastResult.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.diff.HitListSize.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.diff.PvalueDistribution.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.ExpressionExperimentSet.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.pca.Eigenvalue.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.pca.Eigenvector.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.pca.ProbeLoading.Factory
Factory() - Constructor for class ubic.gemma.model.association.Gene2GOAssociation.Factory
Factory() - Constructor for class ubic.gemma.model.association.ReferenceAssociation.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEvent.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditTrail.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.Contact.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.Ticket.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.GroupAuthority.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.JobInfo.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.User.Factory
Factory() - Constructor for class ubic.gemma.model.common.auditAndSecurity.UserGroup.Factory
Factory() - Constructor for class ubic.gemma.model.common.description.BibliographicReference.Factory
Factory() - Constructor for class ubic.gemma.model.common.description.Characteristic.Factory
Factory() - Constructor for class ubic.gemma.model.common.description.DatabaseEntry.Factory
Factory() - Constructor for class ubic.gemma.model.common.description.ExternalDatabase.Factory
Factory() - Constructor for class ubic.gemma.model.common.description.Keyword.Factory
Factory() - Constructor for class ubic.gemma.model.common.description.MedicalSubjectHeading.Factory
Factory() - Constructor for class ubic.gemma.model.common.measurement.Measurement.Factory
Factory() - Constructor for class ubic.gemma.model.common.measurement.Unit.Factory
Factory() - Constructor for class ubic.gemma.model.common.protocol.Protocol.Factory
Factory() - Constructor for class ubic.gemma.model.common.quantitationtype.QuantitationType.Factory
Factory() - Constructor for class ubic.gemma.model.expression.arrayDesign.AlternateName.Factory
Factory() - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesign.Factory
Factory() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssay.Factory
Factory() - Constructor for class ubic.gemma.model.expression.bioAssayData.BioAssayDimension.Factory
Factory() - Constructor for class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics.Factory
Factory() - Constructor for class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment.Factory
Factory() - Constructor for class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation.Factory
Factory() - Constructor for class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector.Factory
Factory() - Constructor for class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector.Factory
Factory() - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterial.Factory
Factory() - Constructor for class ubic.gemma.model.expression.biomaterial.Compound.Factory
Factory() - Constructor for class ubic.gemma.model.expression.biomaterial.Treatment.Factory
Factory() - Constructor for class ubic.gemma.model.expression.designElement.CompositeSequence.Factory
Factory() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesign.Factory
Factory() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalFactor.Factory
Factory() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperiment.Factory
Factory() - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.Factory
Factory() - Constructor for class ubic.gemma.model.expression.experiment.FactorValue.Factory
Factory() - Constructor for class ubic.gemma.model.expression.experiment.Statement.Factory
Factory() - Constructor for class ubic.gemma.model.genome.biosequence.BioSequence.Factory
Factory() - Constructor for class ubic.gemma.model.genome.Chromosome.Factory
Factory() - Constructor for class ubic.gemma.model.genome.Gene.Factory
Factory() - Constructor for class ubic.gemma.model.genome.gene.GeneAlias.Factory
Factory() - Constructor for class ubic.gemma.model.genome.gene.GeneProduct.Factory
Factory() - Constructor for class ubic.gemma.model.genome.gene.GeneSet.Factory
Factory() - Constructor for class ubic.gemma.model.genome.gene.GeneSetMember.Factory
Factory() - Constructor for class ubic.gemma.model.genome.gene.Multifunctionality.Factory
Factory() - Constructor for class ubic.gemma.model.genome.PhysicalLocation.Factory
Factory() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation.Factory
Factory() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation.Factory
Factory() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResult.Factory
Factory() - Constructor for class ubic.gemma.model.genome.Taxon.Factory
Factory() - Constructor for class ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator.Factory
failed - Variable in class ubic.gemma.rest.AdminWebService.JobsListResponse
FAILED - Enum constant in enum class ubic.gemma.core.job.SubmittedTask.Status
FAILED - Enum constant in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Indicate if a failure occurred for a given value or not.
FAILED - Enum constant in enum class ubic.gemma.model.expression.experiment.GeoScrapeWatermark.Status
FAILED - Enum constant in enum class ubic.gemma.model.pipeline.JobState
FailedBatchInformationFetchingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that the attempt to get batch information failed due to an error.
FailedBatchInformationFetchingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationFetchingEvent
FailedBatchInformationMissingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
use BatchInformationMissingEvent
FailedBatchInformationMissingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent: Deprecated.
FailedDataReplacedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Represents a failed data replace.
FailedDataReplacedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedDataReplacedEvent
FailedDifferentialExpressionAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
FailedDifferentialExpressionAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedDifferentialExpressionAnalysisEvent
FailedLinkAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
FailedLinkAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedLinkAnalysisEvent
FailedMeanVarianceUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
FailedMeanVarianceUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedMeanVarianceUpdateEvent
FailedMissingValueAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
FailedMissingValueAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedMissingValueAnalysisEvent
FailedPCAAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
FailedPCAAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedPCAAnalysisEvent
FailedPipelineRunEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: A pipeline job reached terminal failure on an experiment.
FailedPipelineRunEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedPipelineRunEvent
FailedProcessedVectorComputationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
FailedProcessedVectorComputationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedProcessedVectorComputationEvent
FailedSampleCorrelationAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
FailedSampleCorrelationAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedSampleCorrelationAnalysisEvent
FAILURE - Static variable in class ubic.gemma.cli.util.AbstractCLI: Exit code used for a failed AbstractCLI.doWork() execution.
FAILURE_FROM_ERROR_OBJECTS - Static variable in class ubic.gemma.cli.util.AbstractCLI: Exit code used for a successful doWork execution that resulted in failed error objects.
FAIRE_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
FAMILY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoScope
FAST - Enum constant in enum class ubic.gemma.model.common.search.SearchSettings.SearchMode: Fast search mode, designed for autocompletion.
FastaCmd - Interface in ubic.gemma.core.loader.genome: Interface representing a class that can retrieve sequences from Blast databases.
FastaParser - Class in ubic.gemma.core.loader.genome: FASTA sequence file parser.
FastaParser() - Constructor for class ubic.gemma.core.loader.genome.FastaParser
FASTQHeadersPresentButNotUsableException - Exception Class in ubic.gemma.core.analysis.preprocess.batcheffects: Indicates that FASTQ headers were present, but were not in a format that yields usable information on batches.
FASTQHeadersPresentButNotUsableException(ExpressionExperiment, String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException
fastrow(double[][]) - Static method in class ubic.gemma.core.util.matrix.DoubleMatrixFactory
fastrow(int, int) - Static method in class ubic.gemma.core.util.matrix.DoubleMatrixFactory
FastRowAccessDoubleMatrix<R,C> - Class in ubic.gemma.core.util.matrix: Dense 2D matrix implementation designed for very fast access of entire rows.
FastRowAccessDoubleMatrix(double[][]) - Constructor for class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix: Implementation note: The input matrix is NOT COPIED (due to the way colt DoubleArrayList(double[]) is implemented).F
FastRowAccessDoubleMatrix(int, int) - Constructor for class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
fetch() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonFetcher: Fetch the Taxon bundle from NCBI.
fetch(String) - Method in class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
fetch(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.LocalDatasetFetcher
fetch(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.LocalSeriesFetcher
fetch(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
fetch(String) - Method in class ubic.gemma.core.loader.expression.sra.SraFetcher: Fetch an SRA experiment.
fetch(String) - Method in interface ubic.gemma.core.loader.util.fetcher.Fetcher: Fetch files according to the identifier provided.
fetch(String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
fetch(String) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
fetch(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
fetch(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
fetch(String, EntrezQuery, EntrezRetmode, String, int, int, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Retrieve the results of a previous EntrezUtils.search(String, String, EntrezRetmode, String) query.
fetch(Collection) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher: Main method that iterates through each taxon supplied and calls the fetch method for each taxon.
fetchAllCollectionMetadata() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher: Fetch the metadata for all CELLxGENE collections.
fetchAllDatasetMetadata() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher: Fetch the metadata for all CELLxGENE datasets.
fetchAndLoad(String, boolean, boolean, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService: Load data, no restrictions on superseries or subseries
fetchAndLoad(String, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
fetchAndLoad(String, boolean, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService
fetchAndLoad(String, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl: Given a GEO GSE or GDS (or GPL, but support might not be complete) Check that it doesn't already exist in the system, filter samples Download and parse GDS files and GSE file needed Convert the GDS and GSE into a ExpressionExperiment (or just the ArrayDesigns) Load the resulting ExpressionExperiment and/or ArrayDesigns into Gemma
fetchAndLoad(String, String, String, ArrayDesign, String, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderService: Fetch a CELLxGENE dataset and load it into the database.
fetchAndLoad(String, String, String, ArrayDesign, String, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderServiceImpl
fetchByGeoAccession(String) - Method in class ubic.gemma.core.loader.expression.sra.SraFetcher: Fetch an SRA experiment by its GEO association.
fetchById(String, String, EntrezRetmode, String, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Retrieve a record from an Entrez database by ID.
fetchCollectionMetadata(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher: Fetch the full metadata for a specific CELLxGENE collection.
fetchDatasetAssetDownloadMetadata(String, String) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher: Fetch the download metadata for a specific dataset asset.
fetchDatasetMetadata(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher: Retrieves the metadata for a specific CELLxGENE dataset.
fetchedFile(String) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
fetchedFile(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
Fetcher - Interface in ubic.gemma.core.loader.util.fetcher: Interface for classes that can fetch files from a remote location and copy them to a specified location.
fetchFileForProteinQuery(String) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher: Given a biomart taxon formatted name fetch the file from biomart and save as a local file.
fetchRunInfo(String) - Method in class ubic.gemma.core.loader.expression.sra.SraFetcher: Fetch an SRA experiment in the runinfo format.
fetchSeriesFamilySoftFile(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher2.GeoFetcher
fetchSize(int) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder
FieldAwareSearchSource - Interface in ubic.gemma.core.search: Search source that can retrieve results matching specific fields.
FILE_INDIRECTION_SUFFIX - Static variable in class ubic.gemma.core.config.ConfigUtils: Suffix appended to an env-var name to indicate "value lives in this file on disk".
FileFormatException - Exception Class in ubic.gemma.core.loader.util.parser: Use to indicate a file format error.
FileFormatException(String) - Constructor for exception class ubic.gemma.core.loader.util.parser.FileFormatException
FileFormatException(Throwable) - Constructor for exception class ubic.gemma.core.loader.util.parser.FileFormatException
FileLockInfo - Class in ubic.gemma.core.util.locking: Metadata about a file lock.
FileLockInfo - Class in ubic.gemma.core.util.runtime: Metadata about a file lock.
FileLockInfo(String, boolean, boolean, int, boolean, String, String, long, long, long) - Constructor for class ubic.gemma.core.util.runtime.FileLockInfo: Creates a new FileLockInfo instance.
FileLockInfo(Path, Path, int, int, int, boolean, int, List) - Constructor for class ubic.gemma.core.util.locking.FileLockInfo: Creates a new FileLockInfo instance.
FileLockInfoUtils - Class in ubic.gemma.core.util.locking
FileLockInfoUtils() - Constructor for class ubic.gemma.core.util.locking.FileLockInfoUtils
FileLockManager - Interface in ubic.gemma.core.util.locking: Create shared and exclusive locks for files.
FileLockManagerImpl - Class in ubic.gemma.core.util.locking
FileLockManagerImpl() - Constructor for class ubic.gemma.core.util.locking.FileLockManagerImpl
FileTools - Class in ubic.gemma.core.util: Ported in-tree from ubic.basecode.util.FileTools (baseCode project, Apache 2.0, University of British Columbia).
FileTools() - Constructor for class ubic.gemma.core.util.FileTools
FileType - Enum Class in ubic.gemma.core.loader.expression.cellxgene
FileUtils - Class in ubic.gemma.cli.util
FileUtils - Class in ubic.gemma.core.util
FileUtils() - Constructor for class ubic.gemma.cli.util.FileUtils
FileUtils() - Constructor for class ubic.gemma.core.util.FileUtils
fill(double) - Method in class ubic.gemma.core.util.math.distribution.Histogram: Fill the histogram with x.
fill(double) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix: Set every cell to value using the backing Colt matrix's primitive assign loop.
fill(int, int) - Method in class ubic.gemma.core.util.math.distribution.Histogram: Add the given number of counts to the given bin.
fill(DoubleMatrix1D) - Method in class ubic.gemma.core.util.math.distribution.Histogram
fillBatchInformation(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationService: Attempt to obtain batch information from the data provider and populate it into the given experiment.
fillBatchInformation(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl
fillEventInformation(Collection) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
fillEventInformation(Collection) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl: Fill in event information
fillInDatabaseEntry(DatabaseEntry, Map) - Method in class ubic.gemma.persistence.persister.CommonPersister: Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.
fillInSubsumptionInfo(Collection) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
fillInSubsumptionInfo(Collection) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
fillInValueObjects(Collection) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
fillInValueObjects(Collection) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl: Fill in the probe summary statistics
fillRange(int, int) - Static method in class ubic.gemma.core.util.math.MathUtil: Create an array filled with the integer values from a to b, inclusive.
fillResults(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Indicate if result objects (i.e.
filter() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage: Returns the value of the filter record component.
filter() - Method in class ubic.gemma.rest.util.args.FilterArgParser
filter(ContainerRequestContext) - Method in class ubic.gemma.rest.providers.UnknownQueryParameterFilter
filter(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
filter(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl: returns ids of search results
filter(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: returns ids of search results.
filter(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
filter(M) - Method in interface ubic.gemma.core.util.matrix.datafilter.Filter: Filter the data
filter(M) - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilter
filter(T) - Method in interface ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter: Apply the filter to the given data matrix.
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.LowVarianceFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.OutliersFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter: We do this second because doing it first causes some kind of subtle problem ...
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowsWithSequencesFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.ZeroVarianceFilter
filter(ExpressionDataDoubleMatrix, Collection, ExpressionExperimentFilterResult) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
filter(ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisFilterResult) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
filter(ExpressionDataDoubleMatrix, ExpressionExperimentFilterResult) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
Filter - Class in ubic.gemma.persistence.util: Holds the necessary information to filter an entity with a property, operator and right-hand side value.
Filter<M,R,C,V> - Interface in ubic.gemma.core.util.matrix.datafilter: An interface representing the functionality of a class that can filter 2-d matrix-based data by row-oriented criteria.
FILTER - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
Filter.Operator - Enum Class in ubic.gemma.persistence.util
FilterablePropertiesConfigurer() - Constructor for class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
FilterArg<O> - Class in ubic.gemma.rest.util.args: Represent a filter argument designed to generate a Filters from user input.
FilterArg.Filter - Class in ubic.gemma.rest.util.args: Represents the internal value of a FilterArg.
FilterArgBaseListener - Class in ubic.gemma.rest.util.args: This class provides an empty implementation of FilterArgListener, which can be extended to create a listener which only needs to handle a subset of the available methods.
FilterArgBaseListener() - Constructor for class ubic.gemma.rest.util.args.FilterArgBaseListener
FilterArgLexer - Class in ubic.gemma.rest.util.args
FilterArgLexer(CharStream) - Constructor for class ubic.gemma.rest.util.args.FilterArgLexer
FilterArgListener - Interface in ubic.gemma.rest.util.args: This interface defines a complete listener for a parse tree produced by FilterArgParser.
FilterArgParser - Class in ubic.gemma.rest.util.args
FilterArgParser(TokenStream) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser
FilterArgParser.ClauseContext - Class in ubic.gemma.rest.util.args
FilterArgParser.CollectionContext - Class in ubic.gemma.rest.util.args
FilterArgParser.CollectionOperatorContext - Class in ubic.gemma.rest.util.args
FilterArgParser.DisjunctionContext - Class in ubic.gemma.rest.util.args
FilterArgParser.FilterContext - Class in ubic.gemma.rest.util.args
FilterArgParser.OperatorContext - Class in ubic.gemma.rest.util.args
FilterArgParser.PredicateContext - Class in ubic.gemma.rest.util.args
FilterArgParser.QuantifierContext - Class in ubic.gemma.rest.util.args
FilterArgParser.ScalarContext - Class in ubic.gemma.rest.util.args
FilterArgParser.SubClauseContext - Class in ubic.gemma.rest.util.args
filterByTaxon(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
filterByTaxon(Collection, Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
filterByTaxon(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
filterByTaxon(Collection, Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
filterByTaxon(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Remove IDs of Experiments that are not from the given taxon.
filterByTaxon(Collection, Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
Filter chain summary (translated from the legacy XML) - Section in class ubic.gemma.rest.security.RestSecurityConfig
FilterConfig(boolean, boolean, boolean, boolean, double, double, double, double, double, int) - Constructor for record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Creates an instance of a FilterConfig record class.
FilterContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
FilteredAndCursorPaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util: Cursor-mode counterpart to FilteredAndPaginatedResponseDataObject.
FilteredAndCursorPaginatedResponseDataObject(CursorPage, Filters, String[]) - Constructor for class ubic.gemma.rest.util.FilteredAndCursorPaginatedResponseDataObject
FilteredAndInferredAndCursorPaginatedResponseDataObject(CursorPage, Filters, String[], Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.FilteredAndInferredAndCursorPaginatedResponseDataObject
FilteredAndInferredAndCursorPaginatedResponseDataObjectExpressionExperimentValueObject(CursorPage, Filters, String[], Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.FilteredAndInferredAndCursorPaginatedResponseDataObjectExpressionExperimentValueObject
FilteredAndInferredAndPaginatedResponseDataObject(Slice, Filters, String[], Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject
FilteredAndInferredAndPaginatedResponseDataObjectExpressionExperimentValueObject(Slice, Filters, String[], Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObjectExpressionExperimentValueObject
FilteredAndLimitedResponseDataObject<T> - Class in ubic.gemma.rest.util
FilteredAndLimitedResponseDataObject(List, Filters, String[], Sort, Integer) - Constructor for class ubic.gemma.rest.util.FilteredAndLimitedResponseDataObject
FilteredAndPaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util
FilteredAndPaginatedResponseDataObject(Slice, Filters, String[]) - Constructor for class ubic.gemma.rest.util.FilteredAndPaginatedResponseDataObject
FilteredResponseDataObject<T> - Class in ubic.gemma.rest.util
FilteredResponseDataObject(List, Filters, String[], Sort) - Constructor for class ubic.gemma.rest.util.FilteredResponseDataObject
FilteringDao<O> - Interface in ubic.gemma.persistence.service: Interface for filtering-capable DAO.
FilteringDao.ConjunctSpec - Class in ubic.gemma.persistence.service: One predicate of a conjoined subquery filter.
FilteringException - Exception Class in ubic.gemma.core.analysis.preprocess.filter: Exception raised when there is an issue during the filtering process of expression data.
FilteringException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.filter.FilteringException
FilteringException(String, Throwable) - Constructor for exception class ubic.gemma.core.analysis.preprocess.filter.FilteringException
FilteringRelatedAnalysisException - Exception Class in ubic.gemma.core.analysis.expression.diff: Exception raised when data filtering fails.
FilteringRelatedAnalysisException(DifferentialExpressionAnalysisConfig, DifferentialExpressionAnalysisFilterResult, FilteringException) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.FilteringRelatedAnalysisException
FilteringRelatedPreprocessingException - Exception Class in ubic.gemma.core.analysis.preprocess
FilteringRelatedPreprocessingException(ExpressionExperiment, FilteringException) - Constructor for exception class ubic.gemma.core.analysis.preprocess.FilteringRelatedPreprocessingException
FilteringService<O> - Interface in ubic.gemma.persistence.service: Interface for filtering-capable services.
FilteringVoEnabledDao<O,VO> - Interface in ubic.gemma.persistence.service: Interface for VO-enabled DAO with filtering capabilities.
FilteringVoEnabledService<O,VO> - Interface in ubic.gemma.persistence.service: Interface VO-enabled service with filtering capabilities.
FilterJpaUtils - Class in ubic.gemma.persistence.util: JPA Criteria equivalent of FilterQueryUtils.
filterProbesByPlatform(Collection, Collection, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
FilterQueryUtils - Class in ubic.gemma.persistence.util: Utilities for integrating Filter into Query.
FilterQueryUtils() - Constructor for class ubic.gemma.persistence.util.FilterQueryUtils
Filters - Class in ubic.gemma.persistence.util: Represents a conjunction of disjunctions of Filter.
Filters.FiltersClauseBuilder - Class in ubic.gemma.persistence.util: Builder for a disjunctive sub-clause.
FilterStage(String, boolean, int, Integer) - Constructor for record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage: Creates an instance of a FilterStage record class.
FiltersUtils - Class in ubic.gemma.persistence.util: Utilities for working with Filters and Filter.
FiltersUtils() - Constructor for class ubic.gemma.persistence.util.FiltersUtils
finalColumns() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Returns the value of the finalColumns record component.
finalizeAnnotationSet(Long, String, AnnotationSetsWebService.FinalizeRequest) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Mark an annotation set finalized.
finalizedAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
finalizedAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
finalizedBy - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
finalizedBy - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
finalizedNotes - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse: The curator's closing note on this finalization; cleared on reopen.
FinalizeRequest() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.FinalizeRequest
finalizeSet(Long, String, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: Stamp finalizedAt + finalizedBy on the row, marking a DRAFT as "done editing" or a SNAPSHOT as the polished canonical view.
finalizeSet(Long, String, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
finalRows() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Returns the value of the finalRows record component.
find(C) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
find(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.ChromosomeDao
find(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.ChromosomeDaoImpl
find(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.ChromosomeService: Locate by name e.g.
find(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.ChromosomeServiceImpl
find(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService
find(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
find(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService: Find specific type (T) of vectors that meet the given criteria.
find(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
find(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
find(Collection, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao: Retrieve the processed vectors for a set of design elements within a given quantitation type.
find(Collection, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
find(Collection, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Retrieve the processed vectors for a set of design elements within a given (processed) quantitation type.
find(Collection, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
find(Collection, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao
find(Collection, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl
find(Collection, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService
find(Collection, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorServiceImpl
find(Collection) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao
find(Collection) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
find(Collection) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao
find(Collection) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl
find(O) - Method in class ubic.gemma.persistence.service.AbstractService
find(O) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
find(Session, Gene2GOAssociation) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, Contact) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, Characteristic) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, Unit) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, QuantitationType) - Static method in class ubic.gemma.persistence.util.BusinessKey: Find an existing QuantitationType whose full set of identifying fields equals the input's.
find(Session, ArrayDesign) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, BioAssay) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, BioAssayDimension) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, BioMaterial) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, ExperimentalFactor) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, ExpressionExperimentSubSet) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, FactorValue) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, BioSequence) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, Chromosome) - Static method in class ubic.gemma.persistence.util.BusinessKey: Find an existing Chromosome by its business key (name + taxon, optionally tightened by assemblyDatabase + sequence when present on the input).
find(Session, Gene) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, GeneProduct) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(Session, Taxon) - Static method in class ubic.gemma.persistence.util.BusinessKey
find(ObjectIdentity) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
find(ObjectIdentity) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
find(ObjectIdentity, Session) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
find(ObjectIdentity, Session) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
find(Sid) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
find(Sid) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
find(Sid, Session) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
find(Sid, Session) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
find(T) - Method in class ubic.gemma.persistence.service.AbstractDao
find(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Does a look-up for the given entity in the persistent storage, usually looking for a specific identifier if Identifiable.getId() is set or a business key.
find(AclSid) - Method in interface ubic.gemma.core.security.acl.domain.AclDao: Look up the persisted AclSid row matching the principal/grantedAuthority carried by the given (already-loaded but possibly detached) entity.
find(AclSid) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
find(Investigation, BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationService: The assertion held for this exact pair, or null if the pair has never been ruled on.
find(Investigation, BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
find(Gene2GOAssociation) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
find(Gene2GOAssociation) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
find(Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.ContactDaoImpl
find(Person) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.PersonDaoImpl: Deprecated.
find(User) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
find(UserGroup) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
find(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
find(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService: check to see if the object already exists
find(ExternalDatabase) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl
find(Unit) - Method in interface ubic.gemma.persistence.service.common.measurement.UnitDao
find(Unit) - Method in class ubic.gemma.persistence.service.common.measurement.UnitDaoImpl
find(Protocol) - Method in class ubic.gemma.persistence.service.common.protocol.ProtocolDaoImpl
find(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Find a QT matching the given template as per QuantitationType.equals(Object).
find(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
find(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService
find(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
find(QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService: Find specific type (T) of vectors that meet the given criteria.
find(QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
find(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
find(QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Find a QT matching the given template for the given data vector type as per QuantitationTypeDao.find(QuantitationType).
find(QuantitationType, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
find(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
find(ArrayDesign, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao
find(ArrayDesign, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl
find(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
find(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService
find(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
find(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl: Find a BioAssayDimension with the exact same list of BioAssays, name and description.
find(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService: Find specific type (raw or processed, depending on the service) of vectors that meet the given criteria.
find(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
find(BulkExpressionDataVector) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
find(RawExpressionDataVector) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl
find(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
find(Compound) - Method in class ubic.gemma.persistence.service.expression.biomaterial.CompoundDaoImpl
find(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
find(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
find(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl
find(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDao
find(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl
find(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
find(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
find(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
find(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
find(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
find(ExpressionExperiment, QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService: Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.
find(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
find(ExpressionExperiment, QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService: Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.
find(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
find(ExpressionExperiment, QuantitationType, Set) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Find a QT matching the given template as per QuantitationTypeDao.find(QuantitationType) in a given experiment for and for a given data vector type.
find(ExpressionExperiment, QuantitationType, Set) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
find(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl
find(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
find(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
find(BioSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
find(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao
find(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
find(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationReadService
find(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationReadServiceImpl
find(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
find(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationServiceImpl
find(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao
find(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl
find(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadService
find(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadServiceImpl
find(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
find(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl
find(Chromosome) - Method in class ubic.gemma.persistence.service.genome.ChromosomeDaoImpl
find(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
find(Gene) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao
find(Gene) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
find(Gene) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationReadService
find(Gene) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationReadServiceImpl
find(Gene) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
find(Gene) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationServiceImpl
find(Gene) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao
find(Gene) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl
find(Gene) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadService
find(Gene) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadServiceImpl
find(Gene) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
find(Gene) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl
find(GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
find(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
find(PhysicalLocation) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
find(PhysicalLocation) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
find(PhysicalLocation) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService: Find all genes at a physical location.
find(PhysicalLocation) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
find(PhysicalLocation) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Find all genes at a physical location.
find(PhysicalLocation) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
find(Taxon) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
findActiveByExperiment(Long) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobDao: Non-terminal jobs targeting the given experiment.
findActiveByExperiment(Long) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobDaoImpl
findAlignments(String) - Method in class ubic.gemma.core.goldenpath.GoldenPathQuery: Locate the alignment for the given sequence, if it exists in the goldenpath database.
findAllByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService
findAllByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl
findAllByExternalId(String, String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao: Find ALL references sharing an external id, ordered by id ascending.
findAllByExternalId(String, String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
findAllByExternalId(String, String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService: Retrieve ALL references sharing an identifier (accession + database name), ordered by id ascending.
findAllByExternalId(String, String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
findAllByNameAndVectorType(ExpressionExperiment, String, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
findAllByNameAndVectorType(ExpressionExperiment, String, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
findAllByNameAndVectorType(ExpressionExperiment, String, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
findAllByNameAndVectorType(ExpressionExperiment, String, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
findAllByNameAndVectorType(ExpressionExperiment, String, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService: Find all the QT associated to the given experiment, name and vector type.
findAllByNameAndVectorType(ExpressionExperiment, String, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
findAllByNameIn(Collection) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseDao
findAllByNameIn(Collection) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl
findAllByNameIn(List) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseReadService
findAllByNameIn(List) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseReadServiceImpl
findAllByNameIn(List) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
findAllByNameIn(List) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
findAllGroups() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findAllUsers() - Method in interface ubic.gemma.core.security.authentication.UserDetailsManager
findAllUsers() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findAndThaw(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService
findAndThaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService
findAndThaw(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl
findAndThaw(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService
findAndThaw(QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService: Find and thaw specific type (T) of vectors that meet the given criteria.
findAndThaw(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService
findAndThaw(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService
findAndThaw(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl
findAndThaw(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadService
findAndThaw(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadServiceImpl
findAndThaw(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
findAndThaw(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl
findAssignedTo(Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Find all tickets currently assigned to the given contact, regardless of state.
findAssignedTo(Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findAssignedTo(Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findAssignedTo(Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findAssociationByGene(Gene) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findAssociationByGene(Gene) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findAssociationByGene(Gene) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationReadService
findAssociationByGene(Gene) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl
findAssociationByGene(Gene) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findAssociationByGene(Gene) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findAssociationByGenes(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findAssociationByGenes(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findAssociationByGenes(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationReadService
findAssociationByGenes(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl
findAssociationByGenes(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findAssociationByGenes(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findAssociations(String, Long, Long, String, String, String, ThreePrimeDistanceMethod, ProbeMapperConfig) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis: Given a physical location, identify overlapping genes or predicted genes.
findBestByUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Return the characteristic with the most frequently used non-null value by URI.
findBestByUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findBestByUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Find the best possible characteristic for a given URI.
findBestByUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findBestByUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Find the best possible characteristic for a given URI.
findBestByUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findBioAssayDimensions(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
findBioAssayDimensions(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
findBioAssayDimensions(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService: Locate all BioAssayDimensions in which the selected BioAssay occurs.
findBioAssayDimensions(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
findBioAssayDimensions(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService: Locate all BioAssayDimensions in which the selected BioAssay occurs
findBioAssayDimensions(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
findBlockingRejection(Investigation, BibliographicReference, PublicationAssociationSource) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationService: The standing rejection that would refuse an attempt by source to accept publication for investigation, or null if the write is allowed.
findBlockingRejection(Investigation, BibliographicReference, PublicationAssociationSource) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
findByAccession(String) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
findByAccession(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
findByAccession(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.common.description.DatabaseEntryDao
findByAccession(String) - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.common.description.DatabaseEntryReadService
findByAccession(String) - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryReadServiceImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl
findByAccession(String, ExternalDatabase) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
findByAccession(String, ExternalDatabase) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
findByAccession(String, ExternalDatabase) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByAccession(String, ExternalDatabase) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByAccession(String, ExternalDatabase) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findByAccession(String, ExternalDatabase) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByAccession(String, ExternalDatabase) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
findByAccession(String, ExternalDatabase) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByAccession(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByAccession(DatabaseEntry) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByAccession(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByAccession(DatabaseEntry) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByAccession(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByAccession(DatabaseEntry) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByAccession(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
findByAccession(DatabaseEntry) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
findByAccession(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService
findByAccession(DatabaseEntry) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl
findByAccession(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
findByAccession(DatabaseEntry) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
findByAlias(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByAlias(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByAlias(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findByAlias(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByAlias(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Locate genes that match the given alias string
findByAlias(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl: Gets all the genes referred to by the alias defined by the search string.
findByAlternateName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
findByAlternateName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
findByAlternateName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
findByAlternateName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
findByAlternateName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
findByAlternateName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findByAnyUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Find a characteristic or statement by any URI it contains including its category, value, predicates and objects.
findByAnyUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByAnyUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Find a characteristic or statement by any URI it contains including its category, value, predicates and objects.
findByAnyUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByAnyValue(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Find a characteristic by any value it contains including its category, value, predicates and objects.
findByAnyValue(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByAnyValue(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Find a characteristic by any value it contains including its category, value, predicates and objects.
findByAnyValue(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByAnyValueStartingWith(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Find a characteristic by any value it contains including its category, value, predicates and objects that starts with the given query.
findByAnyValueStartingWith(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByAnyValueStartingWith(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Find a characteristic by any value it contains including its category, value, predicates and objects that starts with the given query.
findByAnyValueStartingWith(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByBatch(Long) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobDao
findByBatch(Long) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobDaoImpl
findByBatchAndStates(PipelineJobBatch, Collection) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobDao: Convenience for the batch service: jobs in the batch in the given states.
findByBatchAndStates(PipelineJobBatch, Collection) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobDaoImpl
findByBibliographicReference(BibliographicReference) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByBibliographicReference(BibliographicReference) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByBibliographicReference(BibliographicReference) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByBibliographicReference(BibliographicReference) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByBibliographicReference(BibliographicReference) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByBibliographicReference(BibliographicReference) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByBioAssay(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByBioAssay(BioAssay) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByBioAssay(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByBioAssay(BioAssay) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByBioAssay(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByBioAssay(BioAssay) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByBioAssay(BioAssay, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByBioAssay(BioAssay, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByBioAssay(BioAssay, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByBioAssay(BioAssay, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByBioAssay(BioAssay, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByBioAssay(BioAssay, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByBioAssayIn(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao
findByBioAssayIn(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl
findByBioAssayIn(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Find every subset that contains any of the supplied bio-assays.
findByBioAssayIn(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
findByBioAssayIn(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
findByBioAssayIn(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
findByBioAssaysContainingAll(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDao: Find all the dimensions that contains all the given assays.
findByBioAssaysContainingAll(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl
findByBioAssaysContainingAll(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
findByBioAssaysContainingAll(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl
findByBioAssaySetInAndDatabaseEntryInByCursor(Collection, Collection, Filters, Cursor, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Cursor-paged counterpart to ExpressionAnalysisResultSetDao.findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort): keyset pagination over the result sets associated to a set of BioAssaySet and external database entries, always sorted by ascending id.
findByBioAssaySetInAndDatabaseEntryInByCursor(Collection, Collection, Filters, Cursor, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
findByBioAssaySetInAndDatabaseEntryInByCursor(Collection, Collection, Filters, Cursor, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService: Cursor-paged counterpart to ExpressionAnalysisResultSetService.findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort).
findByBioAssaySetInAndDatabaseEntryInByCursor(Collection, Collection, Filters, Cursor, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Retrieve result sets associated to a set of BioAssaySet and external database entries.
findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
findByBioMaterial(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByBioMaterial(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByBioMaterial(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByBioMaterial(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByBioMaterial(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByBioMaterial(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByBioMaterial(BioMaterial, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByBioMaterial(BioMaterial, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByBioMaterial(BioMaterial, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByBioMaterial(BioMaterial, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByBioMaterial(BioMaterial, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByBioMaterial(BioMaterial, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByBioMaterials(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByBioMaterials(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByBioMaterials(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByBioMaterials(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByBioMaterials(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByBioMaterials(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByBioSequence(BioSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
findByBioSequence(BioSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByBioSequence(BioSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
findByBioSequence(BioSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findByBioSequence(BioSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByBioSequence(BioSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByBioSequence(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao: Find BLAT results for the given sequence
findByBioSequence(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl
findByBioSequence(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadService
findByBioSequence(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadServiceImpl
findByBioSequence(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService
findByBioSequence(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl
findByBioSequenceName(String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
findByBioSequenceName(String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByBioSequenceName(String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
findByBioSequenceName(String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findByBioSequenceName(String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByBioSequenceName(String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByCategory(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
findByCategory(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByCategoryLike(String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
findByCategoryLike(String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByCategoryStartingWith(String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findByCategoryStartingWith(String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByCategoryStartingWith(String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findByCategoryStartingWith(String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByCategoryUri(String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
findByCategoryUri(String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByCategoryUri(String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findByCategoryUri(String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByCategoryUri(String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findByCategoryUri(String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByCommonName(String) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonDao
findByCommonName(String) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
findByCommonName(String) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonReadService
findByCommonName(String) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonReadServiceImpl
findByCommonName(String) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
findByCommonName(String) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
findByCompositeSequence(CompositeSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
findByCompositeSequence(CompositeSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
findByCompositeSequence(CompositeSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService
findByCompositeSequence(CompositeSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl
findByCompositeSequence(CompositeSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
findByCompositeSequence(CompositeSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
findByCompositeSequenceName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
findByCompositeSequenceName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
findByCompositeSequenceName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
findByCompositeSequenceName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
findByCompositeSequenceName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
findByCompositeSequenceName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findByDesign(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByDesign(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByDesign(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByDesign(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByDesign(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByDesign(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByDesignId(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByDesignId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByDesignId(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByDesignId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByDesignId(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByDesignId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByEE(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao: All link rows attached to the given EE.
findByEE(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl
findByEEAndQt(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao: Look up the link row for (ee, qt), or null.
findByEEAndQt(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl
findByEmail(String) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
findByEmail(String) - Method in interface ubic.gemma.core.security.authentication.UserManager
findByEmail(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findByEmail(String) - Method in interface ubic.gemma.core.security.authentication.UserReadService
findByEmail(String) - Method in class ubic.gemma.core.security.authentication.UserReadServiceImpl
findByEmail(String) - Method in interface ubic.gemma.core.security.authentication.UserService
findByEmail(String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
findByEmail(String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.UserDao
findByEmail(String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
findByEnsemblId(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByEnsemblId(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByEnsemblId(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService: Searches for a gene based on its ensembl ID.
findByEnsemblId(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByEnsemblId(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
findByEnsemblId(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByExperiment(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
findByExperiment(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
findByExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDao
findByExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImpl
findByExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao
findByExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
findByExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService
findByExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
findByExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
findByExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
findByExperiment(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao: Find by associated ExpressionExperiment.
findByExperiment(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
findByExperiment(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
findByExperiment(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
findByExperiment(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
findByExperimentAnalyzed(Collection, boolean, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
findByExperimentAnalyzed(Collection, boolean, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
findByExperimentAnalyzed(Collection, boolean, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findByExperimentAnalyzed(Collection, boolean, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findByExperimentAnalyzed(Collection, boolean, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao: Given a list of experiments and a threshold value finds all the probes that met the cut-off in the given experiments
findByExperimentAnalyzed(Collection, boolean, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByExperimentAnalyzed(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao: Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().
findByExperimentAndAnalysisId(ExpressionExperiment, boolean, Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao: Find an analysis for the given experiment and identifier.
findByExperimentAndAnalysisId(ExpressionExperiment, boolean, Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
findByExperimentAndAnalysisId(ExpressionExperiment, boolean, Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
findByExperimentAndAnalysisId(ExpressionExperiment, boolean, Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
findByExperimentAndAnalysisId(ExpressionExperiment, boolean, Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
findByExperimentIds(Collection, boolean, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
findByExperimentIds(Collection, boolean, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
findByExperimentIds(Collection, boolean, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService: Given a set of ids, find experiments or subsets that have differential expression analyses.
findByExperimentIds(Collection, boolean, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
findByExperimentIds(Collection, boolean, Map, Map) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao: Retrieve analysis for the given experiment or experiment subset IDs.
findByExperiments(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
findByExperiments(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
findByExperiments(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao: Find by associated ExpressionExperiments.
findByExperiments(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
findByExperiments(Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
findByExperiments(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
findByExperiments(Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
findByExpressedGene(Gene, double) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByExpressedGene(Gene, double) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByExpressedGene(Gene, double) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByExpressedGene(Gene, double) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByExpressedGene(Gene, Double) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByExpressedGene(Gene, Double) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByExpressionExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Retrieve all the QTs associated with the given experiment.
findByExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
findByExpressionExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
findByExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
findByExpressionExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService: Find all the QT associated to the given experiment.
findByExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
findByExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
findByExpressionExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
findByExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
findByExpressionExperiment(ExpressionExperiment, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
findByExpressionExperiment(ExpressionExperiment, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
findByExpressionExperiment(ExpressionExperiment, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService: Find all the QT associated to the given experiment and data vector type.
findByExpressionExperiment(ExpressionExperiment, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
findByExpressionExperiment(ExpressionExperiment, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
findByExpressionExperiment(ExpressionExperiment, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
findByExpressionExperiment(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService: Union of QuantitationTypeReadService.findByExpressionExperiment(ExpressionExperiment, Class) across a collection of vector types.
findByExpressionExperiment(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
findByExpressionExperiment(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
findByExpressionExperiment(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Retrieve all the QTs associated with the given experiment and dimension.
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension, Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Retrieve all the QTs associated with the given experiment and dimension.
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension, Collection) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension, Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension, Collection) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension, Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
findByExpressionExperimentAndDimension(ExpressionExperiment, BioAssayDimension, Collection) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
findByExternalId(String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService: Get a reference by the unqualified external id.
findByExternalId(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
findByExternalId(String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService: Get a reference by the unqualified external id.
findByExternalId(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
findByExternalId(String, String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
findByExternalId(String, String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
findByExternalId(String, String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService: Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
findByExternalId(String, String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
findByExternalId(String, String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService: Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
findByExternalId(String, String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
findByExternalId(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao: Find by the external database id, such as for PubMed
findByExternalId(DatabaseEntry) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
findByExternalId(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
findByExternalId(DatabaseEntry) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
findByExternalId(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
findByExternalId(DatabaseEntry) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao: Retrieve analyses associated with the factor, either through the subset factor or as factors for result sets.
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByFactors(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
findByFactors(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByFactors(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByFactors(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByFactors(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByFactors(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByFactors(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByFactorValue(FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByFactorValue(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByFactorValue(FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByFactorValue(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByFactorValue(FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByFactorValue(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByFactorValueId(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByFactorValueId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByFactorValueId(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByFactorValueId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByFactorValueId(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByFactorValueId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByFactorValueIds(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByFactorValueIds(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByFactorValueIds(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByFactorValueIds(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByFactorValueIds(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByFactorValueIds(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByFactorValues(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByFactorValues(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByFactorValues(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByFactorValues(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByFactorValues(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByFactorValues(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByGene(Gene) - Method in interface ubic.gemma.core.search.GeneSetSearch
findByGene(Gene) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findByGene(Gene) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationReadService
findByGene(Gene) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findByGene(Gene) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByGene(Gene) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl: uses GENE2CS table.
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByGene(Gene) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByGene(Gene) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
findByGene(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
findByGene(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Return all sets that contain the given gene.
findByGene(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
findByGene(Gene, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Find composite sequences mapped to a given gene.
findByGene(Gene, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByGene(Gene, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
findByGene(Gene, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findByGene(Gene, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByGene(Gene, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByGene(Gene, boolean, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao: Find differential expression results for a given gene, grouped by experiment.
findByGene(Gene, boolean, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByGene(Gene, boolean, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
findByGene(Gene, boolean, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
findByGene(Gene, boolean, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findByGene(Gene, boolean, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findByGene(Gene, boolean, boolean, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao: Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
findByGene(Gene, boolean, boolean, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByGene(Gene, boolean, boolean, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
findByGene(Gene, boolean, boolean, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
findByGene(Gene, boolean, boolean, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findByGene(Gene, boolean, boolean, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findByGene(Gene, int, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Find a slice of composite sequences mapped to a given gene.
findByGene(Gene, int, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByGene(Gene, ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Find composite sequences mapped to a given gene, restricted to a given platform.
findByGene(Gene, ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByGene(Gene, ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
findByGene(Gene, ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findByGene(Gene, ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByGene(Gene, ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao: Find differential expression results for a given gene and set of experiments, grouped by experiment.
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao: Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByGeneAndExperimentAnalyzed(Gene, Collection, boolean, Map, Map, Map, double, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao: Retrieve differential expression results for a given gene across all the given datasets.
findByGeneAndExperimentAnalyzed(Gene, Collection, boolean, Map, Map, Map, double, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByGeneAndExperimentAnalyzedIds(Gene, boolean, boolean, Collection, boolean, Map, Map, Map, double, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
findByGeneAndExperimentAnalyzedIds(Gene, boolean, boolean, Collection, boolean, Map, Map, Map, double, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
findByGeneAndExperimentAnalyzedIds(Gene, boolean, boolean, Collection, boolean, Map, Map, Map, double, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findByGeneAndExperimentAnalyzedIds(Gene, boolean, boolean, Collection, boolean, Map, Map, Map, double, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findByGeneByCursor(Gene, Cursor, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Cursor-paged listing of CompositeSequences associated with a single Gene across all platforms — see CURSOR_PAGINATION_STEP1_PLAN.md step 1m.
findByGeneByCursor(Gene, Cursor, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByGenes(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findByGenes(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findByGenes(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationReadService
findByGenes(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl
findByGenes(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findByGenes(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findByGenes(Collection) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao: Returns matching biosequences for the given genes in a Map (gene to biosequences).
findByGenes(Collection) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
findByGenes(Collection) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService
findByGenes(Collection) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl
findByGenes(Collection) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
findByGenes(Collection) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
findByGenes(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Find composite sequences mapped to the given genes.
findByGenes(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByGenes(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
findByGenes(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findByGenes(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByGenes(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByGenes(Collection, ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Find composite sequences mapped to the given genes, restricted to a given platform.
findByGenes(Collection, ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByGenes(Collection, ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
findByGenes(Collection, ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findByGenes(Collection, ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByGenes(Collection, ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByGoId(String, Taxon) - Method in interface ubic.gemma.core.search.GeneSetSearch: Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.
findByGoId(String, Taxon) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
findByGoTermName(String, Taxon) - Method in interface ubic.gemma.core.search.GeneSetSearch: finds gene sets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
findByGoTermName(String, Taxon) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
findByGoTermName(String, Taxon, Integer, Integer) - Method in interface ubic.gemma.core.search.GeneSetSearch: finds genesets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
findByGoTermName(String, Taxon, Integer, Integer) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
findByGoTermUris(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findByGoTermUris(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findByGoTermUris(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findByGoTermUris(Collection, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findByGOTermUris(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationReadService: Find all the genes that match any of the terms.
findByGOTermUris(Collection, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl
findByGOTermUris(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService: Find all the genes that match any of the terms.
findByGOTermUris(Collection, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findByGoTermUrisPerTaxon(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findByGoTermUrisPerTaxon(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findByGOTermUrisPerTaxon(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationReadService: Find all genes associated with a given set of GO terms, grouped by taxon.
findByGOTermUrisPerTaxon(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl
findByGOTermUrisPerTaxon(Collection) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService: Find all genes associated with a given set of GO terms, grouped by taxon.
findByGOTermUrisPerTaxon(Collection) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findByInvestigation(Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDao: Every judgement on any set attached to one investigation, most recent first — the per-dataset triage view, without loading the sets.
findByInvestigation(Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDaoImpl
findByInvestigation(Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService: Every ruling on any set of one investigation, most recent first.
findByInvestigation(Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
findByInvestigation(Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDao: Every decision on one experiment, most recent first -- the full log, decisions since reversed included.
findByInvestigation(Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDaoImpl
findByInvestigation(Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionService: Every decision on one experiment, most recent first -- the full log.
findByInvestigation(Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionServiceImpl
findByInvestigation(Investigation, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: All sets attached to the given investigation, newest first.
findByInvestigation(Investigation, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
findByInvestigation(Investigation, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
findByInvestigation(Investigation, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
findByInvestigation(Investigation, PublicationAssociationStatus) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationDao: Every assertion attached to the investigation, accepted before rejected and stable thereafter by id.
findByInvestigation(Investigation, PublicationAssociationStatus) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationDaoImpl
findByInvestigation(Investigation, PublicationAssociationStatus) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationService: Every assertion attached to the investigation, accepted before rejected.
findByInvestigation(Investigation, PublicationAssociationStatus) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
findByInvestigationAndKey(Investigation, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDao: Every decision on one key, most recent first.
findByInvestigationAndKey(Investigation, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDaoImpl
findByInvestigationAndPublication(Investigation, BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationDao: The assertion held for this exact pair, or null if none.
findByInvestigationAndPublication(Investigation, BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationDaoImpl
findByInvestigationAndPublications(Investigation, Collection) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationDao: Assertions for the investigation whose publication is one of publications, in one query.
findByInvestigationAndPublications(Investigation, Collection) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationDaoImpl
findByInvestigationAndRoleAndRunId(Investigation, AnnotationSetRole, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: Find an existing row for the (investigation, role, runId) triple, or null.
findByInvestigationAndRoleAndRunId(Investigation, AnnotationSetRole, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
findByInvestigationAndRoleAndRunId(Investigation, AnnotationSetRole, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
findByInvestigationAndRoleAndRunId(Investigation, AnnotationSetRole, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
findByJob(PipelineJob, Date, int) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobEventDao: Events on the given job, ordered by occurredAt ascending.
findByJob(PipelineJob, Date, int) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobEventDaoImpl
findByManufacturer(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
findByManufacturer(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
findByManufacturer(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
findByManufacturer(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
findByManufacturer(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
findByManufacturer(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findByMeanVarianceRelation(MeanVarianceRelation) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByMeanVarianceRelation(MeanVarianceRelation) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByMeanVarianceRelation(MeanVarianceRelation) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByMeanVarianceRelation(MeanVarianceRelation) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByMeanVarianceRelation(MeanVarianceRelation) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByMeanVarianceRelation(MeanVarianceRelation) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByName(String) - Method in interface ubic.gemma.core.search.GeneSetSearch
findByName(String) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
findByName(String) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
findByName(String) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
findByName(String) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
findByName(String) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
findByName(String) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
findByName(String) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao
findByName(String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseDao
findByName(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseReadService
findByName(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseReadServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
findByName(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolDao
findByName(String) - Method in class ubic.gemma.persistence.service.common.protocol.ProtocolDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolReadService
findByName(String) - Method in class ubic.gemma.persistence.service.common.protocol.ProtocolReadServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolService
findByName(String) - Method in class ubic.gemma.persistence.service.common.protocol.ProtocolServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
findByName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
findByName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
findByName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
findByName(String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
findByName(String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByName(String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: security at DAO level
findByName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
findByName(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService
findByName(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
findByName(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
findByName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
findByName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
findByName(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
findByName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
findByName(String, Taxon) - Method in interface ubic.gemma.core.search.GeneSetSearch
findByName(String, Taxon) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductDao
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductReadService
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductReadServiceImpl
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
findByName(ArrayDesign, String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
findByName(ArrayDesign, String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByName(ArrayDesign, String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
findByName(ArrayDesign, String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findByName(ArrayDesign, String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByName(ArrayDesign, String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByName(ExpressionExperiment, String) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService: Find a QT by name in a given experiment, defaulting to RawExpressionDataVector.
findByName(ExpressionExperiment, String) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
findByName(ExpressionExperiment, String) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
findByName(ExpressionExperiment, String) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
findByNameAndVectorType(ExpressionExperiment, String, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Find a quantitation type by experiment, name and data vector type.
findByNameAndVectorType(ExpressionExperiment, String, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
findByNameAndVectorType(ExpressionExperiment, String, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
findByNameAndVectorType(ExpressionExperiment, String, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
findByNameAndVectorType(ExpressionExperiment, String, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
findByNameAndVectorType(ExpressionExperiment, String, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
findByNamesInArrayDesigns(Collection, Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService: Resolve composite sequence names against a collection of array designs, preserving insertion order and discarding names that don't match any sequence on any of the supplied platforms.
findByNamesInArrayDesigns(Collection, Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findByNamesInArrayDesigns(Collection, Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByNamesInArrayDesigns(Collection, Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl: Checks to see if the CompositeSequence exists in any of the array designs.
findByNameWithAuditTrail(String) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseDao
findByNameWithAuditTrail(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl
findByNameWithAuditTrail(String) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseReadService
findByNameWithAuditTrail(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseReadServiceImpl
findByNameWithAuditTrail(String) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
findByNameWithAuditTrail(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
findByNameWithExternalDatabases(String) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseReadService
findByNameWithExternalDatabases(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseReadServiceImpl
findByNameWithExternalDatabases(String) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
findByNameWithExternalDatabases(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
findByNcbiId(Integer) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
findByNcbiId(Integer) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByNcbiId(Integer) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonDao
findByNcbiId(Integer) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
findByNcbiId(Integer) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonReadService
findByNcbiId(Integer) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonReadServiceImpl
findByNcbiId(Integer) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
findByNcbiId(Integer) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
findByNcbiId(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductDao
findByNcbiId(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
findByNCBIId(Integer) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByNCBIId(Integer) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByNCBIId(Integer) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findByNCBIId(Integer) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByNcbiIds(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByNcbiIds(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByNcbiIds(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService: Quickly load exact matches.
findByNcbiIds(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByNcbiIds(Collection) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Quickly load exact matches.
findByNcbiIds(Collection) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByNCBIIdValueObject(Integer) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByNCBIIdValueObject(Integer) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByNCBIIdValueObject(Integer) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findByNCBIIdValueObject(Integer) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByObject(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findByObject(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByObject(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findByObject(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByObject(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.StatementDao
findByObject(String) - Method in class ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl
findByObjectLike(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.StatementDao
findByObjectLike(String) - Method in class ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl
findByObjectUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findByObjectUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByObjectUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findByObjectUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByObjectUri(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.StatementDao
findByObjectUri(String) - Method in class ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl
findByOfficialName(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByOfficialName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByOfficialName(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findByOfficialName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByOfficialName(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
findByOfficialName(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByOfficialNameInexact(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByOfficialNameInexact(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByOfficialNameInexact(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findByOfficialNameInexact(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByOfficialNameInexact(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
findByOfficialNameInexact(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByOfficialSymbol(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByOfficialSymbol(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByOfficialSymbol(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findByOfficialSymbol(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByOfficialSymbol(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
findByOfficialSymbol(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByOfficialSymbol(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByOfficialSymbol(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByOfficialSymbol(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findByOfficialSymbol(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByOfficialSymbol(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
findByOfficialSymbol(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByOfficialSymbolInexact(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByOfficialSymbolInexact(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByOfficialSymbolInexact(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findByOfficialSymbolInexact(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByOfficialSymbolInexact(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
findByOfficialSymbolInexact(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByOfficialSymbolInexact(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByOfficialSymbolInexact(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByOfficialSymbolInexact(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService: Taxon-pruned variant of GeneService.findByOfficialSymbolInexact(String).
findByOfficialSymbolInexact(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByOfficialSymbolInexact(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Taxon-scoped variant of GeneDao.findByOfficialSymbolInexact(String).
findByOfficialSymbolInexact(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByOfficialSymbols(Collection, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
findByOfficialSymbols(Collection, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
findByOfficialSymbols(Collection, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService: Quickly load exact matches.
findByOfficialSymbols(Collection, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findByOfficialSymbols(Collection, Long) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Quickly load exact matches.
findByOfficialSymbols(Collection, Long) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByOwner(Long, PipelineJobBatch.BatchState, int) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchDao: Batches submitted by the given curator, optionally filtered to a single batch state.
findByOwner(Long, PipelineJobBatch.BatchState, int) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchDaoImpl
findByOwner(Long, PipelineJobBatch.BatchState, int) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService
findByOwner(Long, PipelineJobBatch.BatchState, int) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl
findByParentClasses(Collection, boolean, String, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
findByParentClasses(Collection, boolean, String, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByParentClasses(Collection, boolean, String, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Find characteristics that have a particular parent class or lack thereof.
findByParentClasses(Collection, boolean, String, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByParentClasses(Collection, boolean, String, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Find characteristics that have a particular parent class or lack thereof.
findByParentClasses(Collection, boolean, String, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByPhysicalLocation(PhysicalLocation) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Deprecated.
findByPhysicalLocation(PhysicalLocation) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByPredicate(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findByPredicate(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByPredicate(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findByPredicate(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByPredicate(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.StatementDao
findByPredicate(String) - Method in class ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl
findByPredicateLike(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.StatementDao
findByPredicateLike(String) - Method in class ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl
findByPredicateUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findByPredicateUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByPredicateUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findByPredicateUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByPredicateUri(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.StatementDao
findByPredicateUri(String) - Method in class ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl
findByProperty(String, Object) - Method in class ubic.gemma.persistence.service.AbstractDao
findByPropertyIn(String, Collection) - Method in class ubic.gemma.persistence.service.AbstractDao
findByPublications(Investigation, Collection) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationService: Assertions for the investigation covering publications, in one query, keyed by publication id — the read path's way to decorate a dataset's publication list without a query per row.
findByPublications(Investigation, Collection) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
findByQuantitationType(QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByQuantitationType(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByQuantitationType(QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByQuantitationType(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByQuantitationType(QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByQuantitationType(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByResultSet(ExpressionAnalysisResultSet, double, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao
findByResultSet(ExpressionAnalysisResultSet, double, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByResultSet(ExpressionAnalysisResultSet, double, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
findByResultSet(ExpressionAnalysisResultSet, double, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
findByResultSet(ExpressionAnalysisResultSet, double, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findByResultSet(ExpressionAnalysisResultSet, double, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findBySchedulerHandle(SchedulerKind, String) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobDao: Look up a job by its scheduler-side handle.
findBySchedulerHandle(SchedulerKind, String) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobDaoImpl
findByScientificName(String) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonDao: Searches for a taxon by its scientific name, case insensitive.
findByScientificName(String) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
findByScientificName(String) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonReadService
findByScientificName(String) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonReadServiceImpl
findByScientificName(String) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
findByScientificName(String) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
findBySet(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDao: Every ruling on one set, most recent first — the full log, including rulings that have since been superseded.
findBySet(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDaoImpl
findBySet(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionService: Every ruling on one set, most recent first — the full log, superseded rulings included.
findBySet(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionServiceImpl
findBySet(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDao: Every judgement on one set, most recent first.
findBySet(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDaoImpl
findBySet(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService: Every ruling on one set, most recent first.
findBySet(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
findBySetAndJudge(AnnotationSet, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDao: The judgement judgedBy has standing on this set, or null.
findBySetAndJudge(AnnotationSet, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDaoImpl
findBySetAndTarget(AnnotationSet, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDao: Every ruling on one finding, most recent first.
findBySetAndTarget(AnnotationSet, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDaoImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
findByShortName(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
findByShortName(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByShortName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByShortNameAndThawLite(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByShortNameAndThawLite(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByShortNameAndThawLite(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByShortNameAndThawLite(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByShortNameWithPrimaryPublication(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByShortNameWithPrimaryPublication(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByShortNameWithPrimaryPublication(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByShortNameWithPrimaryPublication(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Find by the primary taxon.
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByUpdatedLimit(int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByUpdatedLimit(int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByUpdatedLimit(int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findByUpdatedLimit(int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findByUpdatedLimit(int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByUpdatedLimit(int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByUpdatedLimit(Collection, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByUpdatedLimit(Collection, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByUri(String, String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Find characteristics with the given URI.
findByUri(String, String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByUri(String, String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Looks for an exact match of the given string to a valueUri in the characteristic database.
findByUri(String, String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByUri(String, String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Looks for an exact match of the give string to a valueUri in the characteristic database
findByUri(String, String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByUriInAnySlot(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Find characteristics carrying the given URI in ANY slot: category, value, predicate, second predicate, object or second object.
findByUriInAnySlot(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByUriInAnySlot(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findByUriInAnySlot(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByUserName(String) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
findByUserName(String) - Method in interface ubic.gemma.core.security.authentication.UserManager
findByUserName(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findByUserName(String) - Method in interface ubic.gemma.core.security.authentication.UserReadService
findByUserName(String) - Method in class ubic.gemma.core.security.authentication.UserReadServiceImpl
findByUserName(String) - Method in interface ubic.gemma.core.security.authentication.UserService
findByUserName(String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
findByUserName(String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.UserDao
findByUserName(String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
findByValue(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
findByValue(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByValueLike(String, String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Finds all Characteristics whose value match the given search term
findByValueLike(String, String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByValueLike(String, String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Returns a collection of characteristics that have a value matching the given SQL LIKE pattern.
findByValueLike(String, String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByValueLike(String, String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Returns a collection of characteristics that have a value matching the given SQL LIKE pattern.
findByValueLike(String, String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByValueLikeGroupedByNormalizedValue(String, Collection, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Find characteristics by value matching the provided LIKE pattern.
findByValueLikeGroupedByNormalizedValue(String, Collection, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByValueStartingWith(String, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Deprecated.
findByValueStartingWith(String, int) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
findByValueStartingWith(String, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService: Deprecated.
because FactorValue.getValue() is deprecated
findByValueStartingWith(String, int) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
findByValueStartingWith(String, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Deprecated.
because FactorValue.getValue() is deprecated
findByValueStartingWith(String, int) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl: Deprecated.
findByValueStartingWith(String, String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Returns a collection of characteristics that have a value starting with the given string.
findByValueStartingWith(String, String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByValueStartingWith(String, String, Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Returns a collection of characteristics that have a value starting with the given string.
findByValueStartingWith(String, String, Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByValueUriGroupedByNormalizedValue(String, Collection, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Find characteristics by URI.
findByValueUriGroupedByNormalizedValue(String, Collection, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByValueUriOrValueStartingWith(String, Collection, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: Find characteristics that have a value (prefix) or value URI (exact match) matching the given string.
findByValueUriOrValueStartingWith(String, Collection, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findByValueUriOrValueStartingWith(String, Collection, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: Find characteristics that have a value (prefix) or value URI (exact match) matching the given string.
findByValueUriOrValueStartingWith(String, Collection, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findCategoryGroupedByCategoryUri(Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Find representative Characteristic.getCategory() labels grouped by Characteristic.getCategoryUri().
findCategoryGroupedByCategoryUri(Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findCategoryGroupedByCategoryUri(Collection, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findCategoryGroupedByCategoryUri(Collection, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findCenter(String, String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Find where the center of a query location is in a gene.
findChildren(ObjectIdentity) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
findChildren(AclObjectIdentity) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
findChildren(AclObjectIdentity) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
findClosestGene(String, Long, Long, String, int) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis: Given a location, find the nearest gene on the same strand, including only "known", "refseq" or "ensembl" transcripts.
findContrastsByAnalysisResultIds(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao: Find contrast results by analysis result IDs.
findContrastsByAnalysisResultIds(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl: Key method for getting contrasts associated with results.
findContrastsByAnalysisResultIds(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
findContrastsByAnalysisResultIds(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
findContrastsByAnalysisResultIds(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findContrastsByAnalysisResultIds(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findDetailMetaAnalysisById(long) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperService: Find meta-analysis by the given id.
findDetailMetaAnalysisById(long) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperServiceImpl
findDimensionByEEAndQt(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao: Look up the SingleCellDimension attached to the given (ee, qt) pair via the link table.
findDimensionByEEAndQt(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl
findEeCountsByUriForOriginalValue(Collection, String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: For each supplied value URI, count the distinct experiments on which a prior curator wrote originalValue as the submitter-facing string for that URI.
findEeCountsByUriForOriginalValue(Collection, String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findEeCountsByUriForOriginalValue(Collection, String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findEeCountsByUriForOriginalValue(Collection, String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findEeCountsByUriForOriginalValue(Collection, String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findEeCountsByUriForOriginalValue(Collection, String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findEeCountsByUriForOriginalValue(Collection, String, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: As CharacteristicDao.findEeCountsByUriForOriginalValue(Collection, String), ignoring the given experiments.
findEeCountsByUriForOriginalValue(Collection, String, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findEeCountsByUriForOriginalValue(Collection, String, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findEeCountsByUriForOriginalValue(Collection, String, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findEeCountsByUriForOriginalValue(Collection, String, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findEeCountsByUriForOriginalValue(Collection, String, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findEeCountsByUriGroupedByCategory(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: For each supplied value URI, return the distinct-experiment count grouped by the category the curator applied when tagging the URI on an experiment.
findEeCountsByUriGroupedByCategory(Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findEeCountsByUriGroupedByCategory(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findEeCountsByUriGroupedByCategory(Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findEeCountsByUriGroupedByCategory(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findEeCountsByUriGroupedByCategory(Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findEffectiveByInvestigationIds(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDao: The effective ruling for each of several INVESTIGATIONS, keyed by investigation id.
findEffectiveByInvestigationIds(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDaoImpl
findEffectiveBySetIds(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDao: The effective (most recent) judgement for each of annotationSetIds.
findEffectiveBySetIds(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDaoImpl
findESTs(String, Long, Long, String) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis: Check to see if there are ESTs that overlap with this region.
findEvents(Long, Date, int) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService: Events on the given job ordered by occurredAt ascending.
findEvents(Long, Date, int) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl
findEventsByCursor(Ticket, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Keyset-pagination counterpart to the Ticket.events collection on a single ticket — cursor mode for GET /tickets/{id}/events (step 1r of CURSOR_PAGINATION_STEP1_PLAN.md).
findEventsByCursor(Ticket, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findEventsByCursor(Ticket, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findEventsByCursor(Ticket, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findExperimentIdsByUriInAnySlot(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Ids of the experiments carrying the given URI in any slot, read from the EE2C denormalization.
findExperimentIdsByUriInAnySlot(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findExperimentIdsByUriInAnySlot(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findExperimentIdsByUriInAnySlot(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findExperimentReferencesByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Similar to CharacteristicDao.findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean), but returns proxies with instead of initializing all the EEs in bulk.
findExperimentReferencesByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl: Since proxies are returned, they cannot be collected in a HashSet which would otherwise cause their initialization by accessing Object.hashCode().
findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: This search looks at direct annotations, factor values and biomaterials in that order.
findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findExperimentsCharacteristicTags(String, int, boolean, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Deprecated.
findExperimentsCharacteristicTags(String, int, boolean, boolean, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl: Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list of possible choices
findExperimentsWithAnalyses(Gene) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao: Find experiments (or subsets) that have differential expression analyses for the given gene.
findExperimentsWithAnalyses(Gene) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
findExperimentsWithAnalyses(Gene) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
findExperimentsWithAnalyses(Gene) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
findExperimentsWithAnalyses(Gene) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
findExpressionExperimentByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService: Look up an existing ExpressionExperiment carrying the given accession.
findExpressionExperimentByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl
findGDSforGDS(String, String) - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombiner: Given a GEO dataset id, find all GDS ids that are associated with it.
findGDSforGSE(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.DatasetCombiner
findGDSforGSE(Collection, String) - Static method in class ubic.gemma.core.loader.expression.geo.DatasetCombiner: Given GEO series ids, find all associated data sets.
findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao: Retrieve differential expression results in bulk.
findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl
findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findGeneSetsByGene(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Given a Gemma Gene Id, find all the gene groups it is a member of (filtering is handled when gene sets are loaded)
findGeneSetsByGene(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
findGeneSetsByName(String, Long) - Method in interface ubic.gemma.core.search.GeneSetSearch: Similar to method of same name in GeneSetController.java but here: - no taxon needed - GO groups always searched - GeneSet objects returned instead of GeneSetValueObjects
findGeneSetsByName(String, Long) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
findGeneSetsByName(String, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
findGeneSetsByName(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
findGeneSetValueObjectByGoId(String, Long) - Method in interface ubic.gemma.core.search.GeneSetSearch: Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.
findGeneSetValueObjectByGoId(String, Long) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
findGOTerms(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
findGOTerms(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
findGroupAuthorities(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findGroupByName(String) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
findGroupByName(String) - Method in interface ubic.gemma.core.security.authentication.UserReadService
findGroupByName(String) - Method in class ubic.gemma.core.security.authentication.UserReadServiceImpl
findGroupByName(String) - Method in interface ubic.gemma.core.security.authentication.UserService
findGroupByName(String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
findGroupsForUser(String) - Method in interface ubic.gemma.core.security.authentication.GroupManager: Find all the group a user is in.
findGroupsForUser(String) - Method in interface ubic.gemma.core.security.authentication.UserManager
findGroupsForUser(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findGroupsForUser(User) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
findGroupsForUser(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
findGroupsForUser(User) - Method in interface ubic.gemma.core.security.authentication.UserReadService
findGroupsForUser(User) - Method in class ubic.gemma.core.security.authentication.UserReadServiceImpl
findGroupsForUser(User) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao
findGroupsForUser(User) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
findGSECorrespondence(Collection) - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombiner: Try to line up samples across datasets.
findGSECorrespondence(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.DatasetCombiner: Try to line up samples across datasets contained in a series.
findGSEforGDS(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.DatasetCombiner: Given a GDS, find the corresponding GSEs (there can be more than one in rare cases).
findIdByBioAssay(BioAssay, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findIdByBioAssay(BioAssay, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findIdByBioAssay(BioAssay, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findIdByBioAssay(BioAssay, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findIdByBioAssay(BioAssay, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findIdByBioAssay(BioAssay, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findIdByDesign(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findIdByDesign(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findIdByDesign(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findIdByDesign(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findIdByDesign(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findIdByDesign(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findIdByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findIdByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findIdByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findIdByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findIdByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findIdByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findIdByFactorValue(FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findIdByFactorValue(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findIdByFactorValue(FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findIdByFactorValue(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findIdByFactorValue(FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findIdByFactorValue(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findIdByMeanVarianceRelation(MeanVarianceRelation) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findIdByMeanVarianceRelation(MeanVarianceRelation) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findIdByMeanVarianceRelation(MeanVarianceRelation) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findIdByMeanVarianceRelation(MeanVarianceRelation) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findIdByMeanVarianceRelation(MeanVarianceRelation) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findIdByMeanVarianceRelation(MeanVarianceRelation) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findIdByProperty(String, Object) - Method in class ubic.gemma.persistence.service.AbstractDao
findIds(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: security at DAO level
findIds(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
findIdsByBioMaterial(BioMaterial, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findIdsByBioMaterial(BioMaterial, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findIdsByBioMaterial(BioMaterial, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findIdsByBioMaterial(BioMaterial, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findIdsByBioMaterial(BioMaterial, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findIdsByBioMaterial(BioMaterial, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findIdsByGeneIds(Collection, Long) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Composite-sequence ids on arrayDesignId that map to any of geneIds.
findIdsByGeneIds(Collection, Long) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findIdsByGeneIds(Collection, Long) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
findIdsByGeneIds(Collection, Long) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
findIdsByGeneIds(Collection, Long) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findIdsByGeneIds(Collection, Long) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findIncludedResultSetsInfoById(long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
findIncludedResultSetsInfoById(long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
findIncludedResultSetsInfoById(long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
findIncludedResultSetsInfoById(long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
findIndividuals(String, int) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Looks for any individuals that match the given search string.
findIndividuals(String, int, boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
findIndividuals(String, int, boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
findIndividuals(String, int, boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
findIndividuals(String, int, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Looks for any individuals that match the given search string.
FindingDisposition - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: A curator's ruling on ONE finding inside an audit.
findingId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionRequest: Which FINDING, when you have a stable id for one.
findingId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse: Null on a target-keyed row; see the request shape.
findKnownGenesByLocation(String, Long, Long, String) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis: Find "Known" genes contained in or overlapping a region.
findLatestByAccession(String) - Method in interface ubic.gemma.persistence.service.common.description.DatabaseEntryReadService: Find the latest (as per its version or ID) database entry by accession.
findLatestByAccession(String) - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryReadServiceImpl
findLatestByAccession(String) - Method in interface ubic.gemma.persistence.service.common.description.DatabaseEntryService: Find the latest (as per its version or ID) database entry by accession.
findLatestByAccession(String) - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryServiceImpl
findLatestByInvestigation(Investigation, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: The most recent set attached to the given investigation matching the role filter (or all roles if null), or null.
findLatestByInvestigation(Investigation, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
findLatestByInvestigation(Investigation, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
findLatestByInvestigation(Investigation, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
findLatestCreatedAt(AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao
findLatestCreatedAt(AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
findLatestCreatedAt(AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
findLatestCreatedAt(AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
findMetaAnalyses(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
findMetaAnalyses(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
findMetaAnalyses(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
findMetaAnalyses(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
FindObsoleteTermsCli - Class in ubic.gemma.apps: Deprecated.
superseded by GET /admin/ontologies/obsolete-terms, which answers the same question from a running application and additionally reports the replacement each ontology asserts.
This command exists only because a CLI has to load the ontologies itself — hence the load.ontologies=false precondition below and the warm-up loop. A running Gemma already holds them.
Two things the endpoint does not carry over. Its Count column is always 1: checkForObsolete increments the count but is only reached inside the checkedUris guard, so no term can be counted twice. And it walks every characteristic in the corpus to answer a question about distinct URIs — the endpoint groups CHARACTERISTIC by URI instead and asks each one once.
Scheduled for removal once the correction path lands; see docs/design/OBSOLETE_TERM_CORRECTION.md.
FindObsoleteTermsCli() - Constructor for class ubic.gemma.apps.FindObsoleteTermsCli: Deprecated.
findObsoleteTermsInUse(long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Report the obsolete terms Gemma's annotations still use, with the replacement each owning ontology asserts.
findObsoleteTermsInUse(long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
findObsoleteTermUsage(long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Locates usages of obsolete terms in Characteristics, ignoring Gene Ontology annotations.
findObsoleteTermUsage(long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
findOldestOpenCreatedAt() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao
findOldestOpenCreatedAt() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findOldestOpenCreatedAt() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findOldestOpenCreatedAt() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findOneByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findOneByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findOneByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findOneByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findOneByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findOneByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findOneByAlternateName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
findOneByAlternateName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
findOneByAlternateName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
findOneByAlternateName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
findOneByAlternateName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
findOneByAlternateName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findOneByName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
findOneByName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
findOneByName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
findOneByName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
findOneByName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
findOneByName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findOneByName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findOneByName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findOneByName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findOneByName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findOneByName(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findOneByName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findOneByProperty(String, Object) - Method in class ubic.gemma.persistence.service.AbstractDao
findOpenForTarget(TicketTargetType, Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Find all tickets that are not in a terminal state and target the given entity.
findOpenForTarget(TicketTargetType, Long) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findOpenForTarget(TicketTargetType, Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findOpenForTarget(TicketTargetType, Long) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findOpenForTargetByCursor(TicketTargetType, Long, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Keyset-pagination counterpart to TicketDao.findOpenForTarget(TicketTargetType, Long) — cursor mode for GET /datasets/{dataset}/tickets and the GET /platforms/{platform}/tickets sibling (step 1p of CURSOR_PAGINATION_STEP1_PLAN.md).
findOpenForTargetByCursor(TicketTargetType, Long, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findOpenForTargetByCursor(TicketTargetType, Long, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findOpenForTargetByCursor(TicketTargetType, Long, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findOpenSummariesForTargets(TicketTargetType, Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Bulk counterpart to TicketDao.findOpenForTarget(TicketTargetType, Long): the same open-ticket question asked about a whole page of targets in one query, keyed by target id.
findOpenSummariesForTargets(TicketTargetType, Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findOpenSummariesForTargets(TicketTargetType, Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findOpenSummariesForTargets(TicketTargetType, Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findOrCreate(C) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService
findOrCreate(Collection) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
findOrCreate(Collection) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
findOrCreate(O) - Method in class ubic.gemma.persistence.service.AbstractService
findOrCreate(O) - Method in interface ubic.gemma.persistence.service.BaseImmutableService
findOrCreate(O) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseImmutableService
findOrCreate(O) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService
findOrCreate(T) - Method in class ubic.gemma.persistence.service.AbstractDao
findOrCreate(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Calls the BaseDao.find(Identifiable) method, and if this method returns null, creates a new entity in the persistent storage pas per BaseDao.create(Identifiable).
findOrCreate(AclSid) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
findOrCreate(AclSid) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
findOrCreate(Gene2GOAssociation) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findOrCreate(Gene2GOAssociation) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findOrCreate(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
findOrCreate(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl: Find an existing BibliographicReference by its pubAccession, or create a new one.
findOrCreate(ExternalDatabase) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
findOrCreate(Unit) - Method in interface ubic.gemma.persistence.service.common.measurement.UnitDao
findOrCreate(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
findOrCreate(QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Find a QT as per QuantitationTypeDao.find(QuantitationType, Class) and if none is found, create a new one with QuantitationTypeDao.create(QuantitationType, Class).
findOrCreate(QuantitationType, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
findOrCreate(QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
findOrCreate(QuantitationType, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
findOrCreate(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
findOrCreate(Compound) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.CompoundService
findOrCreate(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findOrCreate(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDao
findOrCreate(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
findOrCreateByDoi(String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService: Resolve a DOI to a persistent BibliographicReference, fetching it when necessary.
findOrCreateByDoi(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
findOrCreateByPubMedId(String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService: Resolve a PubMed id to a persistent BibliographicReference, fetching it from PubMed and persisting it when it is not already in the system.
findOrCreateByPubMedId(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
findOrFail(C) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
findOrFail(O) - Method in class ubic.gemma.persistence.service.AbstractService
findOrFail(O) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Does a search for the entity in the persistent storage, raising a NullPointerException if not found.
findParseLineMethod(Object, String) - Static method in class ubic.gemma.core.loader.util.ParserAndLoaderTools
findPriorCurationByOriginalValue(String, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: For a value string, return the terms prior curators actually chose when they met it, most used first.
findPriorCurationByOriginalValue(String, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findPriorCurationByOriginalValue(String, int, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: As CharacteristicDao.findPriorCurationByOriginalValue(String, int), ignoring the given experiments.
findPriorCurationByOriginalValue(String, int, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findPriorCurationByOriginalValue(String, int, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findPriorCurationByOriginalValue(String, int, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findPriorCurationByOriginalValue(String, int, Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findPriorCurationByOriginalValue(String, int, Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findRefGenesByLocation(String, Long, Long, String) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis: Find RefSeq genes contained in or overlapping a region.
findRejections(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationService: Every rejection of this publication across all datasets: who ruled it out, where, and why.
findRejections(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
findRejectionsByPublication(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationDao: Every investigation-side rejection of this publication, across all datasets.
findRejectionsByPublication(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationDaoImpl
findRelatedTerms(Collection, Collection, AnnotationRelationDao.Direction, Set, Collection, Long, Collection, int, int) - Method in interface ubic.gemma.persistence.service.common.description.AnnotationRelationDao: Set membership: every term related to any of the seeds, with no counting, no ranking and no ambiguity to resolve.
findRelatedTerms(Collection, Collection, AnnotationRelationDao.Direction, Set, Collection, Long, Collection, int, int) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoImpl
findRelatedTermsForSearch(Collection, Collection, AnnotationRelationDao.Direction, Set, Long, Collection, int, int) - Method in interface ubic.gemma.persistence.service.common.description.AnnotationRelationService: Terms related to the seeds, for widening a query or testing membership.
findRelatedTermsForSearch(Collection, Collection, AnnotationRelationDao.Direction, Set, Long, Collection, int, int) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationServiceImpl
findRelations(AnnotationRelationDao.RelationQuery) - Method in interface ubic.gemma.persistence.service.common.description.AnnotationRelationDao: The ranked, evidenced read.
findRelations(AnnotationRelationDao.RelationQuery) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoImpl
findRelations(AnnotationRelationDao.RelationQuery) - Method in interface ubic.gemma.persistence.service.common.description.AnnotationRelationService: The ranked, evidenced read.
findRelations(AnnotationRelationDao.RelationQuery) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationServiceImpl
findRelationsForExperiment(ExpressionExperiment, AnnotationRelationDao.Direction, Set, int) - Method in interface ubic.gemma.persistence.service.common.description.AnnotationRelationService: What this experiment's own annotations imply, for display beside them.
findRelationsForExperiment(ExpressionExperiment, AnnotationRelationDao.Direction, Set, int) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationServiceImpl
findRepresentativeUsageByValueUris(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: For each supplied value URI, return one representative ACL-visible CharacteristicDao.UsageExample, or omit the URI when no accessible usage exists.
findRepresentativeUsageByValueUris(Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findRepresentativeUsageByValueUris(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService: For each value URI, return one representative ACL-visible usage, or omit URIs with no accessible usage.
findRepresentativeUsageByValueUris(Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findRepresentativeUsageByValueUris(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: For each value URI, return one representative ACL-visible usage (or omit it when none is accessible), so a search hit can be shown in the context it has actually been applied.
findRepresentativeUsageByValueUris(Collection) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findResources(String, int) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Looks for any resources (terms or individuals) that match the given search string
findResources(String, int, boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
findResources(String, int, boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
findResources(String, int, boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
findResources(String, int, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Looks for any resources (terms or individuals) that match the given search string
findResultsById(long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
findResultsById(long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
findResultsById(long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
findResultsById(long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
findRNAs(String, Long, Long, String) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis: Check to see if there are mRNAs that overlap with this region.
findScratchpad(Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Find the curator's scratchpad: the TicketType.SCRATCHPAD ticket they reported.
findScratchpad(Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findSearchHitById(Long, boolean, Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Look one ticket up by id and project it to a TicketSearchHitValueObject, honouring the same visibility rules as TicketDao.findSearchHitsByTitle(String, boolean, Long, int).
findSearchHitById(Long, boolean, Long) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findSearchHitsByTitle(String, boolean, Long, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Find tickets whose title contains titleFragment, case-insensitively, projected to TicketSearchHitValueObject and ordered by updatedAt descending.
findSearchHitsByTitle(String, boolean, Long, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findSequenceLocations(String) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis
findSiblings(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
findSiblings(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
findSiblings(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
findSiblings(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
findSiblings(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService: Find the siblings of a given biomaterial (other direct sub-materials of the same source).
findSiblings(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
findSiblings(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Find the siblings of a given biomaterial.
findSiblings(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
findStaleJobs(int, int) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService: For the reconciler: jobs in non-terminal state whose lastEventAt is older than staleMinutes.
findStaleJobs(int, int) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl
findStaleJobs(JobState, Date, int) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobDao: Jobs in state whose lastEventAt is older than staleSinceCutoff (typically now() − staleMinutes).
findStaleJobs(JobState, Date, int) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobDaoImpl
findStandingByInvestigation(Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDao: The standing decision under each key for one experiment.
findStandingByInvestigation(Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDaoImpl
findStandingBySet(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDao: The standing ruling for each finding in one set — the most recent row per finding id, or per target id for rows carrying no finding id.
findStandingBySet(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDaoImpl
findStandingBySetIds(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDao: Batched AnnotationSetDispositionDao.findStandingBySet(AnnotationSet), for a list view that would otherwise ask once per set.
findStandingBySetIds(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDaoImpl
findSubBioAssays(BioAssay, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
findSubBioAssays(BioAssay, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
findSubBioAssays(BioAssay, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
findSubBioAssays(BioAssay, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
findSubBioMaterials(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao: Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
findSubBioMaterials(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
findSubBioMaterials(BioMaterial, boolean) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao: Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
findSubBioMaterials(BioMaterial, boolean) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
findSubBioMaterials(BioMaterial, boolean) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService
findSubBioMaterials(BioMaterial, boolean) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
findSubBioMaterials(BioMaterial, boolean) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
findSubBioMaterials(BioMaterial, boolean) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
findSummariesByInvestigation(Investigation, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: Thin metadata projection of sets attached to the given investigation, newest first.
findSummariesByInvestigation(Investigation, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
findSummariesByInvestigation(Investigation, AnnotationSetRole) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: Thin metadata projection.
findSummariesByInvestigation(Investigation, AnnotationSetRole) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
findTerm(String, int) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
findTerm(String, int) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Looks for any terms that match the given search string.
findTerm(String, int, boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
findTerm(String, int, boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
findTerm(String, int, boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
findTerm(String, int, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Looks for any terms that match the given search string.
findTerms(String, int, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Given a search string will look through the loaded ontologies for terms that match the search term.
findTerms(String, int, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
findTermsInexact(String, int, Taxon, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Given a search string will first look through the characteristic database for any entries that have a match.
findTermsInexact(String, int, Taxon, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
findTickets(boolean, Long, TicketPriority, int, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Paged, filtered list query for the REST surface (Phase B-2).
findTickets(boolean, Long, TicketPriority, int, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findTickets(boolean, Long, TicketPriority, int, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findTickets(boolean, Long, TicketPriority, int, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, int, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Paged, filtered list query for the REST surface — extended filter set (queue-filter expansion).
findTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, int, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, int, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, int, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findTicketsByCursor(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Extended-filter cursor-mode counterpart to TicketDao.findTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, int, int).
findTicketsByCursor(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findTicketsByCursor(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findTicketsByCursor(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findTicketsByCursor(boolean, Long, TicketPriority, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao: Keyset-pagination counterpart to TicketDao.findTickets(boolean, Long, TicketPriority, int, int) — cursor mode for GET /tickets (step 1o of CURSOR_PAGINATION_STEP1_PLAN.md).
findTicketsByCursor(boolean, Long, TicketPriority, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
findTicketsByCursor(boolean, Long, TicketPriority, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
findTicketsByCursor(boolean, Long, TicketPriority, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
findUpdatedAfter(Date) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Find experiments updated on or after a given date.
findUpdatedAfter(Date) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findUpdatedAfter(Date) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
findUpdatedAfter(Date) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
findUpdatedAfter(Date) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findUpdatedAfter(Date) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findUsersInGroup(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findUsingAlternativeId(String) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
findUsingAlternativeId(String) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
findUsingAlternativeId(String) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
findUsingAlternativeId(String) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Find a term using an alternative ID.
findValueGroupedByValueUri(Collection, boolean, boolean, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Find characteristics Characteristic.getValue() grouped by Characteristic.getValueUri().
findValueGroupedByValueUri(Collection, boolean, boolean, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findValueGroupedByValueUri(Collection, boolean, boolean, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
findValueGroupedByValueUri(Collection, boolean, boolean, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
findValueGroupedByValueUri(Collection, boolean, boolean, boolean, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findValueGroupedByValueUri(Collection, boolean, boolean, boolean, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findVOByExternalId(String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService: Get a reference VO by the unqualified external id.
findVOByExternalId(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
findVOByExternalId(String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService: Get a reference by the unqualified external id.
findVOByExternalId(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
Fine - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdict: Looked at; there is nothing to do.
FINISHING - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
FIRST - Enum constant in enum class ubic.gemma.persistence.util.Sort.NullMode
FIRST - Enum constant in enum class ubic.gemma.rest.util.args.SortArg.Sort.NullMode
FIRST_QUARTILE_COMPARATOR - Static variable in class ubic.gemma.core.analysis.preprocess.OutlierDetails: Compare outliers by first quartile Note: this comparator imposes orderings that are inconsistent with equals
FishCompletionGenerator - Class in ubic.gemma.cli.completion: Generates fish completion script.
FishCompletionGenerator(String, Set, MessageSource, Locale) - Constructor for class ubic.gemma.cli.completion.FishCompletionGenerator
fisherCombineLogPvalues(DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: Fisher's method for combining p values (Cooper and Hedges 15-8)
fisherCombinePvalues(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: Fisher's method for combining p values.
fisherTransform(double) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Compute the Fisher z transform of the Pearson correlation.
fisherTransform(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Fisher-transform a list of Pearson correlations.
fisherTransformedSamplingVariance(double) - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis: Equation 18-8 from CH.
fisherTransformedSamplingVariances(DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis: Run equation CH 18-8 on a list of sample sizes.
Fit(double[], double[]) - Constructor for class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject.Fit
fitFDist(DoubleMatrix1D, DoubleMatrix1D) - Static method in class ubic.gemma.core.util.math.linearmodels.ModeratedTstat
fixOntologyTermLabels(boolean, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Check all system uses of ontology terms for the correct label and fix any mismatches based on the ontology OWL files.
fixOntologyTermLabels(boolean, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
FixOntologyTermLabelsCli - Class in ubic.gemma.apps
FixOntologyTermLabelsCli() - Constructor for class ubic.gemma.apps.FixOntologyTermLabelsCli
FL_CDNA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
flags() - Method in record class ubic.gemma.core.util.runtime.CpuInfo: Returns the value of the flags record component.
FLOAT - Enum constant in enum class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaFieldType
FLOAT - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
FLOAT - Enum constant in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType
floatArrayToBytes(float[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
floatArrayToBytes(float[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
FLUORESCENCE_ACTIVATED_CELL_SORTING - Static variable in class ubic.gemma.model.common.description.Values
flushCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
FOLDCHANGE - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Deprecated.
foldCodeRuns(String) - Static method in class ubic.gemma.core.ontology.search.OntologyAnalyzers: Visible for testing: applies the same folding the analyzer applies, so a test can assert on the normalised form directly rather than round-tripping through an index.
FOOTER - Static variable in class ubic.gemma.cli.util.HelpUtils
forCandidates(Collection) - Method in class ubic.gemma.core.loader.util.mapper.ChainedEntityMapper
forCandidates(Collection) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper: Create a stateful mapper for a set of candidates.
forCandidates(Collection) - Method in class ubic.gemma.core.loader.util.mapper.MapBasedEntityMapper
forCandidates(Collection) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
forCandidates(Collection) - Method in class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper
forCandidates(Collection) - Method in class ubic.gemma.core.loader.util.mapper.AbstractGeneIdentifierBasedDesignElementMapper
forCandidates(ArrayDesign) - Method in interface ubic.gemma.core.loader.util.mapper.DesignElementMapper: Create a mapper for the design elements of a given platform.
forCandidates(BioAssaySet) - Method in interface ubic.gemma.core.loader.util.mapper.BioAssayMapper
force - Variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher: Whether download is required even if the sizes match.
FORCE_OPTION - Static variable in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
forceRelease(Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService: Release whoever holds it.
forceRelease(Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl
forceRequired - Variable in class ubic.gemma.rest.util.args.DatasetArgService.DesignChangeResult
forceRequired(DesignPreflightReport) - Static method in class ubic.gemma.rest.util.args.DatasetArgService.DesignChangeResult
forCreation(AuditEvent) - Static method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject: Build a summary from the dataset's creation row, for a dataset that has never received a typed event.
forEvent(AuditEvent) - Static method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject: Build a summary from the dataset's most recent typed audit event.
forId(Long) - Static method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
forId(Long) - Static method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
formAclRestrictionClause(String) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Create an HQL restriction clause with the BasePermission.READ permission.
formAclRestrictionClause(String, Permission) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Create an HQL restriction clause that limits the result only to objects the current user can access.
formAclRestrictionPredicate(Session, CriteriaBuilder, CommonAbstractCriteria, Expression, Class, Permission) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: JPA Criteria counterpart of AclQueryUtils.formAclRestrictionClause(String, Permission), for DAOs that build their queries with CriteriaBuilder rather than HQL strings.
format(double) - Method in class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix
format(double) - Static method in class ubic.gemma.core.util.TsvUtils
format(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix
format(int) - Static method in class ubic.gemma.core.util.TsvUtils
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix: Format a matrix entry at a particular row/column.
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix: Format the value at the provided indices of the matrix.
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
format(int, int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
format(long) - Static method in class ubic.gemma.core.util.TsvUtils
format(Double) - Static method in class ubic.gemma.core.util.TsvUtils: Format a Double for TSV.
format(Integer) - Static method in class ubic.gemma.core.util.TsvUtils
format(Long) - Static method in class ubic.gemma.core.util.TsvUtils
format(Object) - Static method in class ubic.gemma.core.util.TsvUtils
format(String) - Static method in class ubic.gemma.core.util.TsvUtils: Format a String for TSV.
format(String[]) - Static method in class ubic.gemma.core.util.TsvUtils: Join multiple values into a single string, separated by the TsvUtils.SUB_DELIMITER.
format(Collection) - Static method in class ubic.gemma.core.util.TsvUtils
format(Date) - Static method in class ubic.gemma.core.util.TsvUtils
format(FileLockInfo) - Static method in class ubic.gemma.core.util.locking.FileLockInfoUtils
formatBioAssayFilename(BioAssay) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
formatComment(String) - Static method in class ubic.gemma.core.util.TsvUtils: Format a string as a TSV comment.
formatComment(String, Object...) - Static method in class ubic.gemma.core.util.TsvUtils
formatExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Render an experiment to string, with special handling in case of an uninitialized proxy.
formatFast(double) - Static method in class ubic.gemma.core.util.TsvUtils: Quickly format a double value.
formatFast(float) - Static method in class ubic.gemma.core.util.TsvUtils
formatFast(int) - Static method in class ubic.gemma.core.util.TsvUtils
formatFast(long) - Static method in class ubic.gemma.core.util.TsvUtils
formatInteraction(Set) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Format an interaction of factors.
formatMarkdownCodeSpan(String) - Static method in class ubic.gemma.core.util.MarkdownUtils: Format a string as a Markdown code span.
formatOption(String, String) - Static method in class ubic.gemma.cli.util.OptionsUtils
formatOption(Option) - Static method in class ubic.gemma.cli.util.OptionsUtils
formatOption(Options, String) - Static method in class ubic.gemma.cli.util.OptionsUtils: Format an option for display.
formatQuantitationType(QuantitationType, Class) - Static method in class ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils
formatRepresentation() - Method in class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix: Produce a string representation of the type of values held in the matrix.
formatRepresentation() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
formatStatement(Statement) - Static method in class ubic.gemma.model.expression.experiment.StatementUtils: Format a statement.
formatStatement(Statement, String[]) - Static method in class ubic.gemma.model.expression.experiment.StatementUtils: Format a statement.
formatStatement(StatementValueObject) - Static method in class ubic.gemma.model.expression.experiment.StatementUtils
formatter - Variable in class ubic.gemma.core.util.matrix.MatrixWriter
formFtpDirName(GeoRecordType) - Static method in class ubic.gemma.core.loader.expression.geo.service.GeoUtils: Form the FTP directory name for the given GEO record type.
formIsPubliclyReadableExpression(String) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: An HQL boolean expression that is true when the object is readable by an anonymous caller — that is, when it is PUBLIC.
formLocalFilePath(String, File) - Method in class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
formLocalFilePath(String, File) - Method in class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher
formLocalFilePath(String, File) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.GeoFetcher
formLocalFilePath(String, File) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
formLocalFilePath(String, File) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher
formLocalFilePath(String, File) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
formLocalFilePath(String, File) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonFetcher
formLocalFilePath(String, File) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
formLocalFilePath(String, File) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
formNativeAclRestrictionClause(SessionFactoryImplementor, String) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Native flavour of the ACL restriction clause with a BasePermission.READ permission.
formNativeAclRestrictionClause(SessionFactoryImplementor, String, String) - Static method in class ubic.gemma.persistence.util.EE2CAclQueryUtils
formNativeAclRestrictionClause(SessionFactoryImplementor, String, String, Permission) - Static method in class ubic.gemma.persistence.util.EE2CAclQueryUtils
formNativeAclRestrictionClause(SessionFactoryImplementor, String, Permission) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Native flavour of the ACL restriction clause.
formNativeNonTroubledClause(String, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: Form a native non-troubled clause.
formNonTroubledClause(String, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: Form a non-troubled clause.
formOrderByClause(Sort) - Static method in class ubic.gemma.persistence.util.FilterQueryUtils: Forms an order by clause for a Hibernate query based on given arguments.
formProperty(PropertyMapping) - Static method in class ubic.gemma.persistence.util.PropertyMappingUtils: Form a property suitable for a Criteria or HQL query.
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.DatasetFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.PlatformFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.SeriesFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
formRemoteFilePath(String) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
formRestrictionClause(CriteriaBuilder, CommonAbstractCriteria, Root, Filters) - Static method in class ubic.gemma.persistence.util.FilterJpaUtils: Build a JPA Predicate from a Filters (a conjunction of disjunctions).
formRestrictionClause(CriteriaBuilder, CommonAbstractCriteria, Root, Filters, Map) - Static method in class ubic.gemma.persistence.util.FilterJpaUtils: Variant of FilterJpaUtils.formRestrictionClause(CriteriaBuilder, CommonAbstractCriteria, Root, Filters) that honours a registered objectAlias → dotted-prefix map so alias-prefixed paths (e.g.
formRestrictionClause(CriteriaBuilder, Root, Filters) - Static method in class ubic.gemma.persistence.util.FilterJpaUtils: Deprecated.
prefer FilterJpaUtils.formRestrictionClause(CriteriaBuilder, CommonAbstractCriteria, Root, Filters) so inSubquery filters can resolve.
formRestrictionClause(Filters) - Static method in class ubic.gemma.persistence.util.FilterQueryUtils: Creates a CNF restriction clause from the given Filters list.
formShortenedFtpDirName(String) - Static method in class ubic.gemma.core.loader.expression.geo.service.GeoUtils: Form the shortened FTP directory name for a given GEO accession.
forName(String) - Static method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
forName(String) - Static method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
forNcbiId(Integer) - Static method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
FORWARD - Enum constant in enum class ubic.gemma.persistence.util.Cursor.Direction
fractionDistinctValuesNonNA(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.Stats: Compute the fraction of values which are distinct.
FREE_TEXT - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Special indicator for free-text terms.
FREE_TEXT - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Special indicator for free-text terms.
FREE_TEXT_NOT_HOOKED - Enum constant in enum class ubic.gemma.core.ontology.TermViolation.Reason: A free-text experiment tag that hangs off nothing: no statement on it carries both a predicate and a grounded object, so the annotation is attached to the ontology at no point.
FreeTextExpressionExperimentResultsValueObject - Class in ubic.gemma.model.expression.experiment
FreeTextExpressionExperimentResultsValueObject() - Constructor for class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject: default constructor to satisfy java bean contract
FreeTextExpressionExperimentResultsValueObject(String, String, Long, String, Collection, String) - Constructor for class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject: Method to create a display object from scratch
FreeTextGeneResultsValueObject - Class in ubic.gemma.model.genome.gene: *
FreeTextGeneResultsValueObject() - Constructor for class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject: default constructor to satisfy java bean contract
FreeTextGeneResultsValueObject(String, String, Long, String, Collection, String) - Constructor for class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject: Method to create a display object from scratch
from(int, int, DatasetsWebService.PcLoadingDirection, Map, SVDResult, Function) - Static method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject
from(Class, long, double, Map, Object) - Static method in class ubic.gemma.model.common.search.SearchResult: Create a new provisional search result with a result type and ID.
from(Class, T, double, Map, Object) - Static method in class ubic.gemma.model.common.search.SearchResult: Create a search result from a given identifiable entity.
from(BuildInfo) - Static method in class ubic.gemma.rest.util.BuildInfoValueObject
from(Ticket) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: Project the ticket WITHOUT its event log (cheap, for list views).
from(TicketEvent) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
from(Ticket, boolean) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: Project the ticket; include events iff includeEvents.
from(TicketTarget) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
from(User) - Static method in class ubic.gemma.rest.GroupsWebService.GroupMemberValueObject
from(UserGroup) - Static method in class ubic.gemma.rest.GroupsWebService.GroupSummaryValueObject
from(UserGroup) - Static method in class ubic.gemma.rest.GroupsWebService.GroupValueObject
from(UserGroup) - Static method in class ubic.gemma.rest.GroupsWebService.GroupWithMembersValueObject
fromAccession(String, String) - Static method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
FromArrayDesignValueObject() - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject.FromArrayDesignValueObject
fromBaseUrl(String) - Method in class ubic.gemma.persistence.util.EntityUrlBuilder: Obtain an EntityUrlBuilder.EntityUrlChooser for generating a URL relative to a base URL.
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetRole: Parse the lowercase external form back into the enum.
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSource: Parse the lowercase external form back into the enum.
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionScope: Parse the external form, accepting either case.
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionType: Parse the external form, accepting either case.
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.FindingDisposition: Parse the external form, accepting either case and the snake_case and kebab-case spellings other producers emit (needs_more_info, needs-more-info).
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageJudgeKind
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdict: Parse the external form, accepting either case and the snake_case and kebab-case spellings other producers emit (wont_fix, might-fix).
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.description.PublicationAssociationRole: Parse the lowercase external form back into the enum.
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.description.PublicationAssociationSource: Parse the lowercase external form back into the enum.
fromDbValue(String) - Static method in enum class ubic.gemma.model.common.description.PublicationAssociationStatus: Parse the lowercase external form back into the enum.
fromDbValue(String) - Static method in enum class ubic.gemma.model.expression.experiment.AgentCurationKind: Parse the lowercase external form back into the enum.
fromDesignElements(ExpressionExperiment, BioAssayDimension, Slice, List) - Static method in class ubic.gemma.core.visualization.ExpressionDataHeatmap: Create a heatmap for a given set of design elements.
fromDesignElements(ExpressionExperimentSubSet, BioAssayDimension, Slice, List) - Static method in class ubic.gemma.core.visualization.ExpressionDataHeatmap: Create a heatmap for a subset using design elements.
fromEntities(Collection) - Static method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
fromEntity(Collection) - Static method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
fromEntity(BlacklistedEntity) - Static method in class ubic.gemma.model.blacklist.BlacklistedValueObject
fromEntity(CompositeSequence) - Static method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
fromEntity(BioSequence) - Static method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
fromEntity(Taxon) - Static method in class ubic.gemma.model.genome.TaxonValueObject
fromEnv() - Static method in class ubic.gemma.cli.pipeline.PipelineJobReporter: Resolve a reporter from the process environment.
fromExactIdentifier(Class, T, double, Map, Object) - Static method in class ubic.gemma.model.common.search.SearchResult: Same as SearchResult.from(Class, Identifiable, double, Map, Object), but flags the result as an exact identifier match.
fromGeoString(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy: Resolve GEO's spelling, case-insensitively.
fromHostUrl() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder: Obtain an EntityUrlBuilder.EntityUrlChooser for generating a URL relative to the host URL.
fromList(DoubleArrayList) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil: Makes a copy
fromManifest() - Static method in class ubic.gemma.core.util.BuildInfo: Retrieve build information directly from the manifest of gemma-core.
fromRow(Object[]) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject: Project one row of the /tickets/search HQL projection.
fromRVFM(RepetitiveValuesFilter.Mode) - Static method in enum class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode
fromSource(OntologyService) - Static method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex: Invert an ontology's cross-references, read from its SOURCE artifact rather than the model it happens to have loaded.
fromVectors(ExpressionExperiment, BioAssayDimension, Slice, List) - Static method in class ubic.gemma.core.visualization.ExpressionDataHeatmap: Create a heatmap for a given set of vectors.
fromVectors(ExpressionExperimentSubSet, BioAssayDimension, Slice, List) - Static method in class ubic.gemma.core.visualization.ExpressionDataHeatmap: Create a heatmap for a subset.
FTP - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSource
FTP_VIA_HTTPS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSource
FtpArchiveFetcher - Class in ubic.gemma.core.loader.util.fetcher: Fetcher that can fetch archives (e.g., tar.gz) and unpack them.
FtpArchiveFetcher() - Constructor for class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
ftpClient - Variable in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
FTPClientAuthenticator - Interface in ubic.gemma.core.loader.util.ftp
ftpClientFactory() - Method in class ubic.gemma.core.loader.util.ftp.FTPConfig
FTPClientFactory - Interface in ubic.gemma.core.loader.util.ftp: Factory and pool for FTPClient.
FTPClientFactoryImpl - Class in ubic.gemma.core.loader.util.ftp: This implementation maintains one pool of FTP clients per URL authority (i.e URL.getAuthority()).
FTPClientFactoryImpl() - Constructor for class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
FTPConfig - Class in ubic.gemma.core.loader.util.ftp
FTPConfig() - Constructor for class ubic.gemma.core.loader.util.ftp.FTPConfig
ftpDownloadFile(FTPClient, String, File, boolean) - Static method in class ubic.gemma.core.util.NetUtils: Download a file via FTP, skipping if a complete local copy already exists.
ftpDownloadFile(FTPClient, String, String, boolean) - Static method in class ubic.gemma.core.util.NetUtils: Download a file via FTP to the given local path.
FtpFetcher - Class in ubic.gemma.core.loader.util.fetcher: Download files by FTP.
FtpFetcher() - Constructor for class ubic.gemma.core.loader.util.fetcher.FtpFetcher
ftpFileSize(FTPClient, String) - Static method in class ubic.gemma.core.util.NetUtils: Get the size of a remote file.
full - Enum constant in enum class ubic.gemma.rest.DatasetsWebService.CorrelationMatrixChoice
FULL - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoAmount: Add all data tables.
FULL - Enum constant in enum class ubic.gemma.core.ontology.providers.OntologyService.InferenceMode: Complete inference.
FULL - Enum constant in enum class ubic.gemma.core.ontology.providers.OntologyService.LanguageLevel: The full OWL language.
FutureUtils - Class in ubic.gemma.core.util.concurrent
FutureUtils() - Constructor for class ubic.gemma.core.util.concurrent.FutureUtils

G

G - Enum constant in enum class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
GBS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
GE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
GE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
GE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
Geeq - Class in ubic.gemma.model.expression.experiment: Represents quality information about a data set.
Geeq() - Constructor for class ubic.gemma.model.expression.experiment.Geeq
GeeqAdminValueObject - Class in ubic.gemma.model.expression.experiment: Represents administrative geeq information.
GeeqAdminValueObject() - Constructor for class ubic.gemma.model.expression.experiment.GeeqAdminValueObject: Required when using the class as a spring bean
GeeqAdminValueObject(Geeq) - Constructor for class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
GeeqAuditService - Interface in ubic.gemma.persistence.service.expression.experiment: Co-bean carrying the GeeqEvent emission that GeeqServiceImpl.calculateScore(ExpressionExperiment, GeeqService.ScoreMode) records at the end of each scoring run.
GeeqAuditServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of GeeqAuditService: a thin co-bean that exists so GeeqAuditServiceImpl.recordGeeqScoring(ExpressionExperiment, String, String) is invoked through a Spring proxy and the Audited aspect can intercept its return path and emit the GeeqEvent.
GeeqAuditServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.GeeqAuditServiceImpl
GeeqCli - Class in ubic.gemma.apps: Generate or update GEEQ scores
GeeqCli() - Constructor for class ubic.gemma.apps.GeeqCli
GeeqDao - Interface in ubic.gemma.persistence.service.expression.experiment
GeeqDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
GeeqDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.GeeqDaoImpl
GeeqEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
GeeqEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.GeeqEvent
GeeqRecomputeRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.GeeqRecomputeRequest
GeeqService - Interface in ubic.gemma.persistence.service.expression.experiment
GeeqService.ScoreMode - Enum Class in ubic.gemma.persistence.service.expression.experiment: Modes for filling GEEQ scores.
GeeqServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
GeeqServiceImpl(GeeqDao, ExpressionExperimentService, ExpressionExperimentBatchInformationService, OutlierDetectionService, GeeqAuditService, SampleCoexpressionAnalysisService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
GeeqTask - Interface in ubic.gemma.core.tasks.analysis.expression
GeeqTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression: Async-task wrapper around GeeqService.calculateScore(ExpressionExperiment, GeeqService.ScoreMode).
GeeqTaskCommand(ExpressionExperiment, GeeqService.ScoreMode) - Constructor for class ubic.gemma.core.tasks.analysis.expression.GeeqTaskCommand
GeeqTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression
GeeqTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.GeeqTaskImpl
GeeqValueObject - Class in ubic.gemma.model.expression.experiment: Represents publicly available geeq information
GeeqValueObject() - Constructor for class ubic.gemma.model.expression.experiment.GeeqValueObject: Required when using the class as a spring bean
GeeqValueObject(Geeq) - Constructor for class ubic.gemma.model.expression.experiment.GeeqValueObject
GEMMA_CITATION_NOTICE - Static variable in class ubic.gemma.core.util.Constants: Citation notice to include in every data files we generate.
GEMMA_CLI_EXE - Static variable in class ubic.gemma.cli.main.GemmaCLI: Name of the Gemma CLI executable.
GEMMA_COPYRIGHT_NOTICE - Static variable in class ubic.gemma.core.util.Constants
GEMMA_INTAKE - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSource
GEMMA_LICENSE_NOTICE - Static variable in class ubic.gemma.core.util.Constants: Notice to include in all generated files.
GEMMA_PAINT_SCALE - Static variable in interface ubic.gemma.core.visualization.Heatmap: Borrowed from Heatmap.js
GemmaAclConfiguration - Class in ubic.gemma.core.security.acl: Spring-native ACL stack, replacing gsec's Hibernate-backed AclServiceImpl/AclDaoImpl.
GemmaAclConfiguration() - Constructor for class ubic.gemma.core.security.acl.GemmaAclConfiguration
gemmaAfterAclMyDataRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig: Gemma-owned replacement for gsec's afterAclMyDataRead.
gemmaAfterAclMyPrivateDataRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig: Gemma-owned replacement for gsec's afterAclMyPrivateDataRead.
gemmaAfterAclReadQuiet(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig: Gemma-owned replacement for gsec's afterAclReadQuiet.
gemmaAfterAclStreamRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig: Gemma-owned replacement for gsec's afterAclStreamRead.
gemmaAfterAclValueObjectCollectionRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig: Gemma-owned replacement for gsec's afterAclValueObjectCollection.
gemmaAfterAclValueObjectMapRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig: Gemma-owned replacement for gsec's afterAclValueObjectMap.
gemmaAfterAclValueObjectRead(AclService, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy) - Method in class ubic.gemma.core.security.SecurityConfig: Gemma-owned replacement for gsec's afterAclValueObject.
GemmaCLI - Class in ubic.gemma.cli.main: Generic command line for Gemma.
GemmaCLI() - Constructor for class ubic.gemma.cli.main.GemmaCLI
GemmaLegacyAwarePasswordEncoder - Class in ubic.gemma.core.security.authentication: Spring Security 6 PasswordEncoder that understands three formats: Legacy SHA-1 + username-as-salt: stored as a bare 40-char hex digest with no prefix, computed as SHA-1(rawPassword + "{" + username + "}") (the exact output of Spring Security 3/4's ShaPasswordEncoder configured with ReflectionSaltSource(userPropertyToUse="username") — see Gemma's pre-Phase-2 applicationContext-security.xml).
GemmaLegacyAwarePasswordEncoder() - Constructor for class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder
GemmaLegacyAwarePasswordEncoder(BCryptPasswordEncoder) - Constructor for class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder
gemmaOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
GemmaOntologyService - Class in ubic.gemma.core.ontology.providers: Ontology created for Gemma.
GemmaOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.GemmaOntologyService
gemmaRestApiClient(String) - Method in class ubic.gemma.cli.config.GemmaRestApiClientConfig
GemmaRestApiClient - Interface in ubic.gemma.core.util: A minimalist client for accessing Gemma's RESTful API.
GemmaRestApiClient.DataResponse - Interface in ubic.gemma.core.util
GemmaRestApiClient.EmptyResponse - Interface in ubic.gemma.core.util: For endpoints that return no data (i.e.
GemmaRestApiClient.ErrorResponse - Interface in ubic.gemma.core.util: For endpoints that may return an error.
GemmaRestApiClient.ErrorResponse.Error - Interface in ubic.gemma.core.util
GemmaRestApiClient.Response - Interface in ubic.gemma.core.util: A response from the API, which is either a GemmaRestApiClient.DataResponse or GemmaRestApiClient.ErrorResponse.
GemmaRestApiClientAuthenticator - Class in ubic.gemma.cli.authentication
GemmaRestApiClientAuthenticator(GemmaRestApiClient) - Constructor for class ubic.gemma.cli.authentication.GemmaRestApiClientAuthenticator
GemmaRestApiClientConfig - Class in ubic.gemma.cli.config
GemmaRestApiClientConfig() - Constructor for class ubic.gemma.cli.config.GemmaRestApiClientConfig
GemmaRestApiClientException - Exception Class in ubic.gemma.core.util
GemmaRestApiClientException(String, Throwable) - Constructor for exception class ubic.gemma.core.util.GemmaRestApiClientException
GemmaRestApiClientImpl - Class in ubic.gemma.core.util
GemmaRestApiClientImpl(String) - Constructor for class ubic.gemma.core.util.GemmaRestApiClientImpl
GemmaRestApiClientImpl(String, ObjectMapper) - Constructor for class ubic.gemma.core.util.GemmaRestApiClientImpl
GemmaRestOnly - Annotation Interface in ubic.gemma.model.annotations: Indicate that a property or type is only visible not visible outside of Gemma REST.
GemmaSessionBackedValueObject - Interface in ubic.gemma.model.common
GENBANK - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
GenBankUtils - Class in ubic.gemma.core.loader.util: Provides convenience methods for GenBank.
GenBankUtils() - Constructor for class ubic.gemma.core.loader.util.GenBankUtils
gender - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
Gene - Class in ubic.gemma.model.genome: Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Gene() - Constructor for class ubic.gemma.model.genome.Gene: No-arg constructor added to satisfy javabean contract
GENE - Enum constant in enum class ubic.gemma.core.visualization.SingleCellSparsityHeatmap.SingleCellHeatmapType
GENE - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
GENE_EXPRESSION_ASSAYS - Static variable in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils: List of all known gene expression assays from CELLxGENE.
Gene.Factory - Class in ubic.gemma.model.genome
GENE2CS - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
GENE2CS_BATCH_SIZE - Static variable in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Recommended batch size to use when retrieving entries from the GENE2CS table either by gene or design element.
GENE2CS_QUERY_SPACE - Static variable in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Query space used by the GENE2CS table.
Gene2CsStatus - Class in ubic.gemma.persistence.service.maintenance: Used to store information about what happened when the GENE2CS table was updated.
Gene2CsStatus() - Constructor for class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
gene2CsUpdateTrigger(TableMaintenanceUtil, SecurityContext) - Method in class ubic.gemma.core.config.SchedulerConfig: Every day at 00:40.
Gene2GeneAssociation - Class in ubic.gemma.model.association: Entity representing a relationship between two genes.
Gene2GeneAssociation() - Constructor for class ubic.gemma.model.association.Gene2GeneAssociation
Gene2GOAssociation - Class in ubic.gemma.model.association
Gene2GOAssociation() - Constructor for class ubic.gemma.model.association.Gene2GOAssociation
Gene2GOAssociation.Factory - Class in ubic.gemma.model.association
Gene2GOAssociationDao - Interface in ubic.gemma.persistence.service.association
Gene2GOAssociationDaoImpl - Class in ubic.gemma.persistence.service.association
Gene2GOAssociationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
Gene2GOAssociationReadService - Interface in ubic.gemma.persistence.service.association: Read-only retrieval service for Gene2GOAssociation.
Gene2GOAssociationReadServiceImpl - Class in ubic.gemma.persistence.service.association: Implementation of Gene2GOAssociationReadService.
Gene2GOAssociationReadServiceImpl(Gene2GOAssociationDao, CacheManager) - Constructor for class ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl
Gene2GOAssociationService - Interface in ubic.gemma.persistence.service.association
Gene2GOAssociationServiceImpl - Class in ubic.gemma.persistence.service.association
Gene2GOAssociationServiceImpl(Gene2GOAssociationDao, Gene2GOAssociationReadService) - Constructor for class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
GeneAlias - Class in ubic.gemma.model.genome.gene: Hibernate Search 7 mapping: contributes its GeneAlias.getAlias() as a keyword (non-tokenized) field via @IndexedEmbedded from Gene.
GeneAlias() - Constructor for class ubic.gemma.model.genome.gene.GeneAlias
GeneAlias.Factory - Class in ubic.gemma.model.genome.gene
GeneAliasDao - Interface in ubic.gemma.persistence.service.genome.gene
GeneAliasDaoImpl - Class in ubic.gemma.persistence.service.genome.gene: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.gene.GeneAlias.
GeneAliasDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneAliasDaoImpl
GeneArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for Gene API.
GeneArg(String, Class, T) - Constructor for class ubic.gemma.rest.util.args.GeneArg
GeneArgService - Class in ubic.gemma.rest.util.args
GeneArgService(GeneService, GeneOntologyService, CompositeSequenceService) - Constructor for class ubic.gemma.rest.util.args.GeneArgService
GeneArrayArg - Class in ubic.gemma.rest.util.args
GeneDao - Interface in ubic.gemma.persistence.service.genome
GeneDaoImpl - Class in ubic.gemma.persistence.service.genome: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type Gene.
GeneDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.GeneDaoImpl
GeneDifferentialExpressionGroupValueObject(BioAssaySetValueObject, List) - Constructor for class ubic.gemma.rest.GeneWebService.GeneDifferentialExpressionGroupValueObject
GeneDifferentialExpressionMetaAnalysis - Class in ubic.gemma.model.analysis.expression.diff: Represents an analysis that combines the results of other analyses of differential expression.
GeneDifferentialExpressionMetaAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
GeneDifferentialExpressionMetaAnalysis.Factory - Class in ubic.gemma.model.analysis.expression.diff
GeneDifferentialExpressionMetaAnalysisDetailValueObject - Class in ubic.gemma.model.analysis.expression.diff
GeneDifferentialExpressionMetaAnalysisDetailValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
GeneDifferentialExpressionMetaAnalysisResult - Class in ubic.gemma.model.analysis.expression.diff
GeneDifferentialExpressionMetaAnalysisResult() - Constructor for class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
GeneDifferentialExpressionMetaAnalysisResult.Factory - Class in ubic.gemma.model.analysis.expression.diff
GeneDifferentialExpressionMetaAnalysisResultValueObject - Class in ubic.gemma.model.analysis.expression.diff
GeneDifferentialExpressionMetaAnalysisResultValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
GeneDifferentialExpressionMetaAnalysisSummaryValueObject - Class in ubic.gemma.model.analysis.expression.diff
GeneDifferentialExpressionMetaAnalysisSummaryValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
GeneDifferentialExpressionService - Interface in ubic.gemma.core.analysis.expression.diff
GeneDifferentialExpressionServiceImpl - Class in ubic.gemma.core.analysis.expression.diff: Provides access to DifferentialExpressionAnalysisResults and meta-analysis results.
GeneDifferentialExpressionServiceImpl(DifferentialExpressionResultService) - Constructor for class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
GeneDiffExMetaAnalysisDao - Interface in ubic.gemma.persistence.service.analysis.expression.diff
GeneDiffExMetaAnalysisDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
GeneDiffExMetaAnalysisDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
GeneDiffExMetaAnalysisHelperService - Interface in ubic.gemma.core.analysis.expression.diff
GeneDiffExMetaAnalysisHelperServiceImpl - Class in ubic.gemma.core.analysis.expression.diff: * @author frances
GeneDiffExMetaAnalysisHelperServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperServiceImpl
GeneDiffExMetaAnalysisService - Interface in ubic.gemma.persistence.service.analysis.expression.diff
GeneDiffExMetaAnalysisServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
GeneDiffExMetaAnalysisServiceImpl(GeneDiffExMetaAnalysisDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
GeneDiffExStats(Double, Double, Double) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneDiffExStats
GeneElementExpressionsValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
GeneElementExpressionsValueObject(String, Integer, List, boolean, String) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
GeneElementExpressionsValueObject(String, String, Integer, String, Double, Double, Double, List, boolean, String) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
GeneEnsemblIdArg - Class in ubic.gemma.rest.util.args: Long argument type for Gene API, referencing the Gene Ensembl ID.
geneExpressionArraybased - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
geneExpressionMPSSBased - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
geneExpressionRTPCRbased - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
geneExpressionSAGEbased - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
GENELIST - Enum constant in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType: Indicates that this "platform" is just a list of genes (we use this for RNA-seq)
GeneMappingSummary - Class in ubic.gemma.model.analysis.sequence: This is a convenience value object to hold a BlatResult and its associated gene products and genes.
GeneMappingSummary() - Constructor for class ubic.gemma.model.analysis.sequence.GeneMappingSummary
GeneMappingSummaryValueObject - Class in ubic.gemma.model.analysis.sequence: One probe-to-gene mapping, as it goes over the wire: a single alignment plus the genes it supports.
GeneMappingSummaryValueObject() - Constructor for class ubic.gemma.model.analysis.sequence.GeneMappingSummaryValueObject
GeneMappingSummaryValueObject(BlatResultValueObject, List) - Constructor for class ubic.gemma.model.analysis.sequence.GeneMappingSummaryValueObject
GeneMultifunctionalityPopulationService - Interface in ubic.gemma.core.analysis.service: Populate/update the gene multifunctionality information in the system.
GeneMultifunctionalityPopulationServiceImpl - Class in ubic.gemma.core.analysis.service: Compute gene multifunctionality and store it in the database.
GeneMultifunctionalityPopulationServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceImpl
GeneNameDesignElementMapper - Class in ubic.gemma.core.loader.util.mapper
GeneNameDesignElementMapper(Map) - Constructor for class ubic.gemma.core.loader.util.mapper.GeneNameDesignElementMapper
GeneNcbiIdArg - Class in ubic.gemma.rest.util.args: Long argument type for Gene API, referencing the Gene NCBI ID.
GeneOntologySearchSource - Class in ubic.gemma.core.search.source: GO-based search source.
GeneOntologySearchSource() - Constructor for class ubic.gemma.core.search.source.GeneOntologySearchSource
GeneOntologyService - Interface in ubic.gemma.core.ontology.providers
GeneOntologyServiceImpl - Class in ubic.gemma.core.ontology.providers: Gene Ontology
GeneOntologyServiceImpl(String, boolean) - Constructor for class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
GeneOntologyServiceImpl.GOAspect - Enum Class in ubic.gemma.core.ontology.providers
GeneOntologyTermValueObject - Class in ubic.gemma.model.genome
GeneOntologyTermValueObject() - Constructor for class ubic.gemma.model.genome.GeneOntologyTermValueObject
GeneOntologyTermValueObject(String, OntologyTerm) - Constructor for class ubic.gemma.model.genome.GeneOntologyTermValueObject
GeneOntologyUtils - Class in ubic.gemma.core.ontology.providers
GeneOntologyUtils() - Constructor for class ubic.gemma.core.ontology.providers.GeneOntologyUtils
GENEPIX_DATETIME_HEADER_REGEXP - Static variable in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
GeneProduct - Class in ubic.gemma.model.genome.gene: Hibernate Search 7 mapping: contributes name (tokenized), ncbiGi (keyword), and its accessions (via @IndexedEmbedded -> DatabaseEntry.accession) up to Gene's document via the Gene.getProducts() embedded path.
GeneProduct() - Constructor for class ubic.gemma.model.genome.gene.GeneProduct
GeneProduct.Factory - Class in ubic.gemma.model.genome.gene
GeneProductDao - Interface in ubic.gemma.persistence.service.genome.gene
GeneProductDaoImpl - Class in ubic.gemma.persistence.service.genome.gene
GeneProductDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
GeneProductReadService - Interface in ubic.gemma.persistence.service.genome.gene: Read-only retrieval service for GeneProduct.
GeneProductReadServiceImpl - Class in ubic.gemma.persistence.service.genome.gene: Implementation of GeneProductReadService.
GeneProductReadServiceImpl(GeneProductDao) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneProductReadServiceImpl
GeneProductService - Interface in ubic.gemma.persistence.service.genome.gene
GeneProductServiceImpl - Class in ubic.gemma.persistence.service.genome.gene
GeneProductServiceImpl(AnnotationAssociationDao, BioSequenceDao, BlatAssociationDao, GeneProductDao) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
GeneProductValueObject - Class in ubic.gemma.model.genome.gene
GeneProductValueObject() - Constructor for class ubic.gemma.model.genome.gene.GeneProductValueObject: Required when using the class as a spring bean.
GeneProductValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.GeneProductValueObject
GeneProductValueObject(GeneProduct) - Constructor for class ubic.gemma.model.genome.gene.GeneProductValueObject: Populates the VO properties with values from the given entity.
GeneralType - Enum Class in ubic.gemma.model.common.quantitationtype
generate(String) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
generate(String) - Method in interface ubic.gemma.core.loader.util.sdo.SourceDomainObjectGenerator: Combines the necessary data fetching and parsing steps to get a collection of source domain objects.
generate(Collection) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator: Main method to generate a map of biomartEnsembleNcbiIds, involves optional fetch from biomart if no file is provided then returns results of parse method.
generate(BlockingQueue) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
generateAllArrayDesignReport() - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
generateAllArrayDesignReport() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
generateAnnotationFile(Writer, Collection, Boolean) - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService: Generate an annotation for a list of genes, instead of probes.
generateAnnotationFile(Writer, Collection, Boolean) - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
generateArrayDesignReport() - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService: Generate reports for all array designs, as well as the "global" report.
generateArrayDesignReport() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
generateArrayDesignReport(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
generateArrayDesignReport(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
generateArrayDesignReport(ArrayDesignValueObject) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
generateArrayDesignReport(ArrayDesignValueObject) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
generateBeanName(BeanDefinition, BeanDefinitionRegistry) - Method in class ubic.gemma.core.context.BeanNameGenerator: Automatically produce camel-case names for the beans.
generateCompleteCommand(CompletionType, String...) - Static method in class ubic.gemma.cli.completion.CompletionUtils: Generate a complete command suitable for EnumeratedByCommandConverter.
generateCompletion(Options, PrintWriter) - Method in class ubic.gemma.cli.completion.BashCompletionGenerator
generateCompletion(Options, PrintWriter) - Method in interface ubic.gemma.cli.completion.CompletionGenerator: Generate completion for the given options.
generateCompletion(Options, PrintWriter) - Method in class ubic.gemma.cli.completion.FishCompletionGenerator
generateCompletion(Options, PrintWriter) - Method in class ubic.gemma.cli.completion.WikiCompletionGenerator
generatedAt - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta
GenerateDatabaseUpdateCli - Class in ubic.gemma.apps: Generate a database update script.
GenerateDatabaseUpdateCli() - Constructor for class ubic.gemma.apps.GenerateDatabaseUpdateCli
generateGeneralPage(SortedMap, Options) - Method in class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator
generateLocal(String, String, String, String, BlockingQueue) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
generateRemote(Collection) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
generateSeriesMetadataOnly(String) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator: Fetch and parse only the METADATA of a series: its own record plus its sample records, with no data tables and no platform record.
generateSignupToken(String) - Method in interface ubic.gemma.core.security.authentication.UserDetailsManager: Generate a token that can be used to check if the user's email is valid.
generateSignupToken(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in class ubic.gemma.cli.completion.BashCompletionGenerator
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in interface ubic.gemma.cli.completion.CompletionGenerator: Generate completions for the given subcommand.
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in class ubic.gemma.cli.completion.FishCompletionGenerator
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in class ubic.gemma.cli.completion.WikiCompletionGenerator
generateSubcommandPage(String, Options, String, boolean) - Method in class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator
generateSummary(Long) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: Generate a value object that contain summary information about links, biomaterials, and datavectors
generateSummary(Long) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
generateSummaryObjects() - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: Generates reports on ALL experiments, including 'private' ones.
generateSummaryObjects() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
GeneReadService - Interface in ubic.gemma.persistence.service.genome.gene: Read-only retrieval service for Gene.
GeneReadServiceImpl - Class in ubic.gemma.persistence.service.genome.gene: Implementation of GeneReadService.
GeneReadServiceImpl(GeneDao) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
GeneRef() - Constructor for class ubic.gemma.rest.HeatmapDataValueObject.GeneRef
GeneRef(Long, String, String, Integer) - Constructor for class ubic.gemma.rest.HeatmapDataValueObject.GeneRef
GeneReferenceValueObject - Class in ubic.gemma.model.genome.gene: Compact gene identity — just enough to label a row and link to the gene page.
GeneReferenceValueObject() - Constructor for class ubic.gemma.model.genome.gene.GeneReferenceValueObject
GeneReferenceValueObject(Long, String, Integer) - Constructor for class ubic.gemma.model.genome.gene.GeneReferenceValueObject: Creates a new GeneReferenceValueObject instance.
GENERIC - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: Catch-all for tickets that don't fit a more specific category.
GenericAnovaResult - Interface in ubic.gemma.core.util.math.linearmodels
GenericCellLevelCharacteristics - Class in ubic.gemma.model.expression.bioAssayData: Generic cell-level characteristics.
GenericCellLevelCharacteristics() - Constructor for class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
GenericCuratableDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Service that simplifies operation with curatable entities of unknown types.
GenericCuratableDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation
GenericCuratableDaoImpl() - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDaoImpl
GenericExecutorMetrics - Class in ubic.gemma.core.metrics.binder: A meter binder that delegates to the appropriate Executor implementation.
GenericExecutorMetrics(Executor, String) - Constructor for class ubic.gemma.core.metrics.binder.GenericExecutorMetrics
GenericGenelistDesignGenerator - Class in ubic.gemma.apps: Create (or update) an array design based on a list of NCBI gene IDs desired to be on the platform.
GenericGenelistDesignGenerator() - Constructor for class ubic.gemma.apps.GenericGenelistDesignGenerator
GENERICLM - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.AnalysisType
GenericMetadataSingleCellDataLoader - Class in ubic.gemma.core.loader.expression.singleCell.metadata: A generic loader that can be used to load single-cell data with a tabular metadata file.
GenericMetadataSingleCellDataLoader(SingleCellDataLoader, Path, Path, List, List, List) - Constructor for class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
GenericMetadataSingleCellDataLoaderConfigurer - Class in ubic.gemma.core.loader.expression.singleCell
GenericMetadataSingleCellDataLoaderConfigurer(SingleCellDataLoaderConfigurer, BioAssayMapper) - Constructor for class ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderConfigurer
genericMeterRegistryConfigurer(MeterRegistry, SessionFactory, DataSource, TaskExecutor, TaskRunningService, List) - Method in class ubic.gemma.core.config.MetricsConfig: Aggregate all the MeterBinders the legacy XML registered (basic JVM metrics, logging metrics, two Hibernate session-factory binders, one Hikari pool binder, one task-executor binder) plus the TaskRunningService bean (which itself implements MeterBinder).
GenericMeterRegistryConfigurer - Class in ubic.gemma.core.metrics: Attach all the given MeterBinder to the registry.
GenericMeterRegistryConfigurer(MeterRegistry, List) - Constructor for class ubic.gemma.core.metrics.GenericMeterRegistryConfigurer
GenericOntologyService - Class in ubic.gemma.core.ontology.providers: A way to create ad-hoc in-memory ontology services.
GenericOntologyService(String, String) - Constructor for class ubic.gemma.core.ontology.providers.GenericOntologyService
GenericOntologyService(String, String, String) - Constructor for class ubic.gemma.core.ontology.providers.GenericOntologyService
GenericScanFileDateExtractor - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Looks through text file looking for a date near the top of the file in a reasonable format.
GenericScanFileDateExtractor() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractor
GenericTaskExecutorMetrics - Class in ubic.gemma.core.metrics.binder: A meter binder that delegates to the appropriate TaskExecutor implementation.
GenericTaskExecutorMetrics(TaskExecutor) - Constructor for class ubic.gemma.core.metrics.binder.GenericTaskExecutorMetrics
geneSearch(String, Taxon) - Static method in class ubic.gemma.model.common.search.SearchSettings: Convenience method to get pre-configured settings.
GeneSearchService - Interface in ubic.gemma.persistence.service.genome.gene: Service for searching genes (and gene sets)
GeneSearchServiceImpl - Class in ubic.gemma.persistence.service.genome.gene: Service for searching genes (and gene sets)
GeneSearchServiceImpl() - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
GeneSearchServiceImpl(SearchService, SecurityService, TaxonService, GeneSetSearch, GeneSetService, GeneSetReadService, GeneService, GeneOntologyService, GeneSetValueObjectHelper) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
GeneService - Interface in ubic.gemma.persistence.service.genome.gene
GeneServiceImpl - Class in ubic.gemma.persistence.service.genome.gene
GeneServiceImpl(GeneDao, GeneReadService) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
GeneSet - Class in ubic.gemma.model.genome.gene: A grouping of genes that share a common relationship.
GeneSet() - Constructor for class ubic.gemma.model.genome.gene.GeneSet
GeneSet.Factory - Class in ubic.gemma.model.genome.gene
GeneSetDao - Interface in ubic.gemma.persistence.service.genome.gene: The interface for managing groupings of genes.
GeneSetDaoImpl - Class in ubic.gemma.persistence.service.genome.gene: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.gene.GeneSet.
GeneSetDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
GeneSetMember - Class in ubic.gemma.model.genome.gene: Hibernate Search 7 mapping: contributes its referenced Gene via @IndexedEmbedded from GeneSet.
GeneSetMember() - Constructor for class ubic.gemma.model.genome.gene.GeneSetMember
GeneSetMember.Factory - Class in ubic.gemma.model.genome.gene
GeneSetMemberDaoImpl - Class in ubic.gemma.persistence.service.genome.gene
GeneSetMemberDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSetMemberDaoImpl
GeneSetReadService - Interface in ubic.gemma.persistence.service.genome.gene: Read-only retrieval service for GeneSet.
GeneSetReadServiceImpl - Class in ubic.gemma.persistence.service.genome.gene: Implementation of GeneSetReadService.
GeneSetReadServiceImpl(GeneSetDao, GeneService) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
GeneSetSearch - Interface in ubic.gemma.core.search
GeneSetSearchImpl - Class in ubic.gemma.core.search
GeneSetSearchImpl() - Constructor for class ubic.gemma.core.search.GeneSetSearchImpl
GeneSetService - Interface in ubic.gemma.persistence.service.genome.gene: Service for managing gene sets
GeneSetServiceImpl - Class in ubic.gemma.persistence.service.genome.gene: Service for managing gene sets
GeneSetServiceImpl(GeneSetDao) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
GeneSetValueObject - Class in ubic.gemma.model.genome.gene: Represents a Gene group gene set
GeneSetValueObject() - Constructor for class ubic.gemma.model.genome.gene.GeneSetValueObject: default constructor to satisfy java bean contract
GeneSetValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.GeneSetValueObject: Create a lightweight wrapper that can be used for security filtering
GeneSetValueObject(GeneSet, Taxon, Long) - Constructor for class ubic.gemma.model.genome.gene.GeneSetValueObject
GeneSetValueObjectHelper - Interface in ubic.gemma.persistence.service.genome.gene: * @author tvrossum
GeneSetValueObjectHelperImpl - Class in ubic.gemma.persistence.service.genome.gene: This class will handle population of GeneSetValueObjects.
GeneSetValueObjectHelperImpl() - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
GeneSymbolArg - Class in ubic.gemma.rest.util.args: String argument type for Gene API.
GeneValueObject - Class in ubic.gemma.model.genome.gene
GeneValueObject() - Constructor for class ubic.gemma.model.genome.gene.GeneValueObject: Required when using the class as a spring bean.
GeneValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.GeneValueObject
GeneValueObject(Long, String, String, Taxon) - Constructor for class ubic.gemma.model.genome.gene.GeneValueObject
GeneValueObject(Gene) - Constructor for class ubic.gemma.model.genome.gene.GeneValueObject
GeneValueObject(GeneValueObject) - Constructor for class ubic.gemma.model.genome.gene.GeneValueObject: Copies constructor from other GeneValueObject
GeneValueObject(Gene, boolean) - Constructor for class ubic.gemma.model.genome.gene.GeneValueObject
GeneWebService - Class in ubic.gemma.rest: RESTful interface for genes.
GeneWebService() - Constructor for class ubic.gemma.rest.GeneWebService
GeneWebService.CompositeSequenceSummaryValueObject - Class in ubic.gemma.rest: Enriched per-probe row returned by GeneWebService.getGeneProbes(GeneArg, OffsetArg, LimitArg, CursorArg, boolean) when summary=true.
GeneWebService.GeneDifferentialExpressionGroupValueObject - Class in ubic.gemma.rest: One experiment's DEA results for the requested gene.
GeneWriteService - Interface in ubic.gemma.persistence.service.genome.gene: Gene write-side business logic lifted out of GenomePersister as part of the Phase 3 persisterHelper retirement (Chunk 5.3 PREP).
GeneWriteServiceImpl - Class in ubic.gemma.persistence.service.genome.gene: Implementation of GeneWriteService.
GeneWriteServiceImpl() - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl
GENOME - Enum constant in enum class ubic.gemma.model.common.description.DatabaseType: Represents a genome database such as Golden Path or Ensembl
GENOME_BINDING_PROFILING_BY_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
GENOME_BINDING_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
GENOME_BINDING_PROFILING_BY_SNP_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
GENOME_BINDING_PROFILING_BY_TILING_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
GENOME_VARIATION_PROFILING_BY_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
GENOME_VARIATION_PROFILING_BY_GENOME_TILING_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
GenomePersister - Class in ubic.gemma.persistence.persister: Persister-shrink S2b: lifted out of the CommonPersister inheritance chain into a concrete @Component.
GenomePersister() - Constructor for class ubic.gemma.persistence.persister.GenomePersister
genomic - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
GENOMIC - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoLibrarySource
GENOMIC - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType
genomicDNA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
genomicDNA - Enum constant in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule
GENOTYPE - Static variable in class ubic.gemma.model.common.description.Categories
genotypeOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
GenotypeOntologyService - Class in ubic.gemma.core.ontology.providers: Genotype Ontology (GENO) — zygosity, alleles and genotype structure.
GenotypeOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.GenotypeOntologyService
genotypeOrVariation - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
GEO - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
GEO_ACCESSION - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
GEO_CEL_FILE_NAME_REGEX - Static variable in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize: Look for patterns like GSM476194_SK_09-BALBcJ_622.CEL or GSM289913.CEL.gz or GSM1525415_C1.cel.gz and not GSM12343.EXP.gz
GEO_SCRAPE_WATERMARK - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetType: A GeoScrapeWatermark row.
GEO_SUBMITTER_LINK - Enum constant in enum class ubic.gemma.model.common.description.PublicationAssociationSource: GEO's !Series_pubmed_id, as written by the submitter and carried through GeoConverterImpl.convertPubMedIds.
geoAccession - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
GeoAmount - Enum Class in ubic.gemma.core.loader.expression.geo.service: Amounts of data that can be retrieved from GEO.
GeoBioAssayMapper - Class in ubic.gemma.core.loader.expression.geo.singleCell: Strategy to match a BioAssay against a sample name provided by GEO.
GeoBioAssayMapper() - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.GeoBioAssayMapper
GeoBrowser - Interface in ubic.gemma.core.loader.expression.geo.service: Gets records from GEO and compares them to Gemma.
GeoBrowserImpl - Class in ubic.gemma.core.loader.expression.geo.service
GeoBrowserImpl(String) - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl
GeoChannel - Class in ubic.gemma.core.loader.expression.geo.model: Represents data for one channel on a microarray in GEO.
GeoChannel() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoChannel
GeoChannel.ChannelMolecule - Enum Class in ubic.gemma.core.loader.expression.geo.model
GeoCharacteristicKey - Class in ubic.gemma.core.loader.expression.geo: Where a GEO "key: value" characteristic actually divides.
GeoConstants - Class in ubic.gemma.core.loader.expression.geo.util: Constants used to help decipher GEO data files.
GeoConstants() - Constructor for class ubic.gemma.core.loader.expression.geo.util.GeoConstants
GeoContact - Class in ubic.gemma.core.loader.expression.geo.model
GeoContact() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoContact
GeoConverter - Interface in ubic.gemma.core.loader.expression.geo
GeoConverterImpl - Class in ubic.gemma.core.loader.expression.geo: Convert GEO domain objects into Gemma objects.
GeoConverterImpl() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
GeoData - Class in ubic.gemma.core.loader.expression.geo.model: Abstract class from which other GEO objects are descended.
GeoData() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoData
GeoDataset - Class in ubic.gemma.core.loader.expression.geo.model: A GEO-curated dataset.
GeoDataset() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoDataset
GeoDataset.ExperimentType - Enum Class in ubic.gemma.core.loader.expression.geo.model
GeoDataset.PlatformType - Enum Class in ubic.gemma.core.loader.expression.geo.model
GeoDataset.SampleType - Enum Class in ubic.gemma.core.loader.expression.geo.model
GeoDataset.ValueType - Enum Class in ubic.gemma.core.loader.expression.geo.model
GeoDomainObjectGenerator - Class in ubic.gemma.core.loader.expression.geo: Handle fetching and parsing GEO files.
GeoDomainObjectGenerator() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
GeoDomainObjectGenerator(DatasetFetcher, SeriesFetcher, Fetcher) - Constructor for class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
GeoDomainObjectGeneratorLocal - Class in ubic.gemma.core.loader.expression.geo: GEO object generator that works on local files.
GeoDomainObjectGeneratorLocal(String) - Constructor for class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal
GeoFamilyParser - Class in ubic.gemma.core.loader.expression.geo: Class for parsing GSE and GDS files from NCBI GEO.
GeoFamilyParser() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoFamilyParser
GeoFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher
GeoFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher2
GeoFetcher() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.GeoFetcher
GeoFetcher(SimpleRetryPolicy, Path) - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher2.GeoFetcher
GeoFormat - Enum Class in ubic.gemma.core.loader.expression.geo.service
GeoGrabberCli - Class in ubic.gemma.apps: Scans GEO for experiments that are not in Gemma, subject to some filtering criteria, outputs to a file for further screening.
GeoGrabberCli() - Constructor for class ubic.gemma.apps.GeoGrabberCli
GeoGrabRequest() - Constructor for class ubic.gemma.rest.AdminWebService.GeoGrabRequest
GeoGrabResponse() - Constructor for class ubic.gemma.rest.AdminWebService.GeoGrabResponse
GeoLibrarySource - Enum Class in ubic.gemma.core.loader.expression.geo
GeoLibraryStrategy - Enum Class in ubic.gemma.core.loader.expression.geo.model: SRA's library_strategy controlled vocabulary, as GEO reports it in !Sample_library_strategy.
geometricMean(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the geometric mean of a data sequence.
GeoMexSingleCellDataLoaderConfigurer - Class in ubic.gemma.core.loader.expression.geo.singleCell
GeoMexSingleCellDataLoaderConfigurer(Path, GeoSeries, SingleCellDataTransformationFactory) - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurer
GeoParseResult - Class in ubic.gemma.core.loader.expression.geo: This simply holds the results obtained from parsing.
GeoParseResult() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoParseResult
GeoPlatform - Class in ubic.gemma.core.loader.expression.geo.model: Bean describing a microarray platform in GEO
GeoPlatform() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
GeoQuery - Class in ubic.gemma.core.loader.expression.geo.service: Represents a GEO query.
GeoQuery(GeoRecordType, String, String, int) - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoQuery
GeoRecord - Class in ubic.gemma.core.loader.expression.geo.model: Used to contain GEO summary information from the 'Browse' views.
GeoRecord() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoRecord
GeoRecordMatcher - Interface in ubic.gemma.core.geoscrape: Pluggable predicate over a GeoRecord for the GEO scrape & preboard pipeline.
GeoRecordMatcher.MatchResult - Class in ubic.gemma.core.geoscrape: Outcome of a single matcher's evaluation.
GeoRecordType - Enum Class in ubic.gemma.core.loader.expression.geo.service: Type of records that can be browsed in GEO.
GeoRecordValueObject() - Constructor for class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
GeoReplication - Class in ubic.gemma.core.loader.expression.geo.model: Represents a group of samples that were replicated.
GeoReplication() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoReplication
GeoReplication.ReplicationType - Enum Class in ubic.gemma.core.loader.expression.geo.model: Permitted types of replication.
GeoRetrieveConfig - Class in ubic.gemma.core.loader.expression.geo.service: Configuration to use to retrieve GEO records from a GeoQuery.
GeoRetrieveConfig.GeoRetrieveConfigBuilder - Class in ubic.gemma.core.loader.expression.geo.service
GeoSample - Class in ubic.gemma.core.loader.expression.geo.model: Represents a sample (GSM) in GEO.
GeoSample() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoSample
GeoSampleCorrespondence - Class in ubic.gemma.core.loader.expression.geo: Holds information about GEO samples that "go together" across datasets (GDS), because they came from the same sample (or so we infer)
GeoSampleCorrespondence() - Constructor for class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
GeoSampleType - Enum Class in ubic.gemma.core.loader.expression.geo
GeoScope - Enum Class in ubic.gemma.core.loader.expression.geo.service: Scope of data that can be retrieved from GEO.
GeoScrapeDryRunCandidate - Class in ubic.gemma.core.geoscrape: Candidate returned from a dry-run GEO scrape.
GeoScrapeDryRunCandidate() - Constructor for class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
GeoScrapeDryRunResponse() - Constructor for class ubic.gemma.rest.AdminWebService.GeoScrapeDryRunResponse
GeoScrapeRequest() - Constructor for class ubic.gemma.rest.AdminWebService.GeoScrapeRequest
GeoScrapeService - Interface in ubic.gemma.core.geoscrape: Deprecated.
Supplanted by the curation agent's own GEO scraping, currently scrape_geo_and_open_triage.py. The agent discovers candidates, decides what is worth preboarding, and opens its own triage ticket, so Gemma no longer needs to run the scrape itself.
Nothing here is removed yet and it still works. What it does that the agent must therefore also do: it creates the PreboardedExperiment rows, writes the GeoScrapeWatermark audit row, and opens ONE SCREENING ticket per batch targeting that watermark -- deliberately not one per candidate.
The preboarded write API the agent uses instead is POST /preboarded + POST /preboarded/{id}/annotation-sets, with GET /workflow/queue?datasetType=preboarded_experiment for the queue.
GeoScrapeService.DryRunResult - Class in ubic.gemma.core.geoscrape: Deprecated.

Outcome of a dry run: the candidates, plus the two things a batching caller cannot work out from the candidate list alone.
GeoScrapeService.ScrapeRequest - Class in ubic.gemma.core.geoscrape: Deprecated.

Parameters for a single scrape run.
GeoScrapeServiceImpl - Class in ubic.gemma.core.geoscrape: Default GeoScrapeService implementation.
GeoScrapeServiceImpl(SessionFactory, PreboardedExperimentService, List, PlatformTransactionManager, TicketService, UserManager) - Constructor for class ubic.gemma.core.geoscrape.GeoScrapeServiceImpl
GeoScrapeSubmitResponse() - Constructor for class ubic.gemma.rest.AdminWebService.GeoScrapeSubmitResponse
GeoScrapeTask - Interface in ubic.gemma.core.tasks.maintenance: Deprecated.
Supplanted by the curation agent's own GEO scraping, currently scrape_geo_and_open_triage.py. The agent discovers candidates, decides what is worth preboarding, and opens its own triage ticket, so Gemma no longer needs to run the scrape itself.
Nothing here is removed yet and it still works. What it does that the agent must therefore also do: it creates the PreboardedExperiment rows, writes the GeoScrapeWatermark audit row, and opens ONE SCREENING ticket per batch targeting that watermark -- deliberately not one per candidate.
The preboarded write API the agent uses instead is POST /preboarded + POST /preboarded/{id}/annotation-sets, with GET /workflow/queue?datasetType=preboarded_experiment for the queue.
GeoScrapeTaskCommand - Class in ubic.gemma.core.tasks.maintenance: Deprecated.
Supplanted by the curation agent's own GEO scraping, currently scrape_geo_and_open_triage.py. The agent discovers candidates, decides what is worth preboarding, and opens its own triage ticket, so Gemma no longer needs to run the scrape itself.
Nothing here is removed yet and it still works. What it does that the agent must therefore also do: it creates the PreboardedExperiment rows, writes the GeoScrapeWatermark audit row, and opens ONE SCREENING ticket per batch targeting that watermark -- deliberately not one per candidate.
The preboarded write API the agent uses instead is POST /preboarded + POST /preboarded/{id}/annotation-sets, with GET /workflow/queue?datasetType=preboarded_experiment for the queue.
GeoScrapeTaskCommand() - Constructor for class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
GeoScrapeTaskImpl - Class in ubic.gemma.core.tasks.maintenance: Async runner for the GEO scrape & preboard pipeline.
GeoScrapeTaskImpl() - Constructor for class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskImpl
GeoScrapeWatermark - Class in ubic.gemma.model.expression.experiment: Append-only record of one GEO scrape run.
GeoScrapeWatermark() - Constructor for class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
GeoScrapeWatermark.Status - Enum Class in ubic.gemma.model.expression.experiment: Lifecycle status of a scrape run.
GeoScrapeWatermarkValueObject() - Constructor for class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
GeoSearchField - Enum Class in ubic.gemma.core.loader.expression.geo.service: Enumeration of possible fields for searching GEO records.
GeoSeries - Class in ubic.gemma.core.loader.expression.geo.model: Represents a set of GEO samples that were submitted together.
GeoSeries() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoSeries
GeoSeriesType - Enum Class in ubic.gemma.core.loader.expression.geo.model
GeoService - Interface in ubic.gemma.core.loader.expression.geo.service
GeoService.GeoUpdateConfig - Class in ubic.gemma.core.loader.expression.geo.service
GeoService.GeoUpdateConfig.GeoUpdateConfigBuilder - Class in ubic.gemma.core.loader.expression.geo.service
GeoServiceImpl - Class in ubic.gemma.core.loader.expression.geo.service: Non-interactive fetching, processing and persisting of GEO data.
GeoServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
GeoSingleCellDataDownloaderCli - Class in ubic.gemma.apps: Download single-cell data from GEO supplementary material.
GeoSingleCellDataDownloaderCli() - Constructor for class ubic.gemma.apps.GeoSingleCellDataDownloaderCli
GeoSingleCellDetector - Class in ubic.gemma.core.loader.expression.geo.singleCell: This is the main single-cell data detector that delegates to other more specific detectors.
GeoSingleCellDetector() - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
GeoSource - Enum Class in ubic.gemma.core.loader.expression.geo.service
GeoSourceMetadataBuilder - Class in ubic.gemma.core.loader.expression.geo: Builds the schema-v1 Investigation.sourceMetadata document from a parsed GeoSeries.
GeoSourceMetadataBuilder(ObjectMapper) - Constructor for class ubic.gemma.core.loader.expression.geo.GeoSourceMetadataBuilder
GeoSourceMetadataBuilder.ExperimentIdentity - Class in ubic.gemma.core.loader.expression.geo: Identity of the experiment the document is being written for.
GeoSubset - Class in ubic.gemma.core.loader.expression.geo.model: Represents a subset of samples.
GeoSubset() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoSubset
GeoUpdateAuditService - Interface in ubic.gemma.core.loader.expression.geo.service: Co-bean carrying the audit emission for GeoServiceImpl.updateFromGEO(ExpressionExperiment, GeoUpdateConfig).
GeoUpdateAuditServiceImpl - Class in ubic.gemma.core.loader.expression.geo.service: Implementation of GeoUpdateAuditService: a thin co-bean that exists so GeoUpdateAuditServiceImpl.recordGeoUpdate(ExpressionExperiment, int, boolean) is invoked through a Spring proxy and the AuditedConditional aspect can intercept its return path.
GeoUpdateAuditServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoUpdateAuditServiceImpl
GeoUtil - Class in ubic.gemma.core.loader.expression.geo.util
GeoUtil() - Constructor for class ubic.gemma.core.loader.expression.geo.util.GeoUtil
GeoUtils - Class in ubic.gemma.core.loader.expression.geo.service
GeoUtils() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoUtils
GeoValues - Class in ubic.gemma.core.loader.expression.geo.model: Class to store the expression data prior to conversion.
GeoValues() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoValues
GeoVariable - Class in ubic.gemma.core.loader.expression.geo.model: A GeoVariable represents variables which were investigated.
GeoVariable() - Constructor for class ubic.gemma.core.loader.expression.geo.model.GeoVariable
GeoVariable.VariableType - Enum Class in ubic.gemma.core.loader.expression.geo.model: Permitted descriptions of terms.
GEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
GEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
GEQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
get() - Static method in class ubic.gemma.core.security.util.ActingIdentity
get() - Method in class ubic.gemma.rest.analytics.ga4.AuthenticationBasedUserIdRetrievalStrategy
get() - Method in interface ubic.gemma.rest.analytics.ga4.ClientIdRetrievalStrategy
get() - Method in class ubic.gemma.rest.analytics.ga4.CompositeClientIdRetrievalStrategy
get() - Method in class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy
get() - Method in class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy
get() - Method in interface ubic.gemma.rest.analytics.ga4.UserIdRetrievalStrategy
get(int) - Method in class ubic.gemma.core.datastructure.sparse.SparseArrayList
get(int) - Method in class ubic.gemma.core.datastructure.sparse.SparseRangeArrayList
get(int) - Method in interface ubic.gemma.core.loader.util.anndata.Array
get(int) - Method in class ubic.gemma.core.loader.util.anndata.CategoricalArray
get(int) - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
get(int) - Method in class ubic.gemma.core.loader.util.anndata.EnumArray
get(int) - Method in class ubic.gemma.core.loader.util.anndata.NullableArray
get(int) - Method in class ubic.gemma.core.loader.util.anndata.NullableBoolArray
get(int) - Method in class ubic.gemma.core.loader.util.anndata.NullableIntArray
get(int) - Method in class ubic.gemma.model.util.UninitializedList
get(int) - Method in class ubic.gemma.persistence.util.CursorPage
get(int) - Method in class ubic.gemma.persistence.util.Slice
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
get(int, int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a single value of the matrix by row and column.
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
get(int, int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
get(int, int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
get(int, int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
get(int, int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
get(int, int) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
get(int, int) - Method in interface ubic.gemma.core.util.matrix.ObjectMatrix
get(int, int) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
get(int, int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
get(int, int) - Method in class ubic.gemma.core.util.matrix.StringMatrix
get(Integer) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParser
get(Long) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService
get(Long) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl
get(Long, Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
get(Long, Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
get(Long, Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
get(Long, Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
get(String) - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
get(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
get(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
get(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
get(String) - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParser
get(String) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser: Method that returns a particular BioMartEnsembleNcbi based on a peptide id.
get(Future) - Static method in class ubic.gemma.core.util.concurrent.FutureUtils: Resolve a future silently, turning any exception into an unchecked RuntimeException.
get(K) - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
get(K) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
get(R, C) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
get(R, C) - Method in class ubic.gemma.core.util.matrix.StringMatrix
get(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
get(CompositeSequence, BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
get(CompositeSequence, BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
get(CompositeSequence, BioAssay) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix: Access a single value of the matrix.
get(CompositeSequence, BioMaterial) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getAbstract_() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
getAbstractText() - Method in class ubic.gemma.model.common.description.BibliographicReference
getAbstractText() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getAcceptedParameters() - Method in exception class ubic.gemma.rest.util.UnknownQueryParameterException: Every query parameter the matched resource method declares, sorted.
getAcceptsTargets() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getAcceptsTargets() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getAccession() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics: The assay's accession (a GSM for GEO data), which is what the report rows are keyed by.
getAccession() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
getAccession() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
getAccession() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
getAccession() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
getAccession() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
getAccession() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getAccession() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
getAccession() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
getAccession() - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
getAccession() - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
getAccession() - Method in class ubic.gemma.model.common.description.DatabaseEntry
getAccession() - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
getAccession() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getAccession() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getAccession() - Method in interface ubic.gemma.model.expression.experiment.BioAssaySetValueObject: Obtain the accession of this set if one exists.
getAccession() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getAccession() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject: Deprecated.
Do not use, there's never been an accession field in the data model.
getAccession() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getAccession() - Method in class ubic.gemma.model.expression.experiment.PreboardedExperiment
getAccession() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
getAccession() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
getAccession() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getAccession() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject
getAccession() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject: The assay's accession — a GSM for GEO data — which is what the report keys its rows by.
getAccession() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
getAccessions() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
getAccessions() - Method in class ubic.gemma.model.genome.gene.GeneProduct
getAccessions() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getAccessions() - Method in class ubic.gemma.model.genome.Gene
getAccessionToBioAssayMap(ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
getAccessionVersion() - Method in class ubic.gemma.model.common.description.DatabaseEntry
getAceOrder() - Method in class ubic.gemma.core.security.acl.domain.AclEntry
getAcl() - Method in class ubic.gemma.core.security.acl.domain.AclEntry
getAclIsAuthenticatedAnonymouslyMask() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getAclService() - Method in class ubic.gemma.core.security.acl.BaseAclAdvice: For use by other overridden methods.
getAction() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getAction() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
getActionName() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject: Deprecated.
getActiveExperiments() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getActor() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
getActorId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
getActorName() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProvider: Obtain the associated domain object for which ACLs should be evaluated.
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProvider: Obtain the associated domain object for which ACLs should be evaluated.
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationByAssociationCollectionFilteringProvider: Obtain the associated (parent) domain object for which ACLs should be evaluated.
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationByAssociationFilteringProvider: Obtain the associated (parent) domain object for which ACLs should be evaluated.
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCompositeSequenceByArrayDesignFilteringProvider
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCompositeSequenceCollectionByArrayDesignFilteringProvider
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationDataVectorCollectionByExpressionExperimentFilteringProvider
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationDifferentialExpressionAnalysisResultCollectionByResultSetFilteringProvider
getActuallyTroubled() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getActualOutlierBioAssayIds() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject: BioAssay ids the curator has explicitly flagged as outliers (BioAssay.getIsOutlier()).
getAdded() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport
getAdded() - Method in class ubic.gemma.rest.TicketsWebService.AddTargetsResult
getAdditionalPropertyUris() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getAdditionalPropertyUris() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getAdditionalPropertyUris() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getAdditionalPropertyUris() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain the URIs used as additional properties when inferring parents and children.
getAdditionalSupplementaryFiles(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector
getAdditionalSupplementaryFiles(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
getAdditionalSupplementaryFiles(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
getAdditionalSupplementaryFiles(GeoSample) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Obtain a list of all additional supplementary files.
getAdditionalSupplementaryFiles(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector
getAdditionalSupplementaryFiles(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
getAdditionalSupplementaryFiles(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
getAdditionalSupplementaryFiles(GeoSeries) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Obtain a list of all additional supplementary files.
getAdditionalSupplementaryFiles(GeoSeries, GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
getAdditionalSupplementaryFiles(GeoSeries, GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
getAdditionalSupplementaryFiles(GeoSeries, GeoSample) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SeriesAwareSingleCellDetector
getAddress() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getAdjRSquared() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getAdvertisedNumberOfDesignElements() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getAfter() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport
getAfterAffyControlsFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getAfterLowExpressionFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getAfterLowVarianceFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getAfterMinPresentFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getAfterNoSequencesFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getAfterOutliersFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getAfterZeroVarianceFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getAgentName() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getAgentName() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getAgentName() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
getAgentName() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.RunProvenance
getAgentName() - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
getAgentVersion() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getAgentVersion() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getAgentVersion() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.RunProvenance
getAgentVersion() - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
getAggressiveQtRemoval() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getAgreement() - Method in class ubic.gemma.rest.AnnotationsWebService.PriorCurationValueObject: This term's share of every annotation made from this string, in [0, 1].
getAlias() - Method in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
getAlias() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
getAlias() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getAlias() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
getAlias() - Method in class ubic.gemma.model.genome.gene.GeneAlias
getAlias() - Method in class ubic.gemma.persistence.util.Subquery.Alias
getAliases() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Gene aliases, sorted alphabetically.
getAliases() - Method in class ubic.gemma.model.genome.Gene
getAliases() - Method in class ubic.gemma.persistence.util.Subquery: List of aliases for resolving the object alias defined in filter.
getAliasesByGeneId(Collection) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Batch-load the aliases for a set of genes by ID without thawing the entities.
getAliasesByGeneId(Collection) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getAlignments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getAlignments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getAlignments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Retrieves alignments for the platform elements, limited to those which map to a gene product (so not all blat results)
getAlignments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getAllAnnotations(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain all annotations, grouped by applicable level.
getAllAnnotations(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getAllAssociatedBioAssays(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
getAllAssociatedBioAssays(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getAllAssociatedBioAssays(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getAllAssociatedBioAssays(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getAllAssociatedBioAssays(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getAllAssociatedBioAssays(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getAllBioAssaysUsedIn() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial: Obtain all the assays used in the hierarchy of biomaterials via BioMaterial.getSourceBioMaterial().
getAllCharacteristics() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial: Obtain all the Characteristic associated to this biomaterial, including those inherited from its ancestors via BioMaterial.getSourceBioMaterial().
getAllCharacteristics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment: Obtain all characteristics associated to this EE.
getAllDatasetMetadataFromCellXGene(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
getAllDatasetMetadataFromCellXGene(GeoSeries, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
getAllFactorValues() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial: Obtain all the FactorValue associated to this biomaterial, including those inherited from its ancestors via BioMaterial.getSourceBioMaterial().
getAllGeoRecords(GeoRecordType, Collection, int) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Retrieve all GEO records of a given type.
getAllGeoRecords(GeoRecordType, Collection, int) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl
getAllLockInfos() - Method in interface ubic.gemma.core.util.locking.FileLockManager: Get the lock info for all paths known to the lock manager.
getAllLockInfos() - Method in class ubic.gemma.core.util.locking.FileLockManagerImpl
getAllLockInfosByWalking(Path, int) - Method in interface ubic.gemma.core.util.locking.FileLockManager: Get the lock info for all paths obtained by walking the given directory.
getAllLockInfosByWalking(Path, int) - Method in class ubic.gemma.core.util.locking.FileLockManagerImpl
getAllLoggerNames() - Method in class ubic.gemma.cli.logging.log4j.Log4jConfigurer
getAllLoggerNames() - Method in interface ubic.gemma.cli.logging.LoggingConfigurer: Obtain the list of all logger names.
getAllowArrayExpressDesign() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getAllowedNextStates() - Method in exception class ubic.gemma.persistence.service.expression.experiment.DisallowedWorkflowTransitionException
getAllowedValues() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta: A short list of allowed values if that can be determined, or null.
getAllowSuperSeriesLoad() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getAllParents(Collection) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getAllParents(Collection) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getAllParents(Collection, boolean) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getAllParents(Collection, boolean) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getAllSingleCellDataTypes(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Obtain all single-cell data types a GEO series contains.
getAllTaxonExperimentGroup(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService
getAllTaxonExperimentGroup(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl
getAllTreatments() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial: Obtain all treatments, including those inherited from its ancestors via BioMaterial.getSourceBioMaterial().
getAllURIs() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getAllURIs() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getAllURIs() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getAllURIs() - Method in class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService: Empty for the same reason as MeshDiseaseSynonymOntologyService.getTerm(String) — these URIs are MONDO's to enumerate.
getAllURIs() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain all the resource URIs in this ontology.
getAlreadyPresent() - Method in class ubic.gemma.rest.TicketsWebService.AddTargetsResult
getAlternateNames() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getAlternativeIds() - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
getAlternativeIds() - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Obtain alternative IDs for this term.
getAlternativeIds() - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getAlternativeIds() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: Alternative IDs for this term (OBO hasAlternativeId) — merged-in obsolete identifiers.
getAlternativeTo() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getAnalyses(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService
getAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
getAnalysis() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
getAnalysis() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getAnalysisId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getAnalysisId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getAnalysisId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getAnalysisId() - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
getAnalysisNotRun() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getAnalysisResultSetIds() - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
getAnalysisStoragePath() - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getAnalysisType() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Type of analysis to perform.
getAnalysisType() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: Proposed analysis type.
getAnalysisType() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getAnalyticsKey() - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getAnchor() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getAndThen() - Method in class ubic.gemma.persistence.util.Sort
getAnnotatedAbstract() - Method in class ubic.gemma.model.common.description.BibliographicReference: Deprecated.
getAnnotation() - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
getAnnotation(String) - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
getAnnotation(String) - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Obtain an annotation by property URI.
getAnnotation(String) - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getAnnotationCategories() - Method in class ubic.gemma.rest.AnnotationsWebService: List the ontology categories allowed for use in characteristics.
getAnnotationCounts(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getAnnotationCounts(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getAnnotationCountsByIds(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getAnnotationCountsByIds(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getAnnotationCountsByIds(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getAnnotationCountsByIds(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getAnnotationInformation(Collection) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService
getAnnotationInformation(Collection) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl: Populate information about how many annotations there are, and how many factor values there are.
getAnnotationPredicates() - Method in class ubic.gemma.rest.AnnotationsWebService: List the ontology predicates allowed for use in statements.
getAnnotationRelationRowsWritten() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync
getAnnotationRelations(String, String, String, String, String, String, Long, String, Long, String, int, double, boolean, int, int, boolean, boolean, int) - Method in class ubic.gemma.rest.AnnotationsWebService: Relations Gemma knows between annotation terms, with the basis for each.
getAnnotations() - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
getAnnotations() - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Obtain all annotations for this term.
getAnnotations() - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getAnnotations() - Method in class ubic.gemma.model.common.description.BibliographicReference: Deprecated.
getAnnotations() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor: Deprecated.
getAnnotations() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationsReplaceRequest
getAnnotations() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationsUpdateRequest
getAnnotations() - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta: Free-form, gene-shaped annotation bag.
getAnnotations(String) - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
getAnnotations(String) - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Obtain all the annotations for a given property URI.
getAnnotations(String) - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getAnnotations(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getAnnotations(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getAnnotations(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Retrieve annotations for a given experiment.
getAnnotations(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getAnnotations(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getAnnotations(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getAnnotations(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Retrieve annotations for a given experiment, optionally including unmapped ones.
getAnnotations(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getAnnotations(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getAnnotations(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getAnnotations(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Retrieve annotations for a given experiment subset.
getAnnotations(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getAnnotations(ExpressionExperimentSubSet, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getAnnotations(ExpressionExperimentSubSet, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getAnnotations(ExpressionExperimentSubSet, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Retrieve annotations for a given experiment subset, optionally including unmapped ones.
getAnnotations(ExpressionExperimentSubSet, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getAnnotations(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getAnnotations(DatasetArg, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getAnnotationsById(FactorValue) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Create a mapping of annotation IDs to annotations for a FactorValue.
getAnnotationsChildren(String, boolean) - Method in class ubic.gemma.rest.AnnotationsWebService: Obtain the children of a given annotation.
getAnnotationSet() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
getAnnotationSet() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
getAnnotationSet() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
getAnnotationSet() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.AttachedAnnotationSet
getAnnotationSet(Long) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Single annotation set (full payload).
getAnnotationSetId() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationsReplaceRequest
getAnnotationSetsRebound() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PromotionResult
getAnnotationsParents(String, boolean) - Method in class ubic.gemma.rest.AnnotationsWebService
getAnnotationsUsageFrequency(Collection, Class, int, int, String, Collection, Collection, Collection, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain annotations usage frequency for a set of given ExpressionExperiment IDs.
getAnnotationsUsageFrequency(Collection, Class, int, int, String, Collection, Collection, Collection, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl: We're making two assumptions: a dataset cannot have a characteristic more than once and a dataset cannot have the same characteristic at multiple levels to make counting more efficient.
getAnnotationsUsageFrequency(Filters, Set, String, Collection, Collection, int, Collection, int, boolean, boolean, long, TimeUnit) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getAnnotationsUsageFrequency(Filters, Set, String, Collection, Collection, int, Collection, int, boolean, boolean, long, TimeUnit) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl: If the term cannot be resolved via OntologyService.getTerm(String, long, TimeUnit), an attempt is done to resolve its category and assign it as its parent.
getAnnotationsUsageFrequency(Filters, Set, String, Collection, Collection, int, Collection, int, boolean, boolean, long, TimeUnit) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain annotation usage frequency for datasets matching the given filters.
getAnnotationsUsageFrequency(Filters, Set, String, Collection, Collection, int, Collection, int, boolean, boolean, long, TimeUnit) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getAnnotationsUsageFrequencyInternal(Collection, Class, int, int, String, Collection, Collection, boolean, Collection, String, String, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getAnnotationTerm(String, boolean) - Method in class ubic.gemma.rest.AnnotationsWebService
getAnnotationValueObjects() - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
getAnnotDataDir() - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService: Obtain the directory where platform annotations are located.
getAnnotDataDir() - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
getAnova() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getAnswer() - Method in class ubic.gemma.core.job.TaskResult: The answer of this task, may be an Exception or null.
getApiInfo(UriInfo) - Method in class ubic.gemma.rest.RootWebService: Returns an object with API information.
getApiVersion() - Method in class ubic.gemma.rest.util.ResponseErrorObject: API version.
getApplicationContext() - Method in class ubic.gemma.cli.util.AbstractCLI: Obtain the application context.
getApplicationContext(boolean, boolean, String[]) - Static method in class ubic.gemma.core.context.SpringContextUtils: Deprecated.
this method does not support producing Gemma Web contexts, please migrate existing code to use SpringContextUtils.getApplicationContext(String[], String...) instead.
getApplicationContext(String[], String...) - Static method in class ubic.gemma.core.context.SpringContextUtils: Obtain an application context for Gemma.
getApply10xFilter() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig: Filter 10x MEX data to remove low-quality cells.
getApproximateQuantile(int) - Method in class ubic.gemma.core.util.math.distribution.Histogram: Find the bin below which i% of the values are contained.
getArch() - Method in class ubic.gemma.rest.monitoring.InfoWebService.OsBlock
getArgsByPropertyName(AbstractEntityArrayArg) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService: Given a AbstractEntityArrayArg, construct a mapping of properties it refers to values those properties are allowed to take in a filter.
getArgsByPropertyName(AbstractEntityArrayArg) - Method in class ubic.gemma.rest.util.args.TaxonArgService
getArguments() - Method in interface ubic.gemma.cli.util.CLIContext: Obtain the command line arguments for the command.
getArguments() - Method in class ubic.gemma.cli.util.SystemCLIContext
getArray() - Method in class ubic.gemma.core.util.math.distribution.Histogram: Returns the bin heights.
getArrayColumn(String) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain an array column as a H5 dataset.
getArrayDesign() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
getArrayDesign() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
getArrayDesign() - Method in class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskCommand
getArrayDesign() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: The platform this assay was run on, serialized as ArrayDesignReferenceValueObject — id, shortName, name, technologyType.
getArrayDesign() - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
getArrayDesign() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
getArrayDesignCache() - Method in class ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
getArrayDesignCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getArrayDesignId() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getArrayDesignName() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getArrayDesignName() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
getArrayDesignName() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getArrayDesigns() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: Platforms associated to the experiments.
getArrayDesigns() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getArrayDesignShortName() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getArrayDesignsUsageFrequency(int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain dataset usage frequency by platform currently used.
getArrayDesignsUsageFrequency(int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getArrayDesignsUsageFrequency(Collection, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain dataset usage frequency by platform currently for the given dataset IDs.
getArrayDesignsUsageFrequency(Collection, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getArrayDesignsUsed() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
getArrayDesignsUsed() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getArrayDesignsUsed(Collection, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries: Retrieve a list of array designs used by the given experiments.
getArrayDesignsUsed(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getArrayDesignsUsed(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getArrayDesignsUsed(BioAssaySet, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries: Retrieve a list of array designs used in given expression experiment
getArrayDesignsUsed(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getArrayDesignsUsed(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getArrayDesignsUsed(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getArrayDesignsUsed(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getArrayDesignsUsed(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain a collection of ArrayDesign used by a specific set of vectors.
getArrayDesignsUsed(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getArrayDesignsUsed(ExpressionExperiment, QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getArrayDesignsUsed(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getArrayDesignsUsed(ExpressionExperiment, QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain a collection of ArrayDesign used by a specific set of vectors.
getArrayDesignsUsed(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getArrayDesignsUsed(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao
getArrayDesignsUsed(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl
getArrayDesignsUsed(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain the array designs used by the assays in the subset.
getArrayDesignsUsed(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getArrayDesignsUsed(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
getArrayDesignsUsed(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
getArrayDesignsUsedByExperiment(Collection, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries: Retrieve, in one query, a per-experiment map of array designs used.
getArrayDesignsUsedByExperiment(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Per-experiment map variant of ExpressionExperimentDao.getArrayDesignsUsed(Collection): one HQL covers all supplied EEs, the result preserves which platform belongs to which EE.
getArrayDesignsUsedByExperiment(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getArrayDesignsUsedByExperiment(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Per-experiment map of array designs used: one HQL covers all supplied EEs and the result preserves which platform belongs to which EE.
getArrayDesignsUsedByExperiment(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getArrayDesignUsed() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters, Set, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters, Set, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters, Set, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Calculate the usage frequency of platforms by the datasets matching the provided filters.
getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters, Set, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getArrType() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
getAsDouble(int, int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
getAsDouble(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getAsDouble(int, int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveDoubleMatrix: Retrieve the value at the given row and column without boxing.
getAsDouble(int, int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getAsInt(int, int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
getAsInt(int, int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveIntMatrix: Retrieve the value at the given row and column without boxing.
getAsInt(int, int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getAssay() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getAssayDescription() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
getAssayIndex() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getAssayName() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
getAssayProcessingDate() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
getAssays() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getAssemblyDatabase() - Method in class ubic.gemma.model.genome.Chromosome
getAssertedAt() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getAssertedAt() - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
getAssertedBy() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getAssertedBy() - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
getAssertedBy() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssertion
getAssertedBy() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
getAssign() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
getAssignee() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getAssigneeId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getAssigneeId() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
getAssigneeId() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getAssigneeId() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getAssigneeName() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getAssociatedExperimentCount() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: How many experiments "involve" (manipulate, etc.) this gene
getAssociation() - Method in class ubic.gemma.model.common.description.DatasetPublicationValueObject
getATN() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getATN() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getAttempt() - Method in class ubic.gemma.core.util.SimpleRetryContext: Indicate the attempt number (zero for first, 1 for second, etc.)
getAttribute(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
getAttribute(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location
getAttribute(String, String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location
getAttributes() - Method in class ubic.gemma.core.loader.util.hdf5.H5Location
getAttributes(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location
getAuditEvent() - Method in class ubic.gemma.core.security.audit.AuditedEvent
getAuditEventId() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowTransition
getAuditEventIds() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport: Per-row audit-event ids; empty by default — populating these requires capturing the id of the AuditEvent written by the @Audited aspect, which the aspect does not surface back through the call.
getAuditEventIds() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getAuditEvents(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
getAuditEvents(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getAuditEvents(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getAuditEvents(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getAuditTrail() - Method in class ubic.gemma.model.common.auditAndSecurity.AbstractAuditable
getAuditTrail() - Method in interface ubic.gemma.model.common.auditAndSecurity.Auditable
getAuditTrail() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getAuthenticatedUserCount() - Method in interface ubic.gemma.core.security.SecurityService: Obtain the number of authenticated users.
getAuthenticatedUserCount() - Method in class ubic.gemma.core.security.SecurityServiceImpl
getAuthenticatedUserNames() - Method in interface ubic.gemma.core.security.SecurityService
getAuthenticatedUserNames() - Method in class ubic.gemma.core.security.SecurityServiceImpl
getAuthorities() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
getAuthorities() - Method in interface ubic.gemma.core.security.model.UserGroup: A set of authorities conferred by the group membership.
getAuthorities() - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup
getAuthorities() - Method in class ubic.gemma.rest.GroupsWebService.GroupValueObject
getAuthorities() - Method in class ubic.gemma.rest.RootWebService.UserValueObject: Spring Security authorities granted to this user (e.g.
getAuthority() - Method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority
getAuthorList() - Method in class ubic.gemma.model.common.description.BibliographicReference
getAuthorList() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getAutoOptionValue(CommandLine, String, String) - Static method in class ubic.gemma.cli.util.OptionsUtils
getAutoSeekEventType() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Indicate the event to be used for auto-seeking.
getAvailableMemory() - Method in record class ubic.gemma.core.util.runtime.MemInfo
getAvailableSids() - Method in interface ubic.gemma.core.security.SecurityService: Obtain a collection of all availble security IDs (basically, user names and group authorities).
getAvailableSids() - Method in class ubic.gemma.core.security.SecurityServiceImpl
getAverage() - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
getAxiomCount() - Method in class ubic.gemma.core.ontology.providers.OntologySlimExtractor.ExtractResult
getBackgroundChannelA() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getBackgroundChannelB() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getBackgroundSubtracted() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getBaseDifferentialDirectory(String) - Static method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionFileUtils
getBaseline() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: Whether this factor value is a "forced" baseline condition.
getBaseline() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getBaseline() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
getBaseline() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: null = leave the baseline flag unchanged.
getBaseline(String) - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
getBaseline(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Retrieve the baseline for the given result set.
getBaseline(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
getBaseline(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
getBaseline(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
getBaselineConditions(Collection, Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection
getBaselineFactorValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getBaselineFactorValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getBaselineFactorValueId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getBaselineFactorValueId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getBaselineGroup() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
getBaselineGroup() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getBaselineGroup() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.Prefetch
getBaselineGroup() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getBaselineLevels(Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection: Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
getBaselineLevels(Collection, Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection: Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
getBaselineRelevance() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Curator/agent hint about whether this factor warrants picking a baseline factor value.
getBaselineRelevance() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getBaselineRelevance() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject: Curator/agent hint about baseline relevance.
getBaselineRelevance() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Curator/agent hint about whether this factor warrants picking a baseline factor value — the write side of ExperimentalFactorValueObject.baselineRelevance, which was readable and unsettable until now (cab, 2026-09-04: the curation UI offers "Tick to override: no baseline" with a reason box and had nowhere to put the answer).
getBaselineRelevanceReason() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Free-text rationale paired with ExperimentalDesignValueObject.ExperimentalFactorEntry.baselineRelevance.
getBaselineRelevanceReason() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getBaselineRelevanceReason() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject: Free-text rationale paired with ExperimentalFactorValueObject.baselineRelevance.
getBaselineRelevanceReason() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Free-text rationale paired with DatasetsWebService.FactorCommit.baselineRelevance — what the curator typed in the reason box.
getBaselinesForInteractions(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Retrieve baselines for all the given result sets representing factor interactions.
getBaselinesForInteractions(Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
getBaselinesForInteractions(Set, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
getBaselinesForInteractions(Set, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
getBaselinesForInteractionsByIds(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Retrieve baselines using result set IDs representing factor interactions.
getBaselinesForInteractionsByIds(Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
getBaselinesForInteractionsByIds(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
getBaselinesForInteractionsByIds(Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
getBases() - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
getBases() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
getBases() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getBases() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
getBases() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getBasics() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getBasis() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getBasis() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getBasis() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getBasis() - Method in class ubic.gemma.rest.AnnotationsWebService.CanonicalUriValueObject: Why this row decides the way it does — the rule that picked the winner.
getBatch() - Method in class ubic.gemma.model.pipeline.PipelineJob
getBatch(Long) - Method in class ubic.gemma.rest.AdminPipelineWebService
getBatchAccessions(Collection, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getBatchAccessions(Collection, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getBatchConfound() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getBatchConfound() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getBatchConfoundAsHtmlString(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService: Summarize the batch confounds for a given dataset or its subsets in an HTML string.
getBatchConfoundAsHtmlString(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
getBatchConfounds() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
getBatchEffect() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getBatchEffect() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Batch effect type.
getBatchEffect() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
getBatchEffectDetails(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService: Obtain the full batch effect details of a given experiment.
getBatchEffectDetails(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
getBatchEffectStatistics() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails: Obtain an object describing the batch effect if available.
getBatchEffectStatistics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getBatchEffectStatistics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Summary statistics of a batch effect is present.
getBatchEffectStatistics() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
getBatchEffectStatistics(BatchEffectDetails) - Static method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectUtils: Obtain a string describing the summary statistics of a batch effect is present in the given batch details.
getBatchEffectType(BatchEffectDetails) - Static method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectUtils: Obtain a BatchEffectType describing the batch effect state of the given batch details.
getBatchFetchEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getBatchIdentifiers(Collection, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getBatchIdentifiers(Collection, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getBatchInfo(ExpressionExperiment, Collection) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
getBatchSize() - Method in class ubic.gemma.persistence.service.AbstractDao
getBatchSize(Class, SessionFactory) - Static method in class ubic.gemma.persistence.hibernate.HibernateUtils: Obtain the configured default batch fetch size.
getBatchTaskExecutor() - Method in class ubic.gemma.cli.util.AbstractCLI: Obtain an executor for running batch tasks.
getBatchTaskProgressReporter() - Method in class ubic.gemma.cli.util.AbstractCLI
getBefore() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport
getBestBioAssayDimension() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getBestBioAssayDimension() - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix: Obtain the largest BioAssayDimension that covers all the biomaterials in this matrix.
getBestCoexpressionMatrix() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis
getBiggestBinSize() - Method in class ubic.gemma.core.util.math.distribution.Histogram
getBin() - Method in class ubic.gemma.model.genome.PhysicalLocation
getBin() - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
getBinCounts() - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
getBinEdges() - Method in class ubic.gemma.core.util.math.distribution.Histogram
getBinEdgesStrings() - Method in class ubic.gemma.core.util.math.distribution.Histogram
getBinOf(double) - Method in class ubic.gemma.core.util.math.distribution.Histogram
getBins() - Method in class ubic.gemma.rest.PvalueDistributionValueObject
getBioAssay(int) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Obtain the BioAssay for a given cell position.
getBioAssayCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Deprecated.
use ExpressionExperimentValueObject.getNumberOfBioAssays() instead.
getBioAssayDimension() - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getBioAssayDimension() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getBioAssayDimension() - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix: Obtain the dimension for the columns of this matrix.
getBioAssayDimension() - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix: Obtain the dimension for the columns of this matrix.
getBioAssayDimension() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
getBioAssayDimension() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getBioAssayDimension() - Method in class ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector: A dimension of BioAssay the elements of this vector apply to.
getBioAssayDimension() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject: Represents the order of the bioassays for this.
getBioAssayDimension(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getBioAssayDimension(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix: Produce a BioAssayDimension representing the matrix columns for a specific row.
getBioAssayDimension(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Retrieve a dimension for a given experiment and quantitation type.
getBioAssayDimension(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioAssayDimension(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain the dimension associated to the given quantitation type for the given experiment.
getBioAssayDimension(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBioAssayDimension(ExpressionExperiment, QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Retrieve a dimension for a given experiment and quantitation type.
getBioAssayDimension(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioAssayDimension(ExpressionExperiment, QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getBioAssayDimension(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBioAssayDimensionById(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Find a BioAssayDimension by ID.
getBioAssayDimensionById(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBioAssayDimensionById(ExpressionExperiment, Long, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a bioassay dimension by ID.
getBioAssayDimensionById(ExpressionExperiment, Long, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioAssayDimensionById(ExpressionExperiment, Long, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getBioAssayDimensionById(ExpressionExperiment, Long, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBioAssayDimensions() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getBioAssayDimensions() - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix: Obtain all the BioAssayDimensions that are used in this matrix.
getBioAssayDimensions() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getBioAssayDimensions(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getBioAssayDimensions(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioAssayDimensions(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getBioAssayDimensions(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioAssayDimensions(ExpressionExperiment, QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getBioAssayDimensions(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioAssayDimensionsWithAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain all the dimensions associated to the given experiment.
getBioAssayDimensionsWithAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBioAssayDimensionsWithAssays(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain all BioAssayDimensions associated to a particular QuantitationType.
getBioAssayDimensionsWithAssays(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBioAssayExpressionLevels() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
getBioAssayForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getBioAssayForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getBioAssayForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix: Obtain an assay corresponding to a given column.
getBioAssayForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getBioAssayForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getBioAssayForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getBioAssayForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix: Obtain a bioassay applicable to a given column.
getBioAssayId() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
getBioAssayId() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics
getBioAssayId() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject
getBioAssayId() - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta
getBioAssayIds() - Method in class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
getBioAssayIds() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: A list of BioAssay IDs that are applicable to the cells.
getBioAssayIds() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Related BioAssay IDs.
getBioAssayIds() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject: BioAssay ids in the order the rows / columns of DatasetsWebService.SampleCorrelationMatrixValueObject.values appear.
getBioAssayIds() - Method in class ubic.gemma.rest.DatasetsWebService.SimpleSVDValueObject: BioAssay IDs Order same as rows of the v matrix.
getBioAssays() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: Assays used in the SVD analysis.
getBioAssays() - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getBioAssays() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getBioAssays() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getBioAssays() - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix: Obtain the list of bioassays.
getBioAssays() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
getBioAssays() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
getBioAssays() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
getBioAssays() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: List of BioAssays applicable to the cells.
getBioAssays() - Method in class ubic.gemma.model.expression.experiment.BioAssaySet
getBioAssays() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getBioAssays() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
getBioAssays() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getBioAssaysAnalyzed() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject: The BioAssays analyzed in this differential expression analysis.
getBioAssaysAnalyzed() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: List of BioAssays analyzed
getBioAssayScores() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject: Map of bioAssay id to the assay's score on this PC.
getBioAssaySet() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound: Experiment or subset this confound is applicable to.
getBioAssaySet() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getBioAssaySetAnalyzedId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Analyzed BioAssaySet ID.
getBioAssaySetId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject: Deprecated.
use DifferentialExpressionAnalysisValueObject.getExperimentAnalyzedId() instead
getBioAssaySets(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
getBioAssaySets(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
getBioAssaySets(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService: Obtain all the BioAssaySet that contain the given BioAssay.
getBioAssaySets(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
getBioAssaySets(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService: Obtain all the BioAssaySet that contain the given BioAssay.
getBioAssaySets(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
getBioAssaysForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getBioAssaysForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix
getBioassayShortName() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit: Deprecated.
use DatasetsWebService.SampleCharacteristicCommit.bioMaterialId, for the reasons on DatasetsWebService.FactorValueCommit.getBiomaterialShortNames().
getBioAssayShortNames() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject: BioAssay short names parallel to DatasetsWebService.SampleCorrelationMatrixValueObject.bioAssayIds, for axis labels.
getBioAssaysOffset() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Offsets of the BioAssay in SingleCellDimension.cellIds.
getBioAssaysUsedIn() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getBiologicalCharacteristic() - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
getBioMartEnsemblNcbiFetcher() - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator: Should be set
getBioMartFields() - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
getBioMartFieldsPerRow() - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser: Based on what attributes were set on the original file then calculate how many columns should be in file.
getBioMartFileName() - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
getBiomartTaxonName(Taxon) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher: Biomart taxon names are formatted as the scientific name all lowercase with the genus name shortened to one letter and appended to species name E.g.
getBioMaterialAnnotations(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain sample-level annotations.
getBioMaterialAnnotations(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioMaterialAnnotations(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getBioMaterialAnnotations(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioMaterialAssignments() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject: Many-to-many assignment of BioMaterials to FactorValues, materialized as a flat list.
getBioMaterialCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getBioMaterialCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getBioMaterialCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioMaterialCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getBioMaterialCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getBioMaterialCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getBioMaterialCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBioMaterialForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getBioMaterialForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getBioMaterialForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix: Obtain a biomaterial corresponding to a column.
getBioMaterialForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getBioMaterialForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix
getBioMaterialForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getBioMaterialForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getBioMaterialForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix
getBioMaterialId() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
getBioMaterialId() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.BioMaterialFactorValueAssignment
getBioMaterialId() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.SampleCharacteristicAdd
getBioMaterialId() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit: The sample this characteristic belongs to, by BioMaterial id.
getBioMaterialId() - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta
getBiomaterialIds() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: Samples this value applies to, by BioMaterial id — the identifier GET /datasets/{id}/design already reports as bioMaterialAssignments[].bioMaterialId.
getBioMaterialIds() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan.PendingAssignment
getBioMaterialIds() - Method in class ubic.gemma.rest.DatasetsWebService.SimpleSVDValueObject: Order same as the rows of the v matrix.
getBioMaterialName() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.BioMaterialFactorValueAssignment
getBioMaterialProvider() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getBioMaterials() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: Biomaterials used in the SVD analysis.
getBioMaterials() - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getBioMaterials() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getBioMaterials() - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix
getBiomaterialShortNames() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: Deprecated.
use DatasetsWebService.FactorValueCommit.biomaterialIds. Scheduled for removal — Paul, 2026-09-05: "as a choice of way to parameterize, we should not allow it, by removing that as an option for the endpoints. Deprecation is the right step now." Kept working meanwhile so no existing caller breaks.
A name is not an addressing form. It is not guaranteed to EXIST — a single-cell sub-bioassay has no accession of its own — and not guaranteed to be UNIQUE: on GEO-sourced single-cell data every sub-bioassay descends from one GSM, so that accession names fifteen samples rather than one. Such a name is now a 400 rather than an arbitrary pick.
An id, by contrast, always exists here: these endpoints never add or remove a dataset's samples, so every sample a commit can refer to was already persisted and already has one. That is what makes removal safe rather than merely desirable — there is no new-entity case for samples, and clientRef covers the entities a commit genuinely does create.
getBiomaterialsWithChangedAssignments() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
getBioSequence() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getBioSequence2GeneProduct() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getBioSequenceId() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getBioSequenceName() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getBioSequenceNcbiId() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
getBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Return all the (unique) biosequences associated with the array design.
getBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getBkgSubChannelA() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getBlackListed() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getBlacklistedDatasets(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg) - Method in class ubic.gemma.rest.DatasetsWebService: Browse blacklisted datasets.
getBlacklistedDatasetsByCursor(Filters, Cursor, int) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Cursor-mode counterpart to ExpressionExperimentService.loadBlacklistedValueObjects(Filters, Sort, int, int).
getBlacklistedPlatforms(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg) - Method in class ubic.gemma.rest.PlatformsWebService
getBlacklistedPlatformsByCursor(Filters, Cursor, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Cursor-mode counterpart to ArrayDesignService.loadBlacklistedValueObjects(Filters, Sort, int, int).
getBlatResult() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getBlatResult() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummaryValueObject: The alignment this mapping rests on, carrying the scores (identity, score), the genomic coordinates, and the probe's biological sequence under querySequence.
getBlatResult() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
getBlatResultId() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getBlatResults() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
getBlatScoreThreshold() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getBlatScoreThreshold() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getBlockCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getBlockCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getBlockedReason() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
getBlockers() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport: Hard validation errors.
getBlockSizes() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getBlockSizes() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getBody() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket: Curator-facing instructions text — what the reporter writes when filing the ticket, what the detail page renders as multi-line body and the dashboard clamps to 2 lines.
getBody() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: Curator-facing instructions text.
getBody() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
getBody() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getBody() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getBodyParts() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getBodyParts() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
getBool(int) - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
getBool(K) - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
getBoolean(long) - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset: Obtain a single boolean value.
getBoolean(String) - Static method in class ubic.gemma.core.config.Configuration: Obtain a boolean configuration value by key.
getBoolean(String) - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getBoolean(String, boolean) - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getBrokerName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
getBrowserUrl(ExpressionExperiment) - Method in interface ubic.gemma.core.visualization.cellbrowser.CellBrowserService: Obtain a URL for the Cell Browser for a given ExpressionExperiment.
getBrowserUrl(ExpressionExperiment) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserServiceImpl
getBsv() - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
getBsv() - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
getBuckets() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig: Ordered list of explicit buckets.
getBuild() - Method in class ubic.gemma.rest.monitoring.InfoWebService.InfoValueObject
getBuildInfo() - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject
getBuildInfo() - Method in class ubic.gemma.rest.util.ResponseErrorObject: Build information.
getByAccession(String, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getByAccession(String, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getByAnnotationCategory() - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-category distinct-term counts.
getByCategoryAndValueComparator() - Static method in class ubic.gemma.model.common.description.Characteristic: Obtain a comparator to order terms by value URI (or value if null) in a case-insensitive manner.
getByCategoryComparator() - Static method in class ubic.gemma.model.common.description.Characteristic: Obtain a comparator to compare terms by category URI (or category if null) in a case-insensitive manner.
getByIdentifier(int, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getByIdentifier(int, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getByKeys(R, C) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getByKeys(R, C) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
getByKeys(R, C) - Method in interface ubic.gemma.core.util.matrix.Matrix2D
getByKeys(R, C) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
getByKeys(R, C) - Method in class ubic.gemma.core.util.matrix.StringMatrix
getByPlatformType() - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-platform-technology-type dataset counts.
getByResultObjectType(Class) - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap: Obtain results where the result object is of a given type, regardless of the result type.
getByResultType(Class) - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap
getByTaxon() - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-taxon dataset counts, sorted descending by count.
getBytes() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
getCache(CacheManager, String) - Static method in class ubic.gemma.persistence.cache.CacheUtils
getCached() - Method in interface ubic.gemma.core.analysis.report.HomeStatsService: Return the most-recent snapshot, loading from disk on first access.
getCached() - Method in class ubic.gemma.core.analysis.report.HomeStatsServiceImpl
getCacheName() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getCacheName() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getCaches() - Method in class ubic.gemma.rest.AdminWebService: Lists the registered Spring caches by name.
getCandidateIdentifiers(T) - Method in interface ubic.gemma.core.loader.util.mapper.HintingEntityMapper: Obtain a list of possible identifiers for the given entity from higher to lower confidence.
getCandidateIdentifiers(BioAssay) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoBioAssayMapper
getCandidateIdentifiers(BioAssay) - Method in class ubic.gemma.core.loader.util.mapper.SimpleBioAssayMapper
getCandidates() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.DryRunResult: Deprecated.
getCandidates(UriInfo) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Screening queue: redirect to the existing /datasets?filter=curationDetails.needsAttention=true query.
getCanonicalizations() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getCanonicalLabel() - Method in class ubic.gemma.core.ontology.TermCanonicalization: The term's canonical label, now stored (equals TermCanonicalization.getSubmittedLabel() when only the URI changed).
getCanonicalLabel() - Method in class ubic.gemma.rest.DatasetsWebService.Canonicalization: The canonical label now stored — display this (equals submittedLabel when only the URI changed).
getCanonicalUri() - Method in class ubic.gemma.core.ontology.TermCanonicalization: The URI now stored (equals TermCanonicalization.getSubmittedUri() when only the label changed).
getCanonicalUri() - Method in class ubic.gemma.rest.DatasetsWebService.Canonicalization: The URI now stored (equals submittedUri when only the label changed).
getCanonicalUris(String) - Method in class ubic.gemma.rest.AnnotationsWebService: Every URI Gemma resolves to a different one on read, so a caller can hold the same answer we do instead of a hand-copied subset of it.
getCardinality() - Method in interface ubic.gemma.core.ontology.model.OntologyCardinalityRestriction
getCardinalityType() - Method in interface ubic.gemma.core.ontology.model.OntologyCardinalityRestriction
getCatalogNumbers() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getCategoricalColumn(String) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain a categorical column.
getCategoricalColumn(String, Class) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain a categorical column.
getCategories() - Method in class ubic.gemma.core.loader.util.anndata.CategoricalArray
getCategoriesAlias(UriInfo) - Method in class ubic.gemma.rest.RootWebService: Top-level alias for GET /datasets/categories: the curation-UI calls GET /categories for the recently-used annotation-category picker.
getCategoriesUsageFrequency(Collection, Collection, Collection, Collection, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCategoriesUsageFrequency(Collection, Collection, Collection, Collection, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCategoriesUsageFrequency(Filters, Set, Collection, Collection, Collection, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getCategoriesUsageFrequency(Filters, Set, Collection, Collection, Collection, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getCategoriesUsageFrequency(Filters, Set, Collection, Collection, Collection, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain category usage frequency for datasets matching the given filter.
getCategoriesUsageFrequency(Filters, Set, Collection, Collection, Collection, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getCategory() - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Gemma's canonical category label (e.g.
getCategory() - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat: Gemma's canonical category label carried on ExperimentalFactor.category (e.g.
getCategory() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic
getCategory() - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Category label.
getCategory() - Method in class ubic.gemma.model.common.description.Category
getCategory() - Method in class ubic.gemma.model.common.description.Characteristic
getCategory() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
getCategory() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
getCategory() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor: Obtain the category of this experimental factor.
getCategory() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
getCategory() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getCategory() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getCategory() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getCategory() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest.Item
getCategory() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchResultValueObject
getCategory() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: The category a curator has already applied to this URI in the corpus — NOT what kind of thing the term is.
getCategory() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getCategory() - Method in class ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject
getCategory() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
getCategory() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit
getCategory() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
getCategory() - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
getCategory(Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Create a new characteristic that represents the category of a given characteristic.
getCategoryAsCharacteristic(Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils
getCategoryDistribution() - Method in class ubic.gemma.core.analysis.report.HomeStats: Distribution of annotation categories observed across public datasets — the top-N categories Gemma actually uses, with the number of experiments each appears on.
getCategoryTerms() - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain terms which are allowed for use in the category of a Characteristic.
getCategoryTerms() - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getCategoryUri() - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Ontology URI of the category, if any.
getCategoryUri() - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat: Ontology URI of the category, if any.
getCategoryUri() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic
getCategoryUri() - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Category URI.
getCategoryUri() - Method in class ubic.gemma.model.common.description.Category
getCategoryUri() - Method in class ubic.gemma.model.common.description.Characteristic
getCategoryUri() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
getCategoryUri() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
getCategoryUri() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getCategoryUri() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getCategoryUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getCategoryUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: URI of AnnotationsWebService.AnnotationSearchResultValueObject.category, on the same terms: the curated category's URI, null when unused.
getCategoryUri() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getCategoryUri() - Method in class ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject: Named to match Characteristic and the curation write side, which both say category / categoryUri.
getCause() - Method in exception class ubic.gemma.core.analysis.preprocess.FilteringRelatedPreprocessingException
getCause() - Method in exception class ubic.gemma.core.analysis.preprocess.QuantitationTypeConversionRelatedPreprocessingException
getCause() - Method in exception class ubic.gemma.core.analysis.preprocess.QuantitationTypeDetectionRelatedPreprocessingException
getCause() - Method in exception class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException
getCause() - Method in exception class ubic.gemma.core.loader.util.hdf5.H5Exception
getCause() - Method in exception class ubic.gemma.core.search.BaseCodeOntologySearchException
getCause() - Method in exception class ubic.gemma.core.search.SearchTimeoutException
getCause() - Method in exception class ubic.gemma.core.search.source.HibernateSearchException
getCellBrowserDatasetName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getCellBrowserUrl() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: URL for the Cell Browser, if available.
getCellCount() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getCellData() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
getCellIdForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getCellIdForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getCellIdForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getCellIdForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix: Obtain the cell ID of a given column.
getCellIds() - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getCellIds() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getCellIds() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getCellIds() - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix: Note: cell IDs are only unique within a given assay
getCellIds() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Cell identifiers.
getCellIds() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: Cell identifiers.
getCellIdsBySample(int) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Obtain a list of cell IDs for the given sample.
getCellLevelCharacteristicAt(CellLevelCharacteristics, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the characteristic at a given cell index.
getCellLevelCharacteristicAt(CellLevelCharacteristics, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristicAt(CellLevelCharacteristics, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellLevelCharacteristicAt(CellLevelCharacteristics, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristics() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getCellLevelCharacteristics() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Set of cell-level characteristics.
getCellLevelCharacteristics() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: All the other cell-level characteristics.
getCellLevelCharacteristics(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain all cell-level characteristics from all single-cell dimensions.
getCellLevelCharacteristics(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristics(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellLevelCharacteristics(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLevelCharacteristics(ExpressionExperiment, Category) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain all cell-level characteristics from all single-cell dimensions matching the given category.
getCellLevelCharacteristics(ExpressionExperiment, Category) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristics(ExpressionExperiment, Category) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain CLC for given category.
getCellLevelCharacteristics(ExpressionExperiment, Category) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a specific cell-level characteristic by ID.
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a CLC by name.
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, Category) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellLevelCharacteristics(ExpressionExperiment, QuantitationType, Category) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristicsCategory(CellLevelCharacteristics) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the category of a cell-level characteristic.
getCellLevelCharacteristicsCategory(CellLevelCharacteristics) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristicsCategory(ExpressionExperiment, CellLevelCharacteristics) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellLevelCharacteristicsCategory(ExpressionExperiment, CellLevelCharacteristics) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLevelMask(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a mask if one is unambiguously defined for the given experiment and quantitation type.
getCellLevelMask(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellLineType() - Method in class ubic.gemma.rest.AnnotationsWebService.LexicalTermMetadataValueObject: Cellosaurus cell-line category, e.g.
getCellMetadataFileOptionValue(CommandLine, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
getCellMetadataFileOptionValue(CommandLine, boolean, String, boolean) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
getCellRangerExecutable() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation
getCellSize() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getCellSize() - Method in interface ubic.gemma.core.visualization.Heatmap: Get the size of a cell in pixels.
getCellSize() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getCellType() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getCellType(int) - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Obtain the type assignment of a given cell.
getCellTypeAssignment(ExpressionExperiment, QuantitationType, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a cell type assignment by ID.
getCellTypeAssignment(ExpressionExperiment, QuantitationType, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAssignment(ExpressionExperiment, QuantitationType, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a cell type assignment by ID.
getCellTypeAssignment(ExpressionExperiment, QuantitationType, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAssignment(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a cell type assignment by name.
getCellTypeAssignment(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAssignment(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a cell type assignment by name.
getCellTypeAssignment(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAssignmentByProtocol(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellTypeAssignmentByProtocol(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAssignmentByProtocol(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a cell type assignment by a protocol identifier.
getCellTypeAssignmentByProtocol(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAssignmentDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: A description to use for the cell type assignment.
getCellTypeAssignmentFile() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: A location where cell type can be found in a format covered by GenericMetadataSingleCellDataLoader.
getCellTypeAssignmentName() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: A name to use for the cell type assignment.
getCellTypeAssignmentProtocol() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: A protocol to use for the cell type assignment.
getCellTypeAssignmentProtocols() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain all cell type assignment protocols currently used.
getCellTypeAssignmentProtocols() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAssignmentProtocols() - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a collection of protocols used to assign cell types to single-cell vectors.
getCellTypeAssignmentProtocols() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAssignments() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Set of cell types assignment to individual cells.
getCellTypeAssignments() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: All the cell type assignments.
getCellTypeAssignments(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoader
getCellTypeAssignments(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractDelegatingSingleCellDataLoader
getCellTypeAssignments(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getCellTypeAssignments(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
getCellTypeAssignments(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader: MEX does not provide cell type labels.
getCellTypeAssignments(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getCellTypeAssignments(SingleCellDimension) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader: Load single-cell type assignments present in the data.
getCellTypeAssignments(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellTypeAssignments(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAssignments(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain all the cell type labellings from all single-cell vectors.
getCellTypeAssignments(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAssignments(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellTypeAssignments(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAssignments(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellTypeAssignments(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAssignmentsWithoutIndices(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellTypeAssignmentsWithoutIndices(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAssignmentsWithoutIndices(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellTypeAssignmentsWithoutIndices(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a cell type assignment by ID without loading the indices.
getCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a cell type assignment by name without loading the indices.
getCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAt(CellTypeAssignment, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the cell type at a given cell index.
getCellTypeAt(CellTypeAssignment, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAt(CellTypeAssignment, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellTypeAt(CellTypeAssignment, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypeAt(ExpressionExperiment, QuantitationType, Long, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellTypeAt(ExpressionExperiment, QuantitationType, Long, int) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAt(ExpressionExperiment, QuantitationType, Long, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellTypeAt(ExpressionExperiment, QuantitationType, Long, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAt(ExpressionExperiment, QuantitationType, String, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellTypeAt(ExpressionExperiment, QuantitationType, String, int) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeAt(ExpressionExperiment, QuantitationType, String, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getCellTypeAt(ExpressionExperiment, QuantitationType, String, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeFactor(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain the cell type factor.
getCellTypeFactor(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeFactorName() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
getCellTypeIds() - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: A list of IDs, one-per-cell, that refers to one of the cell type labels in CellTypeAssignmentValueObject.cellTypes.
getCellTypeIndices() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Cell types assignment to individual cells from the CellTypeAssignment.cellTypes collections.
getCellTypes() - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: A set of cell types that are assigned to individual cells.
getCellTypes() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: List of cell types.
getCellTypes(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCellTypes(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCellTypes(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain the cell types of a given single-cell dataset.
getCellTypes(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getCellTypeUriFactorName() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
getCenterName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
getChangelogFilePath(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileService: Absolute path of the changelog file for expressionExperiment, whether or not it exists yet.
getChangelogFilePath(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileServiceImpl
getChanges() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getChannel(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getChannelHoldCount() - Method in class ubic.gemma.core.util.locking.FileLockInfo: Number of reentrant holds on the FileChannel.
getChannelNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getChannelNumber() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getChannels() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getCharacteristic() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getCharacteristic() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.SampleCharacteristicAdd
getCharacteristic() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.TagAdd
getCharacteristic() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm: Characteristic.
getCharacteristic(int) - Method in interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics: Obtain the characteristic assigned to a given cell.
getCharacteristic(int) - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Use CellTypeAssignment.getCellType(int) instead.
getCharacteristic(int) - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
getCharacteristicIds() - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
getCharacteristicOriginalValues() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Map of categories to original text values (for this biomaterial).
getCharacteristics() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getCharacteristics() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
getCharacteristics() - Method in class ubic.gemma.model.analysis.Investigation
getCharacteristics() - Method in interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics: List of characteristic.
getCharacteristics() - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
getCharacteristics() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Deprecated.
Use CellTypeAssignment.getCellTypes() instead.
getCharacteristics() - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
getCharacteristics() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getCharacteristics() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
getCharacteristics() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The characteristics associated with this factor value.
getCharacteristics() - Method in interface ubic.gemma.model.expression.experiment.BioAssaySetValueObject
getCharacteristics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getCharacteristics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getCharacteristics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getCharacteristics() - Method in class ubic.gemma.model.expression.experiment.FactorValue: Collection of Statement describing this factor value.
getCharacteristics() - Method in class ubic.gemma.model.genome.gene.GeneSet
getCharacteristicsRewritten() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
getCharacteristicsRewritten() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getCharacteristicValues() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
getCharId() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.

It could be the id of the measurement if there is no characteristic.
getChemblId() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound: ChEMBL's accession for the compound, e.g.
getChemicals() - Method in class ubic.gemma.model.common.description.BibliographicReference
getChemicalsTerms() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getChemistryIdentifiers() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation: Obtain a list of supported chemistry identifiers.
getChildren() - Method in class ubic.gemma.core.loader.util.hdf5.H5Location: Obtain the children of the given H5 location.
getChildren(boolean) - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Obtain the children of this term via subclasses and additional properties.
getChildren(boolean, boolean) - Method in interface ubic.gemma.core.ontology.model.OntologyTerm
getChildren(boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
getChildren(boolean, boolean, boolean) - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Obtain the children of this term via subclass relationships and possibly some additional properties.
getChildren(boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getChildren(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location
getChildren(Collection, boolean, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain all the children of a given set of terms, excluding obsolete terms.
getChildren(Collection, boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getChildren(Collection, boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getChildren(Collection, boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getChildren(Collection, boolean, boolean, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain all the children of a given set of terms.
getChildren(Collection, boolean, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain the children of a collection of terms.
getChildren(Collection, boolean, boolean, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getChildrenOccurrence(Map, String) - Method in interface ubic.gemma.core.ontology.GoMetric
getChildrenOccurrence(Map, String) - Method in class ubic.gemma.core.ontology.GoMetricImpl
getChipTypes(ExpressionExperiment, Collection) - Static method in class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractor: Extract a string like "Rat230_2" from CEL files.
getChiSquare() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
getChiSquared() - Method in class ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
getChromosome() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getChromosome() - Method in class ubic.gemma.model.genome.ChromosomeLocation
getChromosome() - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
getChromosome() - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
getCitation() - Method in class ubic.gemma.model.common.description.BibliographicReference
getCitation() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getCitation() - Method in class ubic.gemma.model.common.description.CitationValueObject
getCitationXrefCount() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: How many literature citations AnnotationsWebService.OntologyTermValueObject.dbXrefs is holding back, or would be holding back if they had not been asked for.
getCity() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getCity() - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
getClassCount() - Method in class ubic.gemma.core.ontology.providers.OntologySlimExtractor.ExtractResult
getCliContext() - Method in class ubic.gemma.cli.util.AbstractCLI: Obtain the CLI context.
getClientRef() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.SampleCharacteristicAdd
getClientRef() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.TagAdd
getClientRef() - Method in class ubic.gemma.rest.DatasetsWebService.Canonicalization: The item's clientRef, so the client can map the rewrite back to its chip without parsing.
getClientRef() - Method in class ubic.gemma.rest.DatasetsWebService.EntityRef
getClosedAt() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
getCluster() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getClusterField() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getClusterName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getCoating() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getCode() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound: The code as asked about.
getCode() - Method in interface ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse.Error
getCode() - Method in class ubic.gemma.rest.TaskStatusValueObject.TaskError: Stable, machine-readable code.
getCode() - Method in class ubic.gemma.rest.util.WellComposedErrorBody
getCodes() - Method in class ubic.gemma.core.loader.util.anndata.CategoricalArray
getCoefficient() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getCoefficient() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
getCoefficients() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: The matrix of coefficients x for Ax = b (parameter estimates).
getCoefficients() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getCoexpressionDataFilename(ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils: Obtain the filename for writing coexpression data.
getCoexpressionMatrix() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
getCol() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getColByName(C) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix: Return a copy of a given column.
getColIndexByName(C) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
getColIndexByName(C) - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Get the index of a column by name.
getCollapsedCount() - Method in class ubic.gemma.rest.CompactAuditEventValueObject
getCollectionId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getCollectionInstance(MethodInvocation) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter: Get the collection from the invocation.
getCollectionInstance(MethodInvocation) - Method in class ubic.gemma.core.security.acl.voter.AclEntryMapValueVoter
getCollectionInstance(MethodInvocation) - Method in class ubic.gemma.core.security.acl.voter.AclEntryMapVoter
getCollectionUri(String) - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils
getColName(int) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
getColName(int) - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Gte the column name for an index.
getColNames() - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
getColNames() - Method in interface ubic.gemma.core.util.matrix.Matrix2D
getColObj(int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
getColObj(int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
getColObj(int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
getColObj(int) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
getColObj(int) - Method in interface ubic.gemma.core.util.matrix.PrimitiveMatrix
getColObj(int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
getColObj(int) - Method in class ubic.gemma.core.util.matrix.StringMatrix
getColor() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Deprecated.
getColor(int) - Method in class ubic.gemma.core.util.graphics.ColorMap
getColor(int, int) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getColor(int, int) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getColorMap() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getColorMap() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getColorMatrix() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getColors() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getColRange(int, int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
getColRange(int, int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
getColRange(int, int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getColRange(int, int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
getColRange(int, int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
getColsCount() - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection
getColumn() - Method in class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult: Affected column or -1 if all columns are affected.
getColumn() - Method in class ubic.gemma.rest.PvalueDistributionValueObject
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a single column of the matrix.
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix: Access a single column of the matrix.
getColumn(int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
getColumn(int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
getColumn(int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getColumn(int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
getColumn(int) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
getColumn(int) - Method in interface ubic.gemma.core.util.matrix.ObjectMatrix
getColumn(int) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
getColumn(int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
getColumn(int) - Method in class ubic.gemma.core.util.matrix.StringMatrix
getColumn(String) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain a column, the element type is guessed as per Dataframe.getColumnType(String)
getColumn(String, Class) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain a column of the given element type.
getColumn(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getColumn(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getColumn(BioAssay) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix: Access a single column of the matrix.
getColumnAsDoubles(int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
getColumnAsDoubles(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getColumnAsDoubles(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveDoubleMatrix: Retrieve the given column without boxing.
getColumnAsDoubles(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getColumnAsDoubles(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
getColumnAsDoubles(BioAssay) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveDoubleMatrix: Retrieve the given column without boxing, or null if the assay is not part of this matrix.
getColumnAsDoubles(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getColumnAsInts(int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
getColumnAsInts(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveIntMatrix: Retrieve the given column without boxing.
getColumnAsInts(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getColumnAsInts(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
getColumnAsInts(BioAssay) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveIntMatrix: Retrieve the given column without boxing.
getColumnByName(C) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getColumnCount() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getColumnCount() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getColumnData(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getColumnData(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getColumnDescriptions() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
getColumnEncodingType(String) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain the encoding type of a column.
getColumnIndex(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getColumnIndex(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix: Obtain the column index of a given assay.
getColumnIndex(BioAssay) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix
getColumnIndex(BioMaterial) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getColumnIndex(BioMaterial) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getColumnIndex(BioMaterial) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix
getColumnIndex(BioMaterial) - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix
getColumnLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getColumnLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix: Obtain a label suitable for describing a column of the matrix.
getColumnLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getColumnLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractSingleCellExpressionDataMatrix
getColumnLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getColumnName() - Method in class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult: Affected column name, if known.
getColumnName(int) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getColumnName(int) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getColumnNames() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData: The column names mean different things in different subclasses.
getColumnNames() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getColumnNames() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getColumns() - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain all the columns defined in the dataframe.
getColumns() - Method in class ubic.gemma.rest.HeatmapDataValueObject: Optional.
getColumnsAfterOutliersFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getColumnType(String) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Guess the type of a given column.
getCommandAliases() - Method in class ubic.gemma.cli.util.AbstractCLI
getCommandAliases() - Method in interface ubic.gemma.cli.util.CLI: A list of aliases for the command that can be used to locate this class.
getCommandGroup() - Method in class ubic.gemma.apps.AclLinterCli
getCommandGroup() - Method in class ubic.gemma.apps.AffyProbeCollapseCli
getCommandGroup() - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli
getCommandGroup() - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
getCommandGroup() - Method in class ubic.gemma.apps.BibRefUpdaterCli
getCommandGroup() - Method in class ubic.gemma.apps.BlacklistCli
getCommandGroup() - Method in class ubic.gemma.apps.CellXGeneDataAdderCli
getCommandGroup() - Method in class ubic.gemma.apps.CellXGeneDataDownloaderCli
getCommandGroup() - Method in class ubic.gemma.apps.ExperimentalDesignViewCli
getCommandGroup() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
getCommandGroup() - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli
getCommandGroup() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli
getCommandGroup() - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI
getCommandGroup() - Method in class ubic.gemma.apps.FindObsoleteTermsCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli
getCommandGroup() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli
getCommandGroup() - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator
getCommandGroup() - Method in class ubic.gemma.apps.GeoGrabberCli
getCommandGroup() - Method in class ubic.gemma.apps.GeoSingleCellDataDownloaderCli
getCommandGroup() - Method in class ubic.gemma.apps.IndexGemmaCLI
getCommandGroup() - Method in class ubic.gemma.apps.InitializeDatabaseCli
getCommandGroup() - Method in class ubic.gemma.apps.ListExpressionDataFIleLocksCli
getCommandGroup() - Method in class ubic.gemma.apps.LoadExpressionDataCli
getCommandGroup() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli
getCommandGroup() - Method in class ubic.gemma.apps.MergeDuplicateBibRefsCli
getCommandGroup() - Method in class ubic.gemma.apps.MultifunctionalityCli
getCommandGroup() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI
getCommandGroup() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI
getCommandGroup() - Method in class ubic.gemma.apps.ProtocolAdderCli
getCommandGroup() - Method in class ubic.gemma.apps.ProtocolDeleterCli
getCommandGroup() - Method in class ubic.gemma.apps.PubMedLoaderCli
getCommandGroup() - Method in class ubic.gemma.apps.PubMedSearcher
getCommandGroup() - Method in class ubic.gemma.apps.SingleCellDataTransformCli
getCommandGroup() - Method in class ubic.gemma.apps.TaxonLoaderCli
getCommandGroup() - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli
getCommandGroup() - Method in class ubic.gemma.apps.UpdateDatabaseCli
getCommandGroup() - Method in class ubic.gemma.apps.UpdateGene2CsCli
getCommandGroup() - Method in class ubic.gemma.apps.UpdateOntologyRelationsCli
getCommandGroup() - Method in class ubic.gemma.apps.UpdatePubMedCli
getCommandGroup() - Method in class ubic.gemma.cli.util.AbstractCLI
getCommandGroup() - Method in interface ubic.gemma.cli.util.CLI: Obtain the command group for this CLI.
getCommandName() - Method in class ubic.gemma.apps.AclLinterCli
getCommandName() - Method in class ubic.gemma.apps.AffyDataFromCelCli
getCommandName() - Method in class ubic.gemma.apps.AffyProbeCollapseCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignAuditTrailCleanupCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignBlatCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignMapSummaryCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignMergeCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignProbeCleanupCLI
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignReportCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli
getCommandName() - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli
getCommandName() - Method in class ubic.gemma.apps.BatchEffectPopulationCli
getCommandName() - Method in class ubic.gemma.apps.BibRefUpdaterCli
getCommandName() - Method in class ubic.gemma.apps.BioSequenceCleanupCli
getCommandName() - Method in class ubic.gemma.apps.BlacklistCli
getCommandName() - Method in class ubic.gemma.apps.CellLevelMetadataWriterCli
getCommandName() - Method in class ubic.gemma.apps.CellXGeneDataAdderCli
getCommandName() - Method in class ubic.gemma.apps.CellXGeneDataDownloaderCli
getCommandName() - Method in class ubic.gemma.apps.CellXGeneGrabberCli
getCommandName() - Method in class ubic.gemma.apps.CompleteCli
getCommandName() - Method in class ubic.gemma.apps.DeleteDiffExCli
getCommandName() - Method in class ubic.gemma.apps.DeleteExperimentsCli
getCommandName() - Method in class ubic.gemma.apps.DetectQuantitationTypeCli
getCommandName() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli
getCommandName() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisWriterCli
getCommandName() - Method in class ubic.gemma.apps.ExperimentalDesignImportCli
getCommandName() - Method in class ubic.gemma.apps.ExperimentalDesignViewCli
getCommandName() - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI
getCommandName() - Method in class ubic.gemma.apps.ExpressionDataCorrMatCli
getCommandName() - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI
getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli
getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli
getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogViewerCli
getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli
getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli
getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli
getCommandName() - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli
getCommandName() - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli
getCommandName() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli
getCommandName() - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI
getCommandName() - Method in class ubic.gemma.apps.FactorValueOntologyWriterCli
getCommandName() - Method in class ubic.gemma.apps.FindObsoleteTermsCli: Deprecated.
getCommandName() - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli
getCommandName() - Method in class ubic.gemma.apps.GeeqCli
getCommandName() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli
getCommandName() - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator
getCommandName() - Method in class ubic.gemma.apps.GeoGrabberCli
getCommandName() - Method in class ubic.gemma.apps.GeoSingleCellDataDownloaderCli
getCommandName() - Method in class ubic.gemma.apps.IndexGemmaCLI
getCommandName() - Method in class ubic.gemma.apps.InitializeDatabaseCli
getCommandName() - Method in class ubic.gemma.apps.ListExpressionDataFIleLocksCli
getCommandName() - Method in class ubic.gemma.apps.ListQuantitationTypesCli
getCommandName() - Method in class ubic.gemma.apps.LoadExpressionDataCli
getCommandName() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli
getCommandName() - Method in class ubic.gemma.apps.LockExpressionDataFileCli
getCommandName() - Method in class ubic.gemma.apps.MakeExperimentPrivateCli
getCommandName() - Method in class ubic.gemma.apps.MakeExperimentsPublicCli
getCommandName() - Method in class ubic.gemma.apps.MergeDuplicateBibRefsCli
getCommandName() - Method in class ubic.gemma.apps.MultifunctionalityCli
getCommandName() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI
getCommandName() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI
getCommandName() - Method in class ubic.gemma.apps.OrderVectorsByDesignCli
getCommandName() - Method in class ubic.gemma.apps.ProcessedDataComputeCLI
getCommandName() - Method in class ubic.gemma.apps.ProcessedDataDeleterCli
getCommandName() - Method in class ubic.gemma.apps.ProtocolAdderCli
getCommandName() - Method in class ubic.gemma.apps.ProtocolDeleterCli
getCommandName() - Method in class ubic.gemma.apps.ProtocolListCli
getCommandName() - Method in class ubic.gemma.apps.PubMedLoaderCli
getCommandName() - Method in class ubic.gemma.apps.PubMedSearcher
getCommandName() - Method in class ubic.gemma.apps.RawDataDeleterCli
getCommandName() - Method in class ubic.gemma.apps.RawExpressionDataWriterCli
getCommandName() - Method in class ubic.gemma.apps.RefreshExperimentCli
getCommandName() - Method in class ubic.gemma.apps.ReplaceDataCli
getCommandName() - Method in class ubic.gemma.apps.RNASeqDataAddCli
getCommandName() - Method in class ubic.gemma.apps.SingleCellCellTypeFactorCreatorCli
getCommandName() - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli
getCommandName() - Method in class ubic.gemma.apps.SingleCellDataDeleterCli
getCommandName() - Method in class ubic.gemma.apps.SingleCellDataLoaderCli
getCommandName() - Method in class ubic.gemma.apps.SingleCellDataTransformCli
getCommandName() - Method in class ubic.gemma.apps.SingleCellDataUpdaterCli
getCommandName() - Method in class ubic.gemma.apps.SingleCellDataWriterCli
getCommandName() - Method in class ubic.gemma.apps.SingleCellSparsityMetricsUpdaterCli
getCommandName() - Method in class ubic.gemma.apps.SplitExperimentCli
getCommandName() - Method in class ubic.gemma.apps.SVDCli
getCommandName() - Method in class ubic.gemma.apps.TaxonLoaderCli
getCommandName() - Method in class ubic.gemma.apps.UcscCellBrowserGrabberCli
getCommandName() - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli
getCommandName() - Method in class ubic.gemma.apps.UpdateDatabaseCli
getCommandName() - Method in class ubic.gemma.apps.UpdateEe2AdCli
getCommandName() - Method in class ubic.gemma.apps.UpdateEE2CCli
getCommandName() - Method in class ubic.gemma.apps.UpdateExternalRelationsCli
getCommandName() - Method in class ubic.gemma.apps.UpdateGene2CsCli
getCommandName() - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCli
getCommandName() - Method in class ubic.gemma.apps.UpdateOntologyRelationsCli
getCommandName() - Method in class ubic.gemma.apps.UpdatePubMedCli
getCommandName() - Method in class ubic.gemma.apps.VectorMergingCli
getCommandName() - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCli
getCommandName() - Method in class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator.CommandMeta
getCommandName() - Method in class ubic.gemma.cli.util.AbstractCLI
getCommandName() - Method in interface ubic.gemma.cli.util.CLI: A short memorable name for the command that can be used to locate this class.
getCommandNameOrAliasUsed() - Method in interface ubic.gemma.cli.util.CLIContext: Command name or alias used to invoke the command, or null if this was invoked using the fully qualified class name.
getCommandNameOrAliasUsed() - Method in class ubic.gemma.cli.util.SystemCLIContext
getComment() - Method in class ubic.gemma.core.ontology.lexical.LexicalAnnotationProperty
getComment() - Method in interface ubic.gemma.core.ontology.model.OntologyResource: A comment for the resource, if available, otherwise null.
getComment() - Method in class ubic.gemma.core.ontology.simple.OntologyIndividualSimple
getComment() - Method in class ubic.gemma.core.ontology.simple.OntologyPropertySimple
getComment() - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getComment() - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
getComment() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getCommitAnnotationSetId() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getCommitAnnotationSetId() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getCommonName() - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
getCommonName() - Method in class ubic.gemma.model.genome.Taxon
getCommonName() - Method in class ubic.gemma.model.genome.TaxonValueObject
getComparator() - Static method in class ubic.gemma.model.common.description.Characteristic: Obtain a full comparator for characteristics that fallbacks on the ID if everything else is equal.
getComparator() - Static method in class ubic.gemma.model.common.description.DatabaseEntry: Compares DatabaseEntry by version.
getCompletedAt() - Method in class ubic.gemma.rest.TaskStatusValueObject
getCompletedTasks() - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter: Obtain the number of completed tasks (either with a success or failure result).
getCompleteness() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getCompletions() - Method in interface ubic.gemma.cli.completion.CompletionSource
getCompletions() - Method in class ubic.gemma.cli.completion.LoggerCompletionSource
getCompletions() - Method in class ubic.gemma.cli.completion.SettingsCompletionSource
getComponent() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails.BatchEffectStatistics: A PCA component that is explained by the batch factor.
getComponent() - Method in class ubic.gemma.rest.DatasetsWebService.BatchEffectStatisticsValueObject
getComponentNumber() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
getComponentNumber() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
getComponentNumber() - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
getComponents() - Method in class ubic.gemma.rest.monitoring.HealthWebService.HealthValueObject
getComponentVarianceProportion() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails.BatchEffectStatistics: The variance explained by the component.
getComponentVarianceProportion() - Method in class ubic.gemma.rest.DatasetsWebService.BatchEffectStatisticsValueObject
getCompositeSequence() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
getCompositeSequence() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getCompositeSequence() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getCompositeSequenceCount() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Number of probes (composite sequences) across all platforms that map to this gene.
getCompositeSequenceCount(Gene, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
getCompositeSequenceCount(Gene, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
getCompositeSequenceCount(Gene, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
getCompositeSequenceCount(Gene, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
getCompositeSequenceCount(Gene, boolean) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Obtain the number of platform elements (e.g.
getCompositeSequenceCount(Gene, boolean) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getCompositeSequenceCountById(long, boolean) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
getCompositeSequenceCountById(long, boolean) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl: Gets a count of the CompositeSequences related to the gene identified by the given id.
getCompositeSequenceCountById(Long, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
getCompositeSequenceCountById(Long, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
getCompositeSequenceCountById(Long, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
getCompositeSequenceCountById(Long, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
getCompositeSequenceDescription() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getCompositeSequenceId() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getCompositeSequenceName() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getCompositeSequences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getCompositeSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getCompositeSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getCompositeSequences(ArrayDesign, int, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getCompositeSequences(ArrayDesign, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getCompositeSequences(ArrayDesign, int, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getCompositeSequences(ArrayDesign, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getCompositeSequences(Gene, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
getCompositeSequences(Gene, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
getCompositeSequences(Gene, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
getCompositeSequences(Gene, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
getCompositeSequences(Gene, boolean) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Get the composite sequences (e.g.
getCompositeSequences(Gene, boolean) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getCompositeSequences(Gene, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries: Given a gene, get all the composite sequences that map to it.
getCompositeSequences(Gene, ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
getCompositeSequences(Gene, ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
getCompositeSequences(Gene, ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
getCompositeSequences(Gene, ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
getCompositeSequences(Gene, ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Get the composite sequences (e.g.
getCompositeSequences(Gene, ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getCompositeSequencesById(long, boolean) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
getCompositeSequencesById(long, boolean) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl: Gets all the CompositeSequences related to the gene identified by the given id.
getCompositeSequencesById(Long, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
getCompositeSequencesById(Long, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
getCompositeSequencesById(Long, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
getCompositeSequencesById(Long, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
getConditions() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
getConfidence() - Method in class ubic.gemma.core.geoscrape.GeoRecordMatcher.MatchResult: Confidence in [0,1]; v1 keyword matchers return 1.0 on a hit.
getConfidence() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getConfidence() - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
getConfidence() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssertion
getConfidence() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
getConfig() - Method in exception class ubic.gemma.core.analysis.expression.diff.AnalysisException
getConfigAttribute() - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManager
getConsider() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: oboInOwl:consider — candidates rather than a replacement, which is what a term that was SPLIT rather than merged leaves behind.
getConsiderUris() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
getConsole() - Method in interface ubic.gemma.cli.util.CLIContext: Obtain the console, if available.
getConsole() - Method in class ubic.gemma.cli.util.SystemCLIContext
getConsole() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig
getConsole() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Console to use for reporting progress.
getConstructionProtocol() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
getContact() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
getContact() - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
getContactName() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getContents() - Method in class ubic.gemma.core.ontology.lexical.LexicalAnnotationProperty
getContents() - Method in interface ubic.gemma.core.ontology.model.AnnotationProperty: The value associated to this annotation as a string.
getContentType() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getContentType() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetMetadataFileValueObject: MIME content type the server will serve the file with.
getContext(Class) - Method in class ubic.gemma.rest.providers.ObjectMapperResolver
getContrastCoefficients() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getContrastCoefficients(String) - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getContrastCoefficientStderr(String) - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary: For the requested factor, return the standard errors associated with the contrast coefficient estimates.
getContrastFactorValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getContrastPValues(String) - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getContrasts() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
getContrasts() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getContrasts() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
getContrasts() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getContrastsFactorValueIds() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getContrastsFactorValues() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getContrastTStats(String) - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getContributer() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getContributors() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getControlGroupTerms() - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection: The control-group terms and URIs themselves, for callers that have to recognise a baseline in SQL rather than over loaded entities.
getControlGroupUris() - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection
getConversionService() - Static method in class ubic.gemma.persistence.util.Filter: Obtain the conversion service used for parsing values.
getConvertibleTypes() - Method in class ubic.gemma.persistence.util.ServiceBasedEntityConverter
getCookie() - Method in class ubic.gemma.core.loader.entrez.EntrezQuery
getCookie(Document) - Static method in class ubic.gemma.core.loader.entrez.EntrezXmlUtils
getCoordFiles() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
getCoords() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getCorrectedPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getCorrectedPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject: Rounded on the way out, as pValue is.
getCorrectedPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getCorrectedPvalue() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject: FDR-corrected p-value for the contrast represented by the result-set used to populate this VO.
getCorrectedPValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getCorrectedPValueBin() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getCorrespondingExperiments() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getCorrespondingSamples(String) - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
getCorrMatIssues() - Method in class ubic.gemma.model.expression.experiment.Geeq
getCorrMatIssues() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getCorrP() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getCount() - Method in class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat: Number of public expression experiments with this accession source.
getCount() - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow: Public experiments whose creation event falls on or after HomeStats.AddedInWindow.since.
getCount() - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
getCount() - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat: Number of expression experiments carrying this term as a treatment annotation.
getCount() - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Annotation-burden metric: Σ numberOfExpressionExperiments over each matched term — a popular drug used in 40 datasets contributes 40, not 1.
getCount() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
getCount() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
getCount() - Method in class ubic.gemma.core.loader.expression.sra.model.SraBase
getCount() - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
getCount() - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
getCount() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
getCount() - Method in class ubic.gemma.rest.PvalueDistributionValueObject.Bin
getCount(Document) - Static method in class ubic.gemma.core.loader.entrez.EntrezXmlUtils
getCountry() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getCountry() - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
getCoverage() - Method in class ubic.gemma.core.loader.util.mapper.EntityMapper.MappingStatistics: Proportion of the candidates that were mapped by an identifier.
getCoveredSeedUris() - Method in class ubic.gemma.core.ontology.providers.OntologySlimExtractor.ExtractResult
getCpuInfo() - Method in class ubic.gemma.core.util.runtime.ExtendedRuntime
getCreated() - Method in class ubic.gemma.rest.DatasetsWebService.CurationSectionChange
getCreatedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getCreatedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getCreatedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getCreatedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getCreateDate() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getCreateDate(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getCreateDate(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
getCreatedBy() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getCreatedBy() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getCreateEvents(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the creation events for the given auditables.
getCreateEvents(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getCreateEvents(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getCreateEvents(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getCriteria() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
getCriteria() - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
getCriteriaApplied() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark: Comma-separated list of matcher names applied (e.g.
getCrossReferences() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getCrossReferences() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getCrossReferences() - Method in interface ubic.gemma.core.ontology.providers.OntologyService
getCrossReferencesFromSource() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService: Read cross-references from the cached SOURCE artifact instead of the loaded model.
getCrossReferencesFromSource() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getCrossReferencesFromSource() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Cross-references read from the ontology's SOURCE artifact on disk, rather than from whatever model happens to be loaded.
getCrossSpeciesExactMatch() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonConstraintValueObject: MONDO's crossSpeciesExactMatch targets — the same disease in another species, typically the human counterpart.
getCs2GeneIdMapForGenes(Collection, Collection, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries: Obtain a mapping of probe to gene IDs for the given gene IDs and platforms IDs.
getCs2GeneMap(Collection, Collection, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getCs2GeneMap(Collection, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getCs2GeneMapForProbes(Collection, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getCurationAgentHealth() - Method in class ubic.gemma.rest.AdminWebService: Out-of-process liveness probe for the gemma-curation-agents Python service.
getCurationDecisions(DatasetArg, boolean) - Method in class ubic.gemma.rest.DatasetsWebService: The standing refusals on a dataset, or the whole decision log.
getCurationDetails() - Method in interface ubic.gemma.model.common.auditAndSecurity.curation.Curatable
getCurationDetails() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getCurationDetails() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getCurationDetails() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getCurationDetailsNote() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getCurationLock(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: 🛑 This route deliberately serves the BARE object, not the {"data": …} envelope the rest of the service uses.
getCurationLocks(DatasetArrayArg) - Method in class ubic.gemma.rest.DatasetsWebService
getCurationLocksBulk(DatasetsWebService.CurationLockBulkRequest) - Method in class ubic.gemma.rest.DatasetsWebService
getCurationNote() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getCurationNote() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getCurationNote() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
getCurationNote() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
getCurationNote() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsUpdateRequest
getCurationNote() - Method in class ubic.gemma.rest.PipelineStatusValueObject: Admin-only; remains null for non-administrators.
getCurationPending() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject: Whether curation of the dataset is under way right now.
getCurationStatus() - Method in class ubic.gemma.rest.AdminWebService: Snapshot of the annotation-set -> ticket lifecycle: per-role AnnotationSet counts in the recent windows, open-ticket counts by TicketType, distinct agent run id count, and latest-createdAt timestamp.
getCurie() - Method in class ubic.gemma.core.ontology.model.OntologyXref: The foreign identifier, normalized by OntologyXref.normalizeCurie(String).
getCurrentAssignee() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
getCurrentId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
getCurrentPassword() - Method in class ubic.gemma.rest.RootWebService.ChangePasswordRequest
getCurrentState() - Method in exception class ubic.gemma.persistence.service.expression.experiment.DisallowedWorkflowTransitionException
getCurrentState() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowTransition
getCurrentState(Investigation) - Method in interface ubic.gemma.persistence.service.expression.experiment.WorkflowService
getCurrentState(Investigation) - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceImpl
getCurrentUser() - Method in interface ubic.gemma.core.security.authentication.UserManager: Obtain the User corresponding to the currently logged in user.
getCurrentUser() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
getCurrentUserHasWritePermission() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getCurrentUserIsOwner() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getCurrentUserIsOwner() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getCurrentUsername() - Method in interface ubic.gemma.core.security.authentication.UserDetailsManager: Returns a String username (the principal).
getCurrentUsername() - Method in interface ubic.gemma.core.security.authentication.UserManager: Obtain the username of the currently logged in user.
getCurrentUsername() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
getCurrentUsername() - Static method in class ubic.gemma.core.security.util.SecurityUtil: Returns the username of the authenticated user
getDailyReport() - Method in interface ubic.gemma.core.analysis.report.WhatsNewService: Generate the report from yesterday.
getDailyReport() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
getData() - Method in exception class ubic.gemma.core.loader.util.AlreadyExistsInSystemException
getData() - Method in class ubic.gemma.core.loader.util.anndata.DenseMatrix
getData() - Method in interface ubic.gemma.core.loader.util.anndata.Matrix: Obtain the H5 dataset underlying this matrix.
getData() - Method in class ubic.gemma.core.loader.util.anndata.SparseMatrix
getData() - Method in interface ubic.gemma.core.util.GemmaRestApiClient.DataResponse
getData() - Method in class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
getData() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getData() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: The data of this vector.
getData() - Method in class ubic.gemma.rest.util.ResponseDataObject
getDataAsBooleans() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsBuffer() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector: Obtain the data as a generic Buffer.
getDataAsChars() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsDoubleBuffer() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector: Obtain the data as a DoubleBuffer.
getDataAsDoubles() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsFloatBuffer() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsFloats() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsIntBuffer() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsInts() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsLongBuffer() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsLongs() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsObjects() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsStrings() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDataAsTabbedStrings() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getDatabaseSupplier() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getDataFile(String, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate any data file in the data directory.
getDataFile(String, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getDataFile(String, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
getDataFile(String, boolean, long, TimeUnit) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getDataFile(ExpressionExperiment, QuantitationType, ExpressionExperimentDataFileType, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
getDataFile(ExpressionExperiment, QuantitationType, ExpressionExperimentDataFileType, boolean, long, TimeUnit) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getDataFileOptionValue(CommandLine, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
getDataFileOptionValue(CommandLine, boolean, boolean, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
getDataFileOptionValue(CommandLine, boolean, boolean, boolean, String, boolean) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils: Obtain the result of the data file options added by DataFileOptionsUtils.addDataFileOptions(Options, String, boolean, boolean, boolean, boolean, boolean, BiConsumer)
getDataFileOptionValue(CommandLine, boolean, String, boolean) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
getDataIndices() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector: Positions of the non-zero data in the DataVector.getData() vector.
getDataOutputFilename(ExpressionExperiment, boolean, String) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils: Obtain a filename for writing the processed data.
getDataOutputFilename(ExpressionExperiment, List, boolean, String) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
getDataOutputFilename(ExpressionExperiment, List, QuantitationType, String) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils: Obtain the filename for writing a specific QT.
getDataOutputFilename(ExpressionExperiment, QuantitationType, String) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils: Obtain the filename for writing a specific QT.
getDataPath() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig: Load data from that specific path instead of looking up standard locations.
getDataProcessing() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getDataset(String) - Static method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils
getDataset(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location
getDataSet() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
getDatasetAllPublications(DatasetArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetAnnotations(DatasetArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the annotations for the given dataset.
getDatasetAssets() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetBatchInformation(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetCellLevelCharacteristics(DatasetArg, QuantitationTypeArg, HttpHeaders) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetCellTypeAssignment(DatasetArg, QuantitationTypeArg, String, String, ExcludeArg, Boolean, HttpHeaders) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetCompletions(String, int) - Method in class ubic.gemma.rest.CompletionsWebService
getDatasetConstraint() - Method in class ubic.gemma.model.common.search.SearchSettings: Constraint results to be related to the given dataset.
getDatasetConstraint() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getDatasetCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Total public expression experiments.
getDatasetCount() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
getDatasetCurationDetails(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetDataMatrix(String, QuantitationType, Map, Map, ProgressReporter) - Static method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils: Create a stream over the expression data matrix of a given dataset.
getDatasetDescription(String) - Static method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils
getDatasetDesign(DatasetArg, QuantitationTypeArg, Boolean, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the design for the given dataset.
getDatasetDesignJson(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the structured experimental design for the given dataset as JSON.
getDatasetDifferentialExpressionAnalyses(DatasetArg, OffsetArg, LimitArg, boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the differential analysis results for the given dataset.
getDatasetDifferentialExpressionAnalysisResultSets(DatasetArg, UriInfo) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the result sets of all the differential expression analyses of a dataset.
getDatasetDiffExAnalysisArchive(DatasetArg, Long, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve the differential-expression analysis archive for a dataset.
getDatasetDraftAnnotationSet(DatasetArg, String) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetExpression(DatasetArg, Boolean, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the data for the given dataset.
getDatasetGeeq(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetGeeqPublic(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Public sibling of DatasetsWebService.getDatasetGeeq(DatasetArg): returns the per-factor GEEQ breakdown without exposing the admin-only detected/manual override scores or the free-text otherIssues curator field, which live on GeeqAdminValueObject.
getDatasetGroupCompletions(String, int) - Method in class ubic.gemma.rest.CompletionsWebService
getDatasetGroups(DatasetArg, boolean, boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Groups that have ANY permission (read or admin) on the given dataset (gap §3c of GEMMA_UI_ENDPOINT_GAP.md).
getDatasetHasBatchInformation(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Indicate if the experiment has batch information.
getDatasetHeatmapData(DatasetArg, String, String, Long, Double, Integer, Integer, Integer, String, Long, QuantitationTypeArg, boolean) - Method in class ubic.gemma.rest.DatasetVisualizationWebService: Resolve raw matrix + metadata for a client-rendered heatmap.
getDatasetId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
getDatasetId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getDatasetId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getDatasetId() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject
getDatasetId() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
getDatasetId() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowTransition
getDatasetId() - Method in class ubic.gemma.rest.DatasetsWebService.StaleDatasetValueObject
getDatasetId() - Method in class ubic.gemma.rest.HeatmapDataValueObject
getDatasetIds() - Method in class ubic.gemma.rest.DatasetsWebService.CurationLockBulkRequest
getDatasetIds() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetTicketsBulkRequest
getDatasetIds() - Method in class ubic.gemma.rest.DatasetsWebService.PipelineStatusBulkRequest
getDatasetLink() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getDatasetMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getDatasetMeanVariance(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the per-probe mean / variance pre-computed by MeanVarianceService.
getDatasetMetadata(String) - Static method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils: Retrieve the metadata for a given dataset.
getDatasetMetadata(String, String) - Static method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils: Retrieve the metadata for a specific field.
getDatasetMetadataFile(DatasetArg, String, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Stream a single preprocessing-metadata file by type for a dataset.
getDatasetMetadataFiles(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: List the preprocessing-metadata files available for a dataset.
getDatasetMetadataFromCellXGene(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
getDatasetMetadataFromCellXGene(GeoSeries, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
getDatasetMetadataFromCellXGene(GeoSeries, String, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
getDatasetName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getDatasetName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getDatasetPermissions(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve the current sharing state of a dataset.
getDatasetPipelineStatus(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetPipelineStatusAlias(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI compatibility alias for DatasetsWebService.getDatasetPipelineStatus(DatasetArg): the UI uses the flatter, hyphenated path /datasets/{id}/pipeline-status; the canonical handler lives at /pipelineStatus.
getDatasetPipelineStatusBulk(DatasetsWebService.PipelineStatusBulkRequest) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetPlatforms(DatasetArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves platforms for the given dataset.
getDatasetProcessedExpression(DatasetArg, Boolean, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve processed expression data.
getDatasetQcMetrics(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the per-sample sequencing QC metrics for a dataset — read depth, mapping rate, duplication and the rest of the RNA-Seq pipeline's MultiQC general statistics — keyed by bioAssay id.
getDatasetQuantitationTypes(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve all available quantitation types for a dataset.
getDatasetRawExpression(DatasetArg, QuantitationTypeArg, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve raw expression data.
getDatasets() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
getDatasets() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getDatasets() - Static method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils: Obtain all the UCSC Cell Browser datasets.
getDatasets(QueryArg, FilterArg, OffsetArg, LimitArg, SortArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDataSets() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getDatasetsAdded() - Method in class ubic.gemma.core.analysis.report.HomeStats: How many public experiments were added to Gemma over each of several trailing windows, newest window first.
getDatasetSampleCorrelation(DatasetArg, DatasetsWebService.CorrelationMatrixChoice) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the sample-sample correlation matrix plus both outlier classifications (curator-flagged + algorithmic), unmasked.
getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the samples for the given dataset.
getDatasetsAnnotationsUsageStatistics(QueryArg, FilterArg, ExcludeArg, LimitArg, Integer, String, StringArrayArg, Boolean, StringArrayArg, Boolean, Boolean, Boolean, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsByAccessionSource() - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-external-database dataset counts — GEO, ArrayExpress, CELLxGENE, etc., plus a "none" bucket for datasets without an external accession (direct lab submissions / Gemma-native).
getDatasetsByCursor(Filters, Cursor, int) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Cursor-mode counterpart to SecurableFilteringVoEnabledService.loadValueObjects(Filters, Sort, int, int).
getDatasetsByIds(DatasetArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves all datasets matching the given identifiers.
getDatasetsCategoriesUsageStatistics(QueryArg, FilterArg, LimitArg, StringArrayArg, Boolean, StringArrayArg, Boolean, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsDifferentialExpression(DatasetArrayArg, Long, Double, LimitArg, Boolean, ExpLevelConsolidationArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the expression levels of genes highly expressed in the given component on given datasets.
getDatasetsDifferentialExpressionAnalysisResultsForGene(GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Double, HttpHeaders) - Method in class ubic.gemma.rest.DatasetsWebService: Obtain differential expression analysis results for a given gene.
getDatasetsDifferentialExpressionAnalysisResultsForGeneInTaxon(TaxonArg, GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Double, HttpHeaders) - Method in class ubic.gemma.rest.DatasetsWebService: Obtain differential expression analysis results for a given gene in a given taxon.
getDatasetsExpressionLevelsForGene(GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve the expression levels of a given gene across all datasets.
getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg, GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve the expression levels of a given gene and taxon across all datasets.
getDatasetsExpressionLevelsForGenes(DatasetArrayArg, GeneArrayArg, Boolean, ExpLevelConsolidationArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsExpressionLevelsForGenesInTaxon(DatasetArrayArg, TaxonArg, GeneArrayArg, Boolean, ExpLevelConsolidationArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the expression levels of given genes on given datasets.
getDatasetsExpressionPca(DatasetArrayArg, Integer, LimitArg, Boolean, ExpLevelConsolidationArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the expression levels of genes highly expressed in the given component on given datasets.
getDatasetShortName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getDatasetShortName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getDatasetShortName() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: The dataset's short name (GSE6966), so a list row can name its experiment.
getDatasetShortName() - Method in class ubic.gemma.rest.HeatmapDataValueObject
getDatasetSingleCellDimension(DatasetArg, QuantitationTypeArg, ExcludeArg, Boolean, HttpHeaders) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve the single-cell dimension for a given quantitation type.
getDatasetSingleCellExpression(DatasetArg, QuantitationTypeArg, Boolean, Boolean, HttpHeaders) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetSourceMetadata(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsPipelineStatus(DatasetArrayArg) - Method in class ubic.gemma.rest.DatasetsWebService: Bulk sibling of DatasetsWebService.getDatasetPipelineStatus(DatasetArg).
getDatasetsPlatformsUsageStatistics(QueryArg, FilterArg, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsTaxaUsageStatistics(QueryArg, FilterArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetSubSetById(DatasetArg, Long) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetSubSetGroup(DatasetArg, Long, boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetSubSetGroups(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve all the "groups" of subsets of a dataset.
getDatasetSubSets(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetSubSetSamples(DatasetArg, Long, CursorArg, LimitArg, boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the samples of a specific subset of a dataset.
getDatasetSvd(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the design for the given dataset.
getDatasetSvdLoadings(DatasetArg, Integer, Integer, DatasetsWebService.PcLoadingDirection) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve the top-N probe loadings on a chosen principal component, plus the bioAssay scores on that PC.
getDatasetTickets(DatasetArg, CursorArg, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetTicketsBulk(DatasetsWebService.DatasetTicketsBulkRequest) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getDatasetType() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
getDatasetUri(String) - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils: FIXME: CELLxGENE does not have a landing page for datasets.
getDatasetUri(String) - Static method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils: Construct a URL to access an UCSC Cell Browser dataset.
getDatasetVisibility(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI compatibility alias for DatasetsWebService.getDatasetPermissions(DatasetArg).
getDatasetWorkflow(Long) - Method in class ubic.gemma.rest.WorkflowWebService: Retrieve the current workflow state and full transition history of a dataset.
getDataSource() - Method in class ubic.gemma.core.goldenpath.GoldenPath
getDataType() - Method in class ubic.gemma.core.loader.util.anndata.DenseMatrix
getDataType() - Method in interface ubic.gemma.core.loader.util.anndata.Matrix: Obtain the data type used for the scalars of this matrix.
getDataType() - Method in class ubic.gemma.core.loader.util.anndata.SparseMatrix
getDataVectorType(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
getDataVectorType(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
getDataVectorType(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
getDataVectorType(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
getDataVectorType(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
getDataVectorType(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
getDataVectorTypes(Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService: Bulk variant of QuantitationTypeReadService.getDataVectorType(QuantitationType) keyed by QT.
getDataVectorTypes(Collection) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
getDataVectorTypes(Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
getDataVectorTypes(Collection) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
getDate() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getDate() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getDate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getDate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
getDate() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject
getDateArrayDesignLastUpdated() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: The date the platform associated with the experiment was last updated.
getDateBatchFetch() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDateCached() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getDateCached() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: The date this object was generated.
getDateCorrelations() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: Map of component to correlation that component with "batch/scan date"
getDateCreated() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: When the dataset was created in Gemma — loaded, not published.
getDateDifferentialAnalysis() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDateLinkAnalysis() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDateMissingValueAnalysis() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDatePcaAnalysis() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDateProcessedDataVectorComputation() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDatePVals() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: P-values associated to the "batch/scan date" component.
getDates() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: Date associated to the SVDResult.bioMaterials.
getDays() - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow: Width of the window in days (7, 30, 90, 365).
getDbPool() - Method in class ubic.gemma.rest.AdminWebService: HikariCP pool snapshot.
getDbValue() - Method in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetRole
getDbValue() - Method in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSource
getDbValue() - Method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionScope
getDbValue() - Method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionType
getDbValue() - Method in enum class ubic.gemma.model.common.auditAndSecurity.curation.FindingDisposition
getDbValue() - Method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageJudgeKind
getDbValue() - Method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdict
getDbValue() - Method in enum class ubic.gemma.model.common.description.PublicationAssociationRole
getDbValue() - Method in enum class ubic.gemma.model.common.description.PublicationAssociationSource
getDbValue() - Method in enum class ubic.gemma.model.common.description.PublicationAssociationStatus
getDbValue() - Method in enum class ubic.gemma.model.expression.experiment.AgentCurationKind
getDbXrefs() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getDbXrefs() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: Database cross-references for this term (OBO hasDbXref) — pointers into other resources such as MESH, OMIM, UMLS, ICD, SNOMED, etc.
getDeaResultSetCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Total distinct differential-expression analysis result sets across public datasets.
getDecidedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
getDecidedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
getDecidedBy() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
getDecidedBy() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
getDecision() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
getDecisionKey() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
getDefaultCountValueAsDouble(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils: Obtain the value that indicates a missing value for counting data.
getDefaultCountValueAsFloat(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils: Obtain the value that indicates a missing value for counting data.
getDefaultSequencingMetadata() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig: Default sequencing metadata to use.
getDefaultSymbol() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getDefaultValue(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils: Obtain the default to use for a given quantitation type.
getDefaultValueAsBytes(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils: Obtain the default value for a vector as an encoded byte[].
getDefaultValueAsDouble(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils
getDefaultValueAsNumber(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils
getDefinition() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Definition of the term, if enriched.
getDefinition() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject
getDefinition(String, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain a definition for the given URI.
getDefinition(String, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getDelegate() - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextAsyncTaskExecutor
getDelegate() - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextExecutor
getDelegate() - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextScheduledExecutorService
getDelegate() - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextSchedulingTaskExecutor
getDelegate() - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextTaskExecutor
getDelegate() - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextAsyncTaskExecutor
getDelegate() - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextExecutorService
getDelegate() - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextSchedulingTaskExecutor
getDelegate() - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextTaskExecutor
getDelegate() - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
getDelegate() - Method in interface ubic.gemma.core.util.concurrent.DelegatingAsyncTaskExecutor: The task executor this is delegating for.
getDelegate() - Method in interface ubic.gemma.core.util.concurrent.DelegatingExecutor: The executor this is delegating for.
getDelegate() - Method in interface ubic.gemma.core.util.concurrent.DelegatingExecutorService
getDelegate() - Method in interface ubic.gemma.core.util.concurrent.DelegatingScheduledExecutorService
getDelegate() - Method in interface ubic.gemma.core.util.concurrent.DelegatingSchedulingTaskExecutor
getDelegate() - Method in interface ubic.gemma.core.util.concurrent.DelegatingTaskExecutor
getDeleted() - Method in class ubic.gemma.rest.DatasetsWebService.CurationSectionChange
getDeletedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.User: Timestamp of the admin soft-delete; null when the account is active.
getDeletedBy() - Method in class ubic.gemma.model.common.auditAndSecurity.User: Username of the admin who soft-deleted this account; null when active.
getDeletedIdentities() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getDeletedIds() - Method in class ubic.gemma.rest.DatasetsWebService.Section
getDenseMatrix() - Method in class ubic.gemma.core.loader.util.anndata.Layer: Obtain the dense matrix encoded in this layer.
getDepartment() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getDescription() - Method in class ubic.gemma.cli.completion.CompletionSource.Completion
getDescription() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition: Longer description, e.g.
getDescription() - Method in class ubic.gemma.core.job.progress.ProgressData
getDescription() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
getDescription() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getDescription() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getDescription() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
getDescription() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getDescription() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
getDescription() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
getDescription() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
getDescription() - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
getDescription() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
getDescription() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
getDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter
getDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataPack
getDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataRewrite
getDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSample
getDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSortBySample
getDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSparsify
getDescription() - Method in interface ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformation: Obtain a short description of what the transformation does.
getDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationPipeline
getDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTranspose
getDescription() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataUnraw
getDescription() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
getDescription() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getDescription() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getDescription() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getDescription() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getDescription() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain a description of this ontology if available.
getDescription() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getDescription() - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
getDescription() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
getDescription() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getDescription() - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
getDescription() - Method in class ubic.gemma.model.analysis.ProtocolValueObject
getDescription() - Method in class ubic.gemma.model.common.AbstractDescribable
getDescription() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getDescription() - Method in interface ubic.gemma.model.common.Describable: Obtain a human-readable description of the object
getDescription() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getDescription() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
getDescription() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getDescription() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getDescription() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getDescription() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getDescription() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getDescription() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject: Deprecated.
getDescription() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
getDescription() - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
getDescription() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getDescription() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getDescription() - Method in class ubic.gemma.model.genome.gene.GeneSet
getDescription() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getDescription() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getDescription() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getDescription() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getDescription() - Method in class ubic.gemma.rest.CompletionsWebService.CompletionValueObject: Human-readable label suitable for UI display alongside the value.
getDescription() - Method in class ubic.gemma.rest.DatasetsWebService.CurationBasics
getDescription() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetBasicsResponse
getDescription() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetBasicsUpdateRequest
getDescription() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
getDescription() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject: Longer description, e.g.
getDescription() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getDescription() - Method in class ubic.gemma.rest.GroupsWebService.GroupCreateRequest
getDescription() - Method in class ubic.gemma.rest.GroupsWebService.GroupSummaryValueObject
getDescription() - Method in class ubic.gemma.rest.GroupsWebService.GroupUpdateRequest
getDescription() - Method in class ubic.gemma.rest.GroupsWebService.GroupValueObject
getDescriptions() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getDescriptions() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta: A short description for this parameter if clarifications are needed.
getDesign() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
getDesign() - Method in class ubic.gemma.model.expression.experiment.DesignApplyOutcome
getDesign() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getDesignAuditEventIds() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getDesignCreated() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getDesignDeleted() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getDesignElement() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
getDesignElement() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
getDesignElement() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
getDesignElementCount() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getDesignElementForRow(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getDesignElementForRow(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getDesignElementForRow(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getDesignElementForRow(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Return a design element for a given index.
getDesignElementForRow(int) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getDesignElementForRow(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getDesignElementForRow(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getDesignElementId() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject.Row
getDesignElementId() - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta
getDesignElementIds() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject: Reserved — Gemma's MeanVarianceRelation does not currently carry design-element ids; the UI indexes the parallel arrays positionally.
getDesignElementName() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
getDesignElementName() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject.Row
getDesignElementName() - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta
getDesignElementNames() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject: Reserved — see DatasetsWebService.MeanVarianceValueObject.designElementIds.
getDesignElements() - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getDesignElements() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getDesignElements() - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getDesignElements() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Obtain all the design elements in this data matrix.
getDesignElements() - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getDesignElements() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getDesignElements() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getDesignElements() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getDesignElements() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getDesignElementsAfterLowVariance() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Number of design elements left after filtering for low variance.
getDesignElementsAfterMinimumCells() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Number of design elements left after filtering for minimum number of cells.
getDesignElementsAfterOutliers() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
getDesignElementsAfterRepetitiveValues() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Number of design elements left after filtering for repetitive values.
getDesignElementsPerSample() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getDesignFileName(ExpressionExperiment, boolean) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils: Obtain the filename for writing experimental design.
getDesignFileName(ExpressionExperiment, QuantitationType) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils: Obtain the filename for writing experimental design for a specific QT.
getDesignFileOptionValue(CommandLine, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
getDesignFileOptionValue(CommandLine, boolean, String, boolean) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
getDesignIdMap() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getDesignPlan() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getDesignProvider() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getDesignReport() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getDesignUnchanged() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getDesignUpdated() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getDest() - Method in class ubic.gemma.core.util.SimpleDownloader.URLAndDestination
getDest(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector: Obtain the download destination for the single-cell data file.
getDetail() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getDetail() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
getDetails() - Method in class ubic.gemma.rest.monitoring.health.HealthResult
getDetails() - Method in class ubic.gemma.rest.monitoring.HealthWebService.ComponentValueObject
getDetectedQualityScore() - Method in class ubic.gemma.model.expression.experiment.Geeq
getDetectedQualityScore() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
getDevelopmentStage() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getDf() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
getDf() - Method in class ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
getDfPrior() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
getDifferentialAnalysisEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDifferentialExpression(Gene, double, int) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService: Get the differential expression results for the given gene across all datasets.
getDifferentialExpression(Gene, double, int) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
getDifferentialExpression(Gene, double, Collection) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService: Get differential expression for a gene, constrained to a specific set of factors.
getDifferentialExpression(Gene, double, Collection) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
getDifferentialExpression(Gene, Collection, boolean) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService: Get the differential expression results for the given gene that is in a specified set of experiments.
getDifferentialExpression(Gene, Collection, boolean) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
getDifferentialExpression(Gene, BioAssaySet, boolean, double, int) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService: Get the differential expression results for the given gene that is in a specified set of experiments.
getDifferentialExpression(Gene, BioAssaySet, boolean, double, int) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
getDifferentialExpressionAnalyses() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDifferentialExpressionAnalysesToDelete() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport
getDifferentialExpressionAnalysesToDelete() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
getDifferentialExpressionMetaAnalysis(double, Gene, Map, Collection, boolean) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService: Get the differential expression analysis results for the gene in the activeExperiments.
getDifferentialExpressionMetaAnalysis(double, Gene, Map, Collection, boolean) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
getDiffExArchiveFileName(DifferentialExpressionAnalysis) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
getDiffExVectors(Long, double, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getDiffExVectors(Long, double, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getDiffValCount() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
getDimension() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getDimension() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getDirection() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getDirection() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getDirection() - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
getDirection() - Method in class ubic.gemma.persistence.util.Cursor
getDirection() - Method in class ubic.gemma.persistence.util.Sort
getDirection() - Method in class ubic.gemma.rest.util.args.SortArg.Sort
getDirection() - Method in class ubic.gemma.rest.util.SortValueObject
getDirectRestrictions() - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Restrictions asserted DIRECTLY on this term, without walking the superclass closure.
getDiscardEmptyCells() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Discard (or keep) empty cells.
getDiscontinuedId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getDisease() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getDiseases() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getDiseases() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
getDiskCachePath(String) - Static method in class ubic.gemma.core.ontology.jena.OntologyLoader: Obtain the on-disk path where the cached source OWL for an ontology lives.
getDisplayLabel() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject: Short display label for the target (e.g.
getDisplayMax() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getDisplayMax() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getDisplayMin() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getDisplayMin() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getDisplayName() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject: Human-readable name for the target (e.g.
getDisplayName() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getDisplayName() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetMetadataFileValueObject: Human-readable label suitable for UI display.
getDisplayRange() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getDisposition() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
getDispositions(Long, boolean) - Method in class ubic.gemma.rest.AnnotationSetsWebService: The rulings on an annotation set's findings — the standing one per finding, or the whole sequence.
getDistinctAccessionCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Distinct external accessions across all public EEs.
getDistribution() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getDocs() - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject: Deprecated.
getDocumentationUrl() - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject
getDof() - Method in class ubic.gemma.core.util.math.linearmodels.AnovaEffect
getDoi() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: DOI of the primary publication, when it is a preprint or otherwise identified by a DOI rather than a PubMed ID.
getDoi() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
getDonorId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getDouble(int) - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
getDouble(long) - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset: Obtain a single double value.
getDouble(K) - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
getDoubleMatrix() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
getDownloadDirectory() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector
getDownloadName() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getDownloadName() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetMetadataFileValueObject: Filename the server will use in the Content-Disposition header on download.
getDownloadName(ExpressionExperiment) - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getDownloadPath() - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getDownloads() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
getDownregulatedCount() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Deprecated.
use DiffExResultSetSummaryValueObject.getNumberOfDownregulatedProbes() instead.
getDownregulatedCount() - Method in class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
getDraftForDataset(DatasetArg, String) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Fetch a curator's DRAFT for the given dataset.
getDrugCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Distinct CHEBI-anchored drug / chemical annotations in use (characteristics whose valueUri starts with http://purl.obolibrary.org/obo/CHEBI_).
getDueDate() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getDueDate() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getDueDate() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getDueDate() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getE() - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
getE() - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
getEditor() - Method in class ubic.gemma.model.common.description.BibliographicReference
getEe2cRowsWritten() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync
getEeId() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
getEeId() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PromotionResult
getEeId() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport
getEffectName() - Method in class ubic.gemma.core.util.math.linearmodels.AnovaEffect
getEffects() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getEfId() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
getEigenGene(int) - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getEigenGenesFilename(ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
getEigenSample(int) - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getEigenvalues() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getEigenValues() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getEigenvectorArrays() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getEigenVectors() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getElementClass() - Method in class ubic.gemma.persistence.service.AbstractDao
getElementClass() - Method in class ubic.gemma.persistence.service.AbstractService
getElementClass() - Method in interface ubic.gemma.persistence.service.BaseDao: Obtain the element class of T.
getElementClass() - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
getElementClass() - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getElementClass() - Method in interface ubic.gemma.rest.util.args.EntityArgService
getElementFilters(PlatformArg, CompositeSequenceArrayArg) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Filters for the /{platform}/elements/{probes} endpoints: the platform scope AND the {probes} id/name set restriction.
getElements(PlatformArg, int, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Retrieves the design elements of the platform that this argument represents.
getElements(PlatformArg, int, int, boolean) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Variant that opt-in hydrates the probe-sequence projection (sequence + length) via a single batch HQL after the main page is fetched.
getElements(PlatformArg, int, int, boolean, boolean, Collection) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Full-projection variant: adds the opt-in gene column (withGenes) and the opt-in gene restriction (geneIds).
getElements(PlatformArg, Filters, Collection, int, int, boolean, boolean) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Widest offset-mode variant: user-supplied filter= conjunct on top of everything else.
getElements(PlatformArg, CompositeSequenceArrayArg, int, int, boolean) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Offset-mode variant of PlatformArgService.getElementsByCursor(PlatformArg, CompositeSequenceArrayArg, Cursor, int, boolean).
getElements(PlatformArg, CompositeSequenceArrayArg, int, int, boolean, boolean) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Probe-set variant with the opt-in gene column.
getElementsByCursor(PlatformArg, Cursor, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Cursor-mode counterpart to PlatformArgService.getElements(PlatformArg, int, int): keyset pagination over the design elements of a single platform, always sorted by ascending id (the primary key, indexed and unique) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1e.
getElementsByCursor(PlatformArg, Cursor, int, boolean) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Cursor-mode variant of PlatformArgService.getElements(PlatformArg, int, int, boolean).
getElementsByCursor(PlatformArg, Cursor, int, boolean, boolean, Collection) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Cursor-mode variant of PlatformArgService.getElements(PlatformArg, int, int, boolean, boolean, Collection).
getElementsByCursor(PlatformArg, Filters, Collection, Cursor, int, boolean, boolean) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Widest cursor-mode variant; see PlatformArgService.getElements(PlatformArg, Filters, Collection, int, int, boolean, boolean).
getElementsByCursor(PlatformArg, CompositeSequenceArrayArg, Cursor, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Cursor-mode counterpart to FilteringVoEnabledService.loadValueObjects(Filters, Sort, int, int) scoped to a single platform AND a fixed set of probe identifiers (the /{platform}/elements/{probes} endpoint) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1j.
getElementsByCursor(PlatformArg, CompositeSequenceArrayArg, Cursor, int, boolean) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Cursor-mode + probe-set variant of PlatformArgService.getElements(PlatformArg, int, int, boolean).
getElementsByCursor(PlatformArg, CompositeSequenceArrayArg, Cursor, int, boolean, boolean) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Cursor-mode + probe-set variant with the opt-in gene column.
getEmail() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getEmail() - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
getEmail() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
getEmail() - Method in interface ubic.gemma.core.security.model.User
getEmail() - Method in class ubic.gemma.model.common.auditAndSecurity.Contact
getEmail() - Method in class ubic.gemma.rest.GroupsWebService.GroupMemberValueObject
getEmail() - Method in class ubic.gemma.rest.RootWebService.UserValueObject
getEncoding() - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection
getEncodingType() - Method in class ubic.gemma.core.loader.util.anndata.Layer
getEndPosition() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getEndTime() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getEnhancedFilters(Filters, Collection, Collection, long, TimeUnit) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getEnhancedFilters(Filters, Collection, Collection, long, TimeUnit) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getEnhancedFilters(Filters, Collection, Collection, long, TimeUnit) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Perform various transformation to the provided filters to enhance it.
getEnhancedFilters(Filters, Collection, Collection, long, TimeUnit) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getEnsembl() - Static method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
getEnsemblGeneId() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getEnsemblId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getEnsemblId() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getEnsemblId() - Method in class ubic.gemma.model.genome.Gene
getEnsemblPeptideId() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getEnsemblTranscriptId() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getEnteredCurrentStateAt() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
getEnteredCurrentStateAt() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowTransition
getEntities(AbstractEntityArg) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getEntities(AbstractEntityArg) - Method in interface ubic.gemma.rest.util.args.EntityArgService: Retrieve the entities represented by this argument.
getEntities(AbstractEntityArrayArg) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getEntities(AbstractEntityArrayArg) - Method in interface ubic.gemma.rest.util.args.EntityArgService: Retrieve each entity represented by the array argument, raising a NotFoundException if any of them is missing.
getEntitiesWithTaxon(GeneArg, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService: Obtain genes from a specific taxon.
getEntitiesWithTaxon(GeneArrayArg, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService: Obtain genes from a specific taxon.
getEntity(AbstractEntityArg) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getEntity(AbstractEntityArg) - Method in interface ubic.gemma.rest.util.args.EntityArgService: Retrieve the entity represented by this argument.
getEntity(AbstractEntityArg) - Method in class ubic.gemma.rest.util.args.GeneArgService: Retrieve the entity represented by this argument.
getEntity(QuantitationTypeArg, ExpressionExperiment) - Method in class ubic.gemma.rest.util.args.QuantitationTypeArgService
getEntity(QuantitationTypeArg, ExpressionExperiment, Class) - Method in class ubic.gemma.rest.util.args.QuantitationTypeArgService
getEntityClass() - Method in class ubic.gemma.core.tasks.EntityTaskCommand
getEntityId() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
getEntityId() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
getEntityId() - Method in class ubic.gemma.core.tasks.EntityTaskCommand
getEntityId(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Retrieve an ID for a given dataset argument.
getEntityName() - Method in class ubic.gemma.persistence.service.AbstractDao
getEntityName() - Method in class ubic.gemma.persistence.util.Subquery: The entity name being queried.
getEntityName(SessionFactory, Class) - Static method in class ubic.gemma.persistence.hibernate.HibernateUtils: Hibernate 6 dropped SessionFactory.getClassMetadata(Class).
getEntityTransformer() - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
getEntityType() - Method in exception class ubic.gemma.persistence.util.UnsupportedEntityUrlException
getEntityWithContrastsAndResults(ExpressionAnalysisResultSetArg) - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgService
getEntityWithContrastsAndResults(ExpressionAnalysisResultSetArg, double, int, int) - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgService
getEntityWithContrastsAndResults(ExpressionAnalysisResultSetArg, int, int) - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgService
getEntityWithPlatform(CompositeSequenceArg, ArrayDesign) - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgService
getEntityWithTaxon(GeneArg, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService: Obtain a gene from a specific taxon.
getEntrezgenes() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getEntries() - Method in class ubic.gemma.core.security.acl.domain.AclImpl
getEntries() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
getEntriesInheriting() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
getEntry(int, int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getEntry(int, int) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
getEntry(int, int) - Method in interface ubic.gemma.core.util.matrix.Matrix2D
getEntry(int, int) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
getEntry(int, int) - Method in class ubic.gemma.core.util.matrix.StringMatrix
getEnumArrayColumn(String) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain an enum array column.
getEnumOptionValue(CommandLine, String) - Static method in class ubic.gemma.cli.util.OptionsUtils: Obtain the value of an enumerated option.
getEnumOptionValue(CommandLine, String, Predicate) - Static method in class ubic.gemma.cli.util.OptionsUtils: Obtain the value of an enumerated option and if present, make sure that it satisfies a predicate.
getEnumSetOptionValue(CommandLine, String) - Static method in class ubic.gemma.cli.util.OptionsUtils
getEnvironment() - Method in interface ubic.gemma.cli.util.CLIContext: Obtain the environment variables for the command.
getEnvironment() - Method in class ubic.gemma.cli.util.SystemCLIContext
getError() - Method in interface ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse
getError() - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
getError() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchResultValueObject
getError() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getError() - Method in class ubic.gemma.rest.TaskStatusValueObject: Structured failure detail.
getError() - Method in class ubic.gemma.rest.util.ResponseErrorObject: Error beign reported.
getErrorMessage() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
getErrorMessage() - Method in class ubic.gemma.model.pipeline.PipelineJob
getErrors() - Method in exception class ubic.gemma.core.loader.entrez.EntrezException
getErrors() - Method in class ubic.gemma.rest.util.WellComposedErrorBody
getErrorStream() - Method in interface ubic.gemma.cli.util.CLIContext
getErrorStream() - Method in class ubic.gemma.cli.util.SystemCLIContext
getEvent() - Method in class ubic.gemma.rest.CompactAuditEventValueObject
getEvents() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
getEvents() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getEvents() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getEvents() - Method in class ubic.gemma.model.pipeline.PipelineJob
getEvents(Auditable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the audit events associated to a given auditable.
getEvents(Auditable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getEvents(Auditable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getEvents(Auditable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getEventsByCursor(Auditable, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Keyset-pagination counterpart to AuditEventDao.getEvents(Auditable) — cursor mode for GET /datasets/{dataset}/auditEvents (step 1q of CURSOR_PAGINATION_STEP1_PLAN.md).
getEventsByCursor(Auditable, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getEventsByCursor(Auditable, Cursor, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService: Keyset-pagination counterpart to AuditEventService.getEvents(Auditable) for the GET /datasets/{dataset}/auditEvents endpoint — see CURSOR_PAGINATION_STEP1_PLAN.md step 1q.
getEventsByCursor(Auditable, Cursor, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getEventsWithType(Auditable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain all events with a non-null event type for a given auditable.
getEventsWithType(Auditable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getEventsWithType(Auditable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService: Retrieve all events with an event type.
getEventsWithType(Auditable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getEventType() - Method in class ubic.gemma.core.security.audit.AuditedEvent
getEventType() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getEventType() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
getEventType() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject: Simple class name of the audit event type (ExpressionExperimentUpdateFromGEOEvent, DifferentialExpressionAnalysisEvent, …).
getEventType() - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: Simple class name of the latest audit event (BatchInformationFetchingEvent, FailedPCAAnalysisEvent, etc.).
getEventTypeName() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
getEvidence() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getEvidence() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getEvidence() - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
getEvidence() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getEvidence() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssertion
getEvidence() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: The one-line basis the source gives, meant to be shown as-is -- PMID:11242117 where MGI cites a paper.
getEvidence() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
getEvidenceCode() - Method in class ubic.gemma.model.association.Gene2GOAssociation
getEvidenceCode() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getEvidenceCode() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getEvidenceCode() - Method in class ubic.gemma.model.common.description.Characteristic
getEvidenceCode() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getEvidenceCode() - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
getEvidenceCode() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: How this statement was arrived at, as a GOEvidenceCode name (IC, IEA, IIA, TAS, …).
getEvidenceCode() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssertion
getEvidenceCode() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getEvidenceCode() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
getEvidenceCode() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit: How this statement was arrived at, as a GOEvidenceCode name.
getEvidenceCode() - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit: How this tag was arrived at, as a GOEvidenceCode name.
getExactLabel() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getExampleDatasetId() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getExampleExperimentId() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getExampleUsage() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: One representative, ACL-visible example of how this term has actually been used in the corpus — so a curator picking an unfamiliar/rare term can see it in context (e.g.
getException() - Method in class ubic.gemma.core.job.TaskResult
getExceptionType() - Method in class ubic.gemma.rest.TaskStatusValueObject.TaskError: Simple class name of the underlying exception, for diagnostics.
getExcludedExperimentIds() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getExcludedPrefixes() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationCategoryValueObject
getExcludedSubjectCategoryUris() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getExcludedUris(StringArrayArg, boolean, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Obtain a list of exclude URIs from an argument containing excluded URIs.
getExcludedWordsFromStemming() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getExcludedWordsFromStemming() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getExcludedWordsFromStemming() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getExcludedWordsFromStemming() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain the words that should be excluded from stemming.
getExistingExperimentId() - Method in class ubic.gemma.rest.TaskStatusValueObject.TaskError: For ALREADY_EXISTS, the id of the experiment that already holds the accession, when resolvable.
getExistingFile(File, String) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher: Wrap the existing file in the required Collection<LocalFile>
getExistingId() - Method in exception class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.AccessionAlreadyExistsException
getExistingType() - Method in exception class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.AccessionAlreadyExistsException: Either "preboarded" or "expression_experiment".
getExitCause() - Method in interface ubic.gemma.cli.util.CLIContext: Obtain the exit cause, if known.
getExitCause() - Method in class ubic.gemma.cli.util.SystemCLIContext
getExitStatus() - Method in interface ubic.gemma.cli.util.CLIContext
getExitStatus() - Method in class ubic.gemma.cli.util.SystemCLIContext
getExons() - Method in class ubic.gemma.model.genome.gene.GeneProduct: Only used for transient instances in sequence analysis, we do not store exon locations in the database.
getExpectedLastUpdated() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getExpectedSize(String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
getExperiment() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
getExperiment() - Method in class ubic.gemma.model.pipeline.PipelineJob
getExperiment() - Method in class ubic.gemma.rest.GeneWebService.GeneDifferentialExpressionGroupValueObject
getExperiment(BioAssaySet) - Static method in class ubic.gemma.persistence.util.CommonQueries: Resolve a BioAssaySet to the ExpressionExperiment that owns its data: itself if it is one, its source experiment if it is a subset.
getExperimentalDesign() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getExperimentalDesign() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getExperimentalDesign() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getExperimentalDesign(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getExperimentalDesignAnnotations(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain experimental design-level annotations.
getExperimentalDesignAnnotations(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getExperimentalDesignDescription() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
getExperimentalDesignName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
getExperimentalDesignValueObject(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getExperimentalDesignValueObject(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getExperimentalDesignValueObject(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Build a full structured representation of an experiment's ExperimentalDesign: factors, factor values (with statements carrying stable database IDs), and per-biomaterial factor-value assignments.
getExperimentalDesignValueObject(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getExperimentalFactor() - Method in class ubic.gemma.model.analysis.expression.diff.Contrast
getExperimentalFactor() - Method in class ubic.gemma.model.expression.experiment.FactorValue
getExperimentalFactorCategories(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao
getExperimentalFactorCategories(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
getExperimentalFactorCategoriesIgnoreAcls(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService: Return the experimental factor categories of the given factor values.
getExperimentalFactorCategoriesIgnoreAcls(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
getExperimentalFactorCategoriesIgnoreAcls(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Obtain the categories of the given factor values.
getExperimentalFactorCategoriesIgnoreAcls(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
getExperimentalFactorCategory() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The experiment factor category.
getExperimentalFactorId() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The ID of the experimental factor this factor value belongs to.
getExperimentalFactors() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
getExperimentalFactors() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getExperimentalFactors() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getExperimentalFactors() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.Prefetch
getExperimentalFactors() - Method in class ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet
getExperimentalFactors() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getExperimentalFactors() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
getExperimentalFactorType() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The experimental factor type.
getExperimentAnalyzed() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: Experiment or subset this is for.
getExperimentAnalyzed() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis
getExperimentAnalyzedId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
getExperimentAnalyzedId() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject: The ID of the experiment analyzed which is either an ExpressionExperiment or an ExpressionExperimentSubSet.
getExperimentAnnotations(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain experiment-level annotations.
getExperimentAnnotations(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getExperimentCount() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
getExperimentCount() - Method in class ubic.gemma.rest.AnnotationsWebService.PriorCurationValueObject: Distinct experiments on which this string was annotated with this term.
getExperimentGroup() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
getExperimentGroupName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getExperimentGroupName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
getExperimentId() - Method in class ubic.gemma.core.pipeline.SubmitRequest
getExperimentId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getExperimentId() - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
getExperimentId() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetBasicsResponse
getExperimentId() - Method in class ubic.gemma.rest.DatasetsWebService.RenameDatasetResponse
getExperimentId() - Method in class ubic.gemma.rest.PipelineStatusValueObject
getExperimentId() - Method in class ubic.gemma.rest.TaskStatusValueObject: Identifier of the experiment the task is operating on, when derivable from the task command.
getExperimentName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getExperimentPackages() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackageSet
getExperiments() - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
getExperiments() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getExperiments(PlatformArg, int, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Retrieves the Datasets of the Platform that this argument represents.
getExperimentsAffected() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
getExperimentsAffected() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getExperimentsByCursor(PlatformArg, Cursor, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Cursor-mode counterpart to PlatformArgService.getExperiments(PlatformArg, int, int): keyset pagination over the datasets that use a single platform, always sorted by ascending id (the primary key, indexed and unique) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1f.
getExperimentSet(Long, boolean) - Method in class ubic.gemma.rest.ExperimentSetsWebService
getExperimentSetDatasets(Long) - Method in class ubic.gemma.rest.ExperimentSetsWebService
getExperimentSets(boolean, String, boolean, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.ExperimentSetsWebService
getExperimentsInSet(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
getExperimentsInSet(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
getExperimentsInSet(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: Get the (security-filtered) list of experiments in a set.
getExperimentsInSet(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
getExperimentsLackingPublications(int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getExperimentsLackingPublications(int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getExperimentsLackingPublications(int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getExperimentsLackingPublications(int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getExperimentsResynced() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync
getExperimentSubSetAnnotations(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the subset annotations.
getExperimentSubSetAnnotations(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getExperimentsWithAnalysis(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
getExperimentsWithAnalysis(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
getExperimentsWithAnalysis(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
getExperimentsWithAnalysis(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
getExperimentsWithAnalysis(Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
getExperimentsWithAnalysis(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService: Obtain IDs of experiments that have analyses.
getExperimentsWithAnalysis(Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
getExperimentsWithOutliers() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getExperimentsWithOutliers() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getExperimentsWithOutliers() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getExperimentsWithOutliers() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getExperimentsWithOutliers() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getExperimentsWithOutliers() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getExperimentType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getExperimentValueObjectsInSet(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
getExperimentValueObjectsInSet(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
getExperimentValueObjectsInSet(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: Get the member experiment value objects for the set id; security filtered.
getExperimentValueObjectsInSet(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
getExpiresAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
getExplicitBaselines(ExperimentalFactor, Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection: The factor values a curator has EXPLICITLY marked as baseline on this factor, restricted to those the given samples actually use.
getExponentialBackoffFactor() - Method in class ubic.gemma.core.util.SimpleRetryPolicy
getExpressionDataFileOptionValue(CommandLine, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
getExpressionDataFileOptionValue(CommandLine, boolean, String, boolean) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
getExpressionExperiment() - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getExpressionExperiment() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getExpressionExperiment() - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getExpressionExperiment() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Return the expression experiment this matrix is holding data for, if known.
getExpressionExperiment() - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getExpressionExperiment() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getExpressionExperiment() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getExpressionExperiment() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.expression.GeeqTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getExpressionExperiment() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getExpressionExperiment() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getExpressionExperiment() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getExpressionExperiment() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
getExpressionExperiment() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
getExpressionExperimentCount() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Deprecated.
use ArrayDesignValueObject.getNumberOfExpressionExperiments() instead.
getExpressionExperimentId() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject: Associated expression experiment ID.
getExpressionExperimentIds() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getExpressionExperimentMetadataDirname(ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils: Forms a folder name where the given experiments metadata will be located (within the ${gemma.appdata.home}/metadata directory).
getExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
getExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getExpressionExperiments(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao: Obtain all the experiments a biomaterial is used in from its hierarchy.
getExpressionExperiments(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
getExpressionExperiments(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService: Return the ExpressionExperiment occurrences of a given biomaterial, organized by BioAssay.
getExpressionExperiments(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
getExpressionExperiments(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
getExpressionExperiments(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
getExpressionExperimentSets() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: EE sets this experiment is part of.
getExpressionExperimentsIgnoreAcls(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao
getExpressionExperimentsIgnoreAcls(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
getExpressionExperimentsIgnoreAcls(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService: Return the ExpressionExperiment that owns each of the given factor values.
getExpressionExperimentsIgnoreAcls(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
getExpressionExperimentsIgnoreAcls(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: For efficiency, only the ID, short name and name of the EEs are populated.
getExpressionExperimentsIgnoreAcls(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
getExpressionLevels(Collection, Collection, boolean, String) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getExpressionLevels(Collection, Collection, boolean, String) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getExpressionLevelsByIds(Collection, Collection, boolean, String) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Retrieve expression levels by dataset IDs.
getExpressionLevelsByIds(Collection, Collection, boolean, String) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getExpressionLevelsDiffEx(Collection, Long, double, int, boolean, String) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getExpressionLevelsDiffEx(Collection, Long, double, int, boolean, String) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getExpressionLevelsPca(Collection, int, int, boolean, String) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getExpressionLevelsPca(Collection, int, int, boolean, String) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getExternalAccession() - Method in class ubic.gemma.model.blacklist.BlacklistedEntity
getExternalAccession() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getExternalDatabase() - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
getExternalDatabase() - Method in class ubic.gemma.model.common.description.DatabaseEntry
getExternalDatabase() - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
getExternalDatabase() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getExternalDatabase() - Method in class ubic.gemma.model.genome.Taxon
getExternalDatabase() - Method in class ubic.gemma.model.genome.TaxonValueObject
getExternalDatabaseId() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
getExternalDatabaseName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
getExternalDatabases() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getExternalDatabases() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
getExternalDatabases() - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject
getExternalDatabaseUri() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getExternalIdentification() - Method in class ubic.gemma.rest.AnnotationsWebService.NegativeEvidenceValueObject: What an external naming authority says this string is, when nothing loaded named it.
getExternalIds() - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
getExternalIssueSyncState() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getExternalIssueSyncState() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getExternalIssueUrl() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getExternalIssueUrl() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getExternalLabel() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getExternalLink(OntologyResource) - Method in class ubic.gemma.core.ontology.OntologyExternalLinks
getExternalReferences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getExternalReferences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Main external reference.
getExternalUri() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getExtractedMolecule() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getExtractedMolecule() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: What was extracted from the sample and assayed — GEO's molecule.
getExtractProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getExtraMissingValueIndicators() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
getFactor() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound: Factor being confounded with the batches.
getFactor() - Method in class ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
getFactor() - Method in class ubic.gemma.rest.HeatmapDataValueObject.FactorEntry: Full factor VO: id, name, description, type, category(+Uri), values (with statements + is_baseline + measurement), baseline_relevance, baseline_relevance_reason.
getFactorAName() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getFactorBName() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getFactorCategory() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getFactorCategory() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getFactorCorrelations() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: Map of component to a map of ExperimentalFactor IDs to correlations of that factor with the component.
getFactorCount() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getFactorCount() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCounts
getFactorCount() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: Derived hint; null means unknown, never zero.
getFactorDescription() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getFactorDescription() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getFactorId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getFactorId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getFactorId() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
getFactorId() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.

ID of the experimental factor this FV belongs to.
getFactorIds() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getFactorIds() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialAnalysisRunRequest
getFactorIdToFactorValueId() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Map of factor ids (factor232) to factor value (id or the actual value) for this biomaterial.
getFactorName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getFactorName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getFactorName() - Method in interface ubic.gemma.core.util.math.linearmodels.OneWayAnovaResult
getFactorNames() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getFactorPVals() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: Map of component to map of ExperimentalFactor IDs to P-values for the association of that factor with the component.
getFactors() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: Map of factors to the double-ized representations of them.
getFactors() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: The factors to actually use in the analysis.
getFactors() - Method in class ubic.gemma.persistence.util.FactorValueVector
getFactors() - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit
getFactors() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetGroupValueObject: List of factors that are associated with the subsets in this group.
getFactors() - Method in class ubic.gemma.rest.HeatmapDataValueObject: Optional.
getFactors(Collection, Map) - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
getFactors(Collection, Map) - Method in interface ubic.gemma.core.loader.expression.DataLoader: Load experimental factors present in the data.
getFactors(Collection, Map) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getFactors(Collection, Map) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader: MEX does not provide experimental factors.
getFactors(Collection, Map) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getFactorsToCreate() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
getFactorsToDelete() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport
getFactorsToDelete() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
getFactorsToInclude() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getFactorsToUpdate() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport: Kept factors whose name, description or category the proposal rewrites.
getFactorsToUpdate() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
getFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.Baseline
getFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.Contrast
getFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
getFactorValue() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getFactorValueAnnotations(String) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyService: Obtain annotations belonging to the given URI representing a factor value.
getFactorValueAnnotations(String) - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl
getFactorValueAnnotations(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain factor value-level annotations.
getFactorValueAnnotations(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getFactorValueAnnotations(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain factor value-level annotations for a given subset.
getFactorValueAnnotations(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getFactorValueAnnotationsWithParents(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain factor value-level annotations together with the owning factor value and experimental factor, so the read VO can carry the term's parent context (parentName = the factor value, parentOfParentName = the factor) without a second query.
getFactorValueAnnotationsWithParents(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getFactorValueAnnotationsWithParents(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Subset variant of ExpressionExperimentDao.getFactorValueAnnotationsWithParents(ExpressionExperiment).
getFactorValueAnnotationsWithParents(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getFactorValueClientRef() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan.PendingAssignment
getFactorValueId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getFactorValueId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
getFactorValueId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
getFactorValueId() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
getFactorValueIds() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.BioMaterialFactorValueAssignment
getFactorValueIds() - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta: factorId -> factorValueId.
getFactorValueMap(Collection, Collection) - Static method in class ubic.gemma.model.expression.experiment.ExperimentalDesignUtils
getFactorValueMap(ExperimentalDesign, Collection) - Static method in class ubic.gemma.model.expression.experiment.ExperimentalDesignUtils: Create a mapping of samples to factor values for all factors in the experimental design.
getFactorValueObjects() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Deprecated.
use BioMaterialValueObject.getFactorValues()
getFactorValues() - Method in class ubic.gemma.model.analysis.expression.diff.Contrast
getFactorValues() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial: Obtain the values that this BioAssay is associated with for the experiment.
getFactorValues() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
getFactorValues() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getFactorValues() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject: Deprecated.
getFactorValues() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject
getFactorValues() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
getFactorValues(int, int) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyService: Obtain all the factor value in the ontology.
getFactorValues(int, int) - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl
getFactorValuesByCategory() - Method in class ubic.gemma.core.analysis.report.HomeStats: Distinct factor-value count per ExperimentalFactor category.
getFactorValueStatements(String) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyService: Obtain statements related to the given URI representing a factor value.
getFactorValueStatements(String) - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl
getFactorValuesToCreate() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
getFactorValuesToDelete() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport
getFactorValuesToDelete() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
getFactorValuesToUpdate() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport: Kept factor values the proposal edits in place: a statement re-termed, evidence attached, the baseline flag flipped, a measurement retimed, the deprecated free-text value rewritten.
getFactorValuesToUpdate() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
getFactorValuesUsed() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject: Deprecated.
This was renamed for clarity.
getFactorValuesUsed(Long, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao
getFactorValuesUsed(Long, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl
getFactorValuesUsed(Long, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
getFactorValuesUsed(Long, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao: Obtain the FactorValue used by the samples from this subset in the given factor.
getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl
getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain the FactorValues used by samples in the given subset for the given factor.
getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
getFactorValuesUsedAsVO(Long, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: VO-form variant of ExpressionExperimentSubSetReadService.getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) accepting plain IDs.
getFactorValuesUsedAsVO(Long, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getFactorValuesUsedByExperimentalFactorId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject: Produce a mapping of ExperimentalFactor IDs to FactorValue VOs used in this analysis.
getFactorValueUris() - Method in interface ubic.gemma.core.ontology.FactorValueOntologyService
getFactorValueUris() - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl
getFactorValueUris(int, int) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyService: Obtain all the factor value URIs in the ontology.
getFactorValueUris(int, int) - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl
getFailedMessage() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getFastqHeaders() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getFastqHeaders() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
getFax() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getFeatureCount() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getFetchSize() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig
getFields(Class, SearchSettings.SearchMode) - Method in interface ubic.gemma.core.search.FieldAwareSearchSource: Obtain a list of fields that can be searched on.
getFields(Class, SearchSettings.SearchMode) - Method in interface ubic.gemma.core.search.SearchService: Obtain a list of fields that can be searched on for the given result type and search mode.
getFields(Class, SearchSettings.SearchMode) - Method in class ubic.gemma.core.search.SearchServiceImpl
getFields(Class, SearchSettings.SearchMode) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
getFileLockInfo() - Method in class ubic.gemma.core.util.runtime.ExtendedRuntime
getFilename() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getFileName() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getFileName(ExpressionExperiment) - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getFiles() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFiles
getFiles() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getFileSize() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
getFiletype() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
getFilter() - Method in class ubic.gemma.persistence.util.Subquery: The sole filter carried by this subquery.
getFilter() - Method in class ubic.gemma.rest.AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
getFilter() - Method in class ubic.gemma.rest.util.FilteredAndCursorPaginatedResponseDataObject
getFilter() - Method in class ubic.gemma.rest.util.FilteredAndPaginatedResponseDataObject
getFilter() - Method in class ubic.gemma.rest.util.FilteredResponseDataObject
getFilter(String, Class, Filter.Operator, Collection) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(String, Class, Filter.Operator, Collection) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(String, Class, Filter.Operator, Collection) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(String, Class, Filter.Operator, Collection) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a Filter with an already parsed collection of values.
getFilter(String, Class, Filter.Operator, Collection) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilter(String, Class, Filter.Operator, T) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(String, Class, Filter.Operator, T) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(String, Class, Filter.Operator, T) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(String, Class, Filter.Operator, T) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a Filter with an already parsed value.
getFilter(String, Class, Filter.Operator, T) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilter(String, Filter.Operator, String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(String, Filter.Operator, String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(String, Filter.Operator, String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(String, Filter.Operator, String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain an Filter for the entity this DAO is providing.
getFilter(String, Filter.Operator, String) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilter(String, Filter.Operator, String, SubqueryMode) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(String, Filter.Operator, String, SubqueryMode) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(String, Filter.Operator, String, SubqueryMode) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(String, Filter.Operator, String, SubqueryMode) - Method in interface ubic.gemma.persistence.service.FilteringDao
getFilter(String, Filter.Operator, String, SubqueryMode) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilter(String, Filter.Operator, Collection) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(String, Filter.Operator, Collection) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(String, Filter.Operator, Collection) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(String, Filter.Operator, Collection) - Method in interface ubic.gemma.persistence.service.FilteringDao: Similar to FilteringDao.getFilter(String, Filter.Operator, String), but with a collection of values.
getFilter(String, Filter.Operator, Collection) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilter(String, Filter.Operator, Collection, SubqueryMode) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(String, Filter.Operator, Collection, SubqueryMode) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(String, Filter.Operator, Collection, SubqueryMode) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(String, Filter.Operator, Collection, SubqueryMode) - Method in interface ubic.gemma.persistence.service.FilteringDao
getFilter(String, Filter.Operator, Collection, SubqueryMode) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilter(List, SubqueryMode) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(List, SubqueryMode) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(List, SubqueryMode) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(List, SubqueryMode) - Method in interface ubic.gemma.persistence.service.FilteringDao: Build a filter requiring a SINGLE element of a to-many relation to satisfy EVERY given predicate.
getFilter(List, SubqueryMode) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterableProperties() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterableProperties() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterableProperties() - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilterableProperties() - Method in interface ubic.gemma.persistence.service.FilteringDao: List all properties availble for filtering.
getFilterableProperties() - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterableProperties() - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterableProperties() - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilterablePropertyAllowedValues(String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a short list of allowed values for the given property, or null if unrestricted.
getFilterablePropertyAllowedValues(String) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyAllowedValues(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyConfigAttributes(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyConfigAttributes(String) - Method in interface ubic.gemma.persistence.service.FilteringService: Obtain the Spring Security config attributes for a given property.
getFilterablePropertyConfigAttributes(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyConfigAttributes(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyDescription(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterablePropertyDescription(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyDescription(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilterablePropertyDescription(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Augments the base service description with a note about ontology inference.
getFilterablePropertyDescription(String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a short description for a given filterable property.
getFilterablePropertyDescription(String) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterablePropertyDescription(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyDescription(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterablePropertyObjectAliases() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao: Expose registered object-alias mappings to subclasses (e.g.
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in interface ubic.gemma.persistence.service.FilteringService: Obtain a list of resolvable MessageSourceResolvables to be used for user display purposes.
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyType(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterablePropertyType(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyType(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilterablePropertyType(String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain the type of the given filterable property.
getFilterablePropertyType(String) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterablePropertyType(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyType(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterAttrition() - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.PreparedCoexMatrices
getFilterAttrition() - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: How many design elements and samples each filter removed while the step ran, and the filter settings that produced those numbers.
getFilterDescription() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject: Currently always null; placeholder for a probe-filter caption once SampleCoexpressionAnalysisService surfaces it.
getFilteredMatrix(Collection, ArrayDesign, ExpressionExperimentFilterConfig, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService
getFilteredMatrix(Collection, ArrayDesign, ExpressionExperimentFilterConfig, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getFilteredMatrix(ExpressionExperiment, Collection, ExpressionExperimentFilterConfig, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService: Provide a filtered expression data matrix.
getFilteredMatrix(ExpressionExperiment, Collection, ExpressionExperimentFilterConfig, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getFilteredMatrix(ExpressionExperiment, Collection, ExpressionExperimentFilterConfig, boolean, ExpressionExperimentFilterResult) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService: Provide a filtered expression data matrix, reporting the per-stage attrition into a caller-supplied result.
getFilteredMatrix(ExpressionExperiment, Collection, ExpressionExperimentFilterConfig, boolean, ExpressionExperimentFilterResult) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getFilteredMatrix(ExpressionExperiment, ExpressionExperimentFilterConfig) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService: Provide a filtered expression data matrix.
getFilteredMatrix(ExpressionExperiment, ExpressionExperimentFilterConfig) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getFilteringCountQuery(Filters) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
getFilteringCountQuery(Filters) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getFilteringCountQuery(Filters) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getFilteringCountQuery(Filters) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getFilteringCountQuery(Filters) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getFilteringCountQuery(Filters) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
getFilteringCriteria(CriteriaBuilder, Class, Filters) - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao: Build a CriteriaQuery of the given result type rooted at the element class and apply the filter restriction.
getFilteringIdQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
getFilteringIdQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getFilteringIdQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getFilteringIdQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getFilteringQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao: Produce a query for retrieving filtered entities or VOs after applying filters and ordering.
getFilteringQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getFilteringQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getFilteringQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getFilteringQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getFilteringQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
getFilters() - Method in class ubic.gemma.persistence.util.Subquery: The filters being nested in the subquery, conjoined.
getFilters(AbstractEntityArg) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilters(AbstractEntityArg) - Method in interface ubic.gemma.rest.util.args.EntityArgService: Translate the provided entity argument into a Filters.
getFilters(AbstractEntityArg) - Method in class ubic.gemma.rest.util.args.TaxonArgService
getFilters(AbstractEntityArrayArg) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilters(AbstractEntityArrayArg) - Method in interface ubic.gemma.rest.util.args.EntityArgService: Translate the provided entity argument into a Filters.
getFilters(FilterArg) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilters(FilterArg) - Method in interface ubic.gemma.rest.util.args.EntityArgService: Obtain a Filters from a filter argument.
getFilters(FilterArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getFilters(FilterArg, Collection, Collection) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getFilters(FilterArg, Collection, Collection, long, TimeUnit) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getFinalColumns() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getFinalDesignElements() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Final number of design elements.
getFinalizedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getFinalizedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getFinalizedBy() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getFinalizedBy() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getFinalizedNotes() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getFinalRows() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getFinalSamples() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Final set of samples.
getFindingId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
getFinishedAt() - Method in class ubic.gemma.model.pipeline.PipelineJob
getFinishTime() - Method in interface ubic.gemma.core.job.SubmittedTask
getFirstBuildTipe() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getFirstGene() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
getFirstName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
getFirstQuartile() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
getFisherContribution() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getFisherPValue() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getFit() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject: Reserved — Gemma's MeanVarianceRelation does not currently expose a fit curve.
getFitted() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
getFittedIncludingMissing() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: Fitted values before the cells whose input was missing are blanked out.
getFittedVariances() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject.Fit
getFlags() - Method in record class ubic.gemma.core.util.runtime.CpuInfo
getFocusedCellLevelCharacteristic() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getFont() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Font to use when rendering diagnostic plots, etc.
getForceOption() - Method in class ubic.gemma.cli.options.DataFileOptionValue: Name of the force option.
getForwardingURL() - Method in class ubic.gemma.core.job.progress.ProgressData
getFractionRepeats() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getFractionRepeats() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getFreeTextIntended() - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit: Declares that this tag is meant to be free text — no value.uri — on purpose.
getFreeTextLabel() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: The value's human-readable label.
getFromCache(CompositeSequence) - Method in class ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
getFromLabel() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getFromUri() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getFromUri() - Method in class ubic.gemma.rest.AnnotationsWebService.CanonicalUriValueObject: The URI as stored on the annotation.
getFStat() - Method in class ubic.gemma.core.util.math.linearmodels.AnovaEffect
getFStat() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getFtpClient(URL) - Method in interface ubic.gemma.core.loader.util.ftp.FTPClientFactory: Create an FTP client for the given URL.
getFtpClient(URL) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
getFtpUri() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getFullCoexpressionMatrix() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis: Note that since you get a full square matrix, all correlations are represented twice, and values on the main diagonal will always be 1.
getFullName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
getFullName() - Method in class ubic.gemma.model.common.auditAndSecurity.Person: Deprecated.
getFullTextUri() - Method in class ubic.gemma.model.common.description.BibliographicReference
getFundamentalType() - Method in class ubic.gemma.core.loader.util.hdf5.H5Type
getFVBasicVOs() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: 🛑 This field's JsonIgnore does not hide it: the payload carries an fvbasicVOs key regardless.
getGeeq() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getGeeq() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getGeeq() - Method in class ubic.gemma.rest.PipelineStatusValueObject
getGemmaChartTheme(String) - Static method in class ubic.gemma.core.visualization.ChartThemeUtils
getGemmaId() - Method in class ubic.gemma.rest.DatasetsWebService.EntityRef
getGemmaJobId() - Method in class ubic.gemma.core.pipeline.SubmitRequest
getGenBank() - Static method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
getGenBank() - Static method in class ubic.gemma.core.loader.util.GenBankUtils
getGenBankAccession(String) - Static method in class ubic.gemma.core.loader.util.GenBankUtils
getGene() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getGene() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getGene() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getGene() - Method in class ubic.gemma.model.association.Gene2GOAssociation
getGene() - Method in class ubic.gemma.model.genome.gene.GeneProduct
getGene() - Method in class ubic.gemma.model.genome.gene.GeneSetMember
getGene(GeneProductValueObject) - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getGene2ProbeMapByOfficialSymbols(Collection, Collection) - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService
getGeneCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Number of distinct genes in the database.
getGeneCount() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Distinct genes annotated with this term (including the descendant terms walked under the request's geneCountMaxTerms cap).
getGeneCount() - Method in class ubic.gemma.rest.GoTermsWebService.GoTermGeneCountValueObject
getGeneCount(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao: This method does not do any permissions filtering.
getGeneCount(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
getGeneCountMaxTerms() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getGeneCountsLastUpdated() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: When the report backing ArrayDesignValueObject.numberOfGenes / ArrayDesignValueObject.numberOfMappedElements was written, as yyyy.MM.dd HH:mm.
getGeneData(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Batch-fetch the compact gene identities mapped to each of the supplied composite-sequence ids, keyed by composite-sequence id.
getGeneData(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getGeneData(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
getGeneData(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
getGeneData(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getGeneData(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGeneDifferentialExpression(GeneArg, double, int) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the differential expression results for the given gene across all experiments the caller has access to (ACL-filtered downstream).
getGeneEnsemblId() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
getGeneExonOverlaps(String, String, String, String, Gene) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Given a gene, find out how much of it overlaps with exons provided as starts and sizes.
getGeneExpressionLevels() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject
getGeneGoTerms(GeneArg) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the GO terms of the given gene.
getGeneGoTerms(GeneArg) - Method in class ubic.gemma.rest.util.args.GeneArgService: Returns GO terms for the gene that this GeneArg represents.
getGeneGoTermsInTaxon(GeneArg, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService: Obtain GO terms for the gene in the given taxon.
getGeneGroup() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
getGeneGroupName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
getGeneHomologues(GeneArg) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the homologues of the given gene.
getGeneId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getGeneId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getGeneId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getGeneId() - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
getGeneIds() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject: Gene IDs part of this gene set.
getGeneIdsInGroup(GeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
getGeneIdsInGroup(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
getGeneIdsInGroup(GeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
getGeneIdsInGroup(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
getGeneInfo() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
getGeneLocation(GeneArg) - Method in class ubic.gemma.rest.util.args.GeneArgService: Returns all known locations of the gene(s) that this GeneArg represents.
getGeneLocationInTaxon(GeneArg, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService: Returns all known locations of the gene that this GeneArg represents.
getGeneLocations(GeneArg) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the physical location of the given gene.
getGeneManipulatedCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Distinct genes annotated as manipulation targets across the corpus — characteristics whose valueUri starts with Gene.NCBI_URI_PREFIX AND whose own categoryUri is genotype.
getGeneManipulatedExperimentCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Companion to HomeStats.geneManipulatedCount: number of distinct experiments carrying at least one genotype-category gene-URI annotation.
getGeneMappingSummaries() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Per-alignment gene mappings for this element, or null when the caller did not ask for them (only GET /platforms/{platform}/elements/{probe}/mappingSummary populates this).
getGeneMappingSummary(BioSequence, CompositeSequenceValueObject) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getGeneMappingSummary(BioSequence, CompositeSequenceValueObject) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGeneName() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getGeneNcbiId() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
getGeneOfficialName() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
getGeneOfficialSymbol() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
getGeneOverview(GeneArg) - Method in class ubic.gemma.rest.GeneWebService: Retrieves a fully-populated overview of the given gene, suitable for rendering the gene-page header in gemma-curation-ui.
getGeneProbes(GeneArg, int, int) - Method in class ubic.gemma.rest.util.args.GeneArgService: Obtain probes for the gene across all platforms.
getGeneProbes(GeneArg, OffsetArg, LimitArg, CursorArg, boolean) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the probes (composite sequences) with this gene.
getGeneProbesByCursor(GeneArg, Cursor, int) - Method in class ubic.gemma.rest.util.args.GeneArgService: Cursor-mode counterpart to GeneArgService.getGeneProbes(GeneArg, int, int): keyset pagination over the probes (composite sequences) mapped to a single gene across all platforms — see CURSOR_PAGINATION_STEP1_PLAN.md step 1m.
getGeneProbesInTaxon(GeneArg, Taxon, int, int) - Method in class ubic.gemma.rest.util.args.GeneArgService: Obtain probes for the gene in the given taxon across all platforms.
getGeneProbesInTaxonByCursor(GeneArg, Taxon, Cursor, int) - Method in class ubic.gemma.rest.util.args.GeneArgService: Cursor-mode counterpart to GeneArgService.getGeneProbesInTaxon(GeneArg, Taxon, int, int): keyset pagination over the probes (composite sequences) mapped to a single gene in the given taxon across all platforms — see CURSOR_PAGINATION_STEP1_PLAN.md step 1n.
getGeneProduct() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getGeneProductExonOverlap(String, String, String, GeneProduct) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Compute the overlap of a physical location with a transcript (gene product).
getGeneProductIdGeneMap() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getGeneProductIdMap() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getGeneProductMap() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getGeneProducts() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
getGeneProducts() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getGeneProducts() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getGeneralType() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
getGeneralType() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getGeneralType() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getGeneralType() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getGeneratedAt() - Method in class ubic.gemma.core.analysis.report.HomeStats: When the snapshot was last refreshed (ISO-8601 in JSON via default Jackson).
getGeneratedAt() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getGenes() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
getGenes() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getGenes() - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
getGenes() - Method in interface ubic.gemma.core.loader.expression.DataLoader: Load gene identifiers present in the data.
getGenes() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getGenes() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
getGenes() - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getGenes() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
getGenes() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap: List of genes to use for display purposes.
getGenes() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
getGenes() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummaryValueObject: Genes this alignment supports, deduplicated — a gene reached through several of its gene products appears once.
getGenes() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
getGenes() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Compact identities of the genes this element maps to, via the denormalized GENE2CS table.
getGenes() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject.Row: Genes the probe maps to, or null if it maps to none.
getGenes() - Method in class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject
getGenes() - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta: Genes mapped to this probe.
getGenes(int, int) - Method in class ubic.gemma.rest.util.args.GeneArgService
getGenes(String, Taxon) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Find genes for a given GO term by GO ID.
getGenes(String, Taxon) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getGenes(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao: Obtain the genes associated to each vector.
getGenes(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getGenes(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Given a collection of composite sequences returns a map of the given composite sequences to a collection of genes
getGenes(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getGenes(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
getGenes(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
getGenes(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getGenes(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGenes(OntologyTerm, Taxon) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Find genes for a given of GO term.
getGenes(OntologyTerm, Taxon) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getGenes(QuantitationType) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: Obtain the genes for a specific QT.
getGenes(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Obtain all the genes associated to the platform.
getGenes(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getGenes(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getGenes(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getGenes(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getGenes(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getGenes(CompositeSequence, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService: Return all genes mapped to the given composite sequence.
getGenes(CompositeSequence, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
getGenes(CompositeSequence, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getGenes(CompositeSequence, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGenes(CompositeSequence, int, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: given a composite sequence returns a collection of genes
getGenes(CompositeSequence, int, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getGenes(CompositeSequence, int, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
getGenes(CompositeSequence, int, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
getGenes(CompositeSequence, int, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getGenes(CompositeSequence, int, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGenes(OffsetArg, LimitArg, CursorArg) - Method in class ubic.gemma.rest.GeneWebService
getGenesByAccession(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
getGenesByAccession(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
getGenesByAccession(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService
getGenesByAccession(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl
getGenesByAccession(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
getGenesByAccession(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
getGenesByCompositeSequence(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
getGenesByCompositeSequence(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getGenesByCompositeSequence(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getGenesByCompositeSequence(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getGenesByCompositeSequence(Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getGenesByCompositeSequence(Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getGenesByCompositeSequence(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Obtain all the genes associated to the platform organized by corresponding design elements.
getGenesByCompositeSequence(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getGenesByCompositeSequence(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getGenesByCompositeSequence(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getGenesByCompositeSequence(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getGenesByCompositeSequence(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getGenesByCursor(CompositeSequence, Cursor, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Cursor-paged listing of Genes associated with a single CompositeSequence — see CURSOR_PAGINATION_STEP1_PLAN.md step 1l.
getGenesByCursor(CompositeSequence, Cursor, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getGenesByCursor(CompositeSequence, Cursor, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
getGenesByCursor(CompositeSequence, Cursor, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
getGenesByCursor(CompositeSequence, Cursor, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService: Cursor-mode counterpart to CompositeSequenceService.getGenes(CompositeSequence, int, int, boolean) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1l.
getGenesByCursor(CompositeSequence, Cursor, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGenesByCursor(Cursor, int) - Method in class ubic.gemma.rest.util.args.GeneArgService: Cursor-mode counterpart to GeneArgService.getGenes(int, int): keyset pagination over genes, always sorted by ascending id (the primary key, indexed and unique).
getGenesByCursor(CompositeSequenceArg, ArrayDesign, Cursor, int) - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgService: Cursor-mode counterpart to CompositeSequenceService.getGenes(CompositeSequence, int, int, boolean) scoped to a single probe on a single platform (the /{platform}/elements/{probe}/genes endpoint) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1l.
getGenesByGOId(String, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSearchService: get all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy
getGenesByGOId(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
getGenesByGoTerm(String, TaxonArg, OffsetArg, LimitArg, boolean, int) - Method in class ubic.gemma.rest.GoTermsWebService: Reverse lookup: genes annotated with the given GO term.
getGenesByIds(GeneArrayArg) - Method in class ubic.gemma.rest.GeneWebService
getGenesByName(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao: For a biosequence name, get the genes
getGenesByName(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
getGenesByName(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService
getGenesByName(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl
getGenesByName(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
getGenesByName(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
getGenesByName(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductDao
getGenesByName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
getGenesByName(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductReadService
getGenesByName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductReadServiceImpl
getGenesByName(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
getGenesByName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
getGenesByNcbiId(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductDao
getGenesByNcbiId(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
getGenesByNcbiId(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductReadService
getGenesByNcbiId(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductReadServiceImpl
getGenesByNcbiId(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
getGenesByNcbiId(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
getGeneSets() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Gene sets this gene belongs to, in their light form (no members).
getGenesInGroup(GeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
getGenesInGroup(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
getGenesInGroup(GeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Get the gene value objects for the members of the group param
getGenesInGroup(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
getGenesInTaxon(Taxon, int, int) - Method in class ubic.gemma.rest.util.args.GeneArgService
getGenesInTaxon(GeneArrayArg, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService
getGenesInTaxonByCursor(Taxon, Cursor, int) - Method in class ubic.gemma.rest.util.args.GeneArgService: Cursor-mode counterpart to GeneArgService.getGenesInTaxon(Taxon, int, int): keyset pagination over the genes belonging to a single taxon, always sorted by ascending id (the primary key, indexed and unique) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1g.
getGenesOnChromosome(TaxonArg, String, String, long, int) - Method in class ubic.gemma.rest.util.args.TaxonArgService: Lists Genes overlapping a location on a specific chromosome on a taxon that this TaxonArg represents.
getGenesUsedByPreferredVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain genes used by the processed vectors of this dataset.
getGenesUsedByPreferredVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getGenesUsedByPreferredVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Retrieve the genes used by the preferred vectors of this experiment.
getGenesUsedByPreferredVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getGenesWithSpecificity(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
getGenesWithSpecificity(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getGenesWithSpecificity(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
getGenesWithSpecificity(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
getGenesWithSpecificity(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getGenesWithSpecificity(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGeneSymbol() - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat: Canonical Gemma gene symbol (e.g.
getGeneSymbol() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getGeneType() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getGenomicNucleotideAccession() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getGenomicNucleotideAccessionVersion() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getGenomicNucleotideGI() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getGeoAccession() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
getGeoAccessions(CollectionMetadata) - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils: Extract GEO accessions from the given collection metadata.
getGeoRecord(GeoRecordType, String) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Retrieve a single GEO series using the default preset.
getGeoRecord(GeoRecordType, String, GeoRetrieveConfig) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Retrieve a single GEO record.
getGeoRecord(GeoRecordType, String, GeoRetrieveConfig) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl
getGeoRecords(GeoRecordType, Collection) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser
getGeoRecords(GeoRecordType, Collection, GeoRetrieveConfig) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Retrieve a collection of GEO series.
getGeoRecords(GeoRecordType, Collection, GeoRetrieveConfig) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl: Retrieve records for experiments
getGeoSeries() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
getGeoSeries(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentGeoService: Obtain the GEO series metadata.
getGeoSeries(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentGeoServiceImpl
getGeoString() - Method in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
getGfClientExe() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getGfServerExe() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getGitHash() - Method in class ubic.gemma.core.util.BuildInfo
getGitHash() - Method in class ubic.gemma.rest.monitoring.InfoWebService.BuildBlock
getGitHash() - Method in class ubic.gemma.rest.util.BuildInfoValueObject
getGOGroupGenes(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSearchService
getGOGroupGenes(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
getGoId() - Method in class ubic.gemma.model.genome.gene.GOGroupValueObject
getGoId() - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
getGOTerms(Gene) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getGOTerms(Gene) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getGOTerms(Gene, boolean, GeneOntologyServiceImpl.GOAspect) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Get all GO terms for a gene, including parents of terms via is-a relationships; and optionally also parents via part-of relationships.
getGOTerms(Gene, boolean, GeneOntologyServiceImpl.GOAspect) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getGrammarFileName() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getGrammarFileName() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getGrantedAuthority() - Method in class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
getGroundedTermLabel() - Method in class ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject: Label of AnnotationsWebService.ExternalIdentificationValueObject.getGroundedTermUri().
getGroundedTermUri() - Method in class ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject: A term Gemma already has whose name equals AnnotationsWebService.ExternalIdentificationValueObject.getName() — the one URI here that is safe to commit.
getGroup() - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Coarse UI grouping carried through from the bucket spec — control, pharmacology, biological, unclassified.
getGroup() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Coarse UI grouping.
getGroup() - Method in class ubic.gemma.rest.RootWebService.UserValueObject
getGroup(Long, boolean, boolean) - Method in class ubic.gemma.rest.GroupsWebService: Retrieve a single group by id.
getGroup(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location
getGroupAuthoritiesNameFromGroupName(String) - Method in interface ubic.gemma.core.security.SecurityService
getGroupAuthoritiesNameFromGroupName(String) - Method in class ubic.gemma.core.security.SecurityServiceImpl: From the group name get the authority which should be underscored with GROUP_
getGroupBy() - Method in class ubic.gemma.rest.AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
getGroupBy() - Method in class ubic.gemma.rest.util.CursorPaginatedResponseDataObject
getGroupBy() - Method in class ubic.gemma.rest.util.FilteredResponseDataObject
getGroupBy() - Method in class ubic.gemma.rest.util.PaginatedResponseDataObject
getGroupMembers() - Method in interface ubic.gemma.core.security.model.UserGroup: A set of users that belong to the group.
getGroupMembers() - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup
getGroupName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
getGroups() - Method in interface ubic.gemma.core.security.model.User
getGroups() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getGroups(String, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.GroupsWebService: List groups (paginated; offset/limit).
getGroupsEditableBy(Collection) - Method in interface ubic.gemma.core.security.SecurityService
getGroupsEditableBy(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
getGroupsEditableBy(Securable) - Method in interface ubic.gemma.core.security.SecurityService
getGroupsEditableBy(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
getGroupsReadableBy(Collection) - Method in interface ubic.gemma.core.security.SecurityService
getGroupsReadableBy(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
getGroupsReadableBy(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Obtain all the groups whose members can read a given object.
getGroupsReadableBy(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
getGroupsUserCanEdit(String) - Method in interface ubic.gemma.core.security.SecurityService: Obtain all the groups that the user can edit.
getGroupsUserCanEdit(String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
getGrowthProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getH5Version() - Static method in class ubic.gemma.core.loader.util.hdf5.H5Utils: Obtain the version of the HDF5 library.
getHasBatchInformation() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getHasBlatAssociations() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getHasBothIntensities() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getHasCoexpressionAnalysis() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getHasDifferentialExpressionAnalysis() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getHasEitherIntensity() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getHasFile() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
getHasFiles() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getHasGeneAssociations() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getHasMultiplePreferredQuantitationTypes() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getHasMultipleTechnologyTypes() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getHasSequenceAssociations() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getHDF5Version() - Method in class ubic.gemma.core.util.BuildInfo: Obtain the version of HDF5 used by Gemma.
getHealth() - Method in class ubic.gemma.rest.monitoring.HealthWebService
getHeldBy() - Method in exception class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService.CurationLockedException
getHelpFooter() - Method in class ubic.gemma.apps.SingleCellDataTransformCli
getHelpFooter() - Method in class ubic.gemma.cli.util.AbstractCLI: Include a detailed help footer in the --help menu.
getHgnc_id() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getHi() - Method in class ubic.gemma.rest.PvalueDistributionValueObject.Bin
getHibernateProperties() - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
getHibernateStats() - Method in class ubic.gemma.rest.AdminWebService: Returns a structured snapshot of Hibernate statistics.
getHighExpressionCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: High cut for expression.
getHighlightedText() - Method in class ubic.gemma.model.common.search.SearchResultValueObject
getHighlighter() - Method in class ubic.gemma.core.search.SearchContext
getHighlights() - Method in class ubic.gemma.model.common.search.SearchResult: Highlights for this result.
getHighlights() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
getHistory() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getHistory(Investigation) - Method in interface ubic.gemma.persistence.service.expression.experiment.WorkflowService: Retrieve the full chronological history of workflow transitions for a dataset, derived from the AUDIT_EVENT stream filtered to WorkflowStateChangedEvent rows.
getHistory(Investigation) - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceImpl
getHitListSizes() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getHomeStats() - Method in class ubic.gemma.rest.StatsWebService
getHomologue(Gene, Taxon) - Method in interface ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService
getHomologue(Gene, Taxon) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl
getHomologues() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Homologues of this gene across taxa.
getHomologues(Long) - Method in interface ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService
getHomologues(Long) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl
getHomologues(Gene) - Method in interface ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService
getHomologues(Gene) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl
getHomologueValueObject(Long, String) - Method in interface ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService
getHomologueValueObject(Long, String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl
getHost() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getHost() - Method in class ubic.gemma.core.util.NetDatasourceUtil
getHostUrl() - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getHostUrl() - Method in interface ubic.gemma.core.util.GemmaRestApiClient
getHostUrl() - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
getHumanSensitiveServerPort() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getHumanSeqFiles() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getHumanServerPort() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getHybProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getId() - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
getId() - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
getId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
getId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
getId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getId() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getId() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getId() - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
getId() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
getId() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExternalId
getId() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
getId() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
getId() - Method in class ubic.gemma.core.pipeline.SchedulerHandle
getId() - Method in class ubic.gemma.core.security.acl.domain.AclEntry
getId() - Method in class ubic.gemma.core.security.acl.domain.AclImpl
getId() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
getId() - Method in class ubic.gemma.core.security.acl.domain.AclSid
getId() - Method in interface ubic.gemma.core.security.model.Securable: Obtain the ID of this object.
getId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
getId() - Method in class ubic.gemma.core.util.runtime.FileLockInfo: Unique identifier for the lock.
getId() - Method in class ubic.gemma.model.analysis.AnalysisResultSet
getId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
getId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getId() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getId() - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
getId() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
getId() - Method in class ubic.gemma.model.common.AbstractIdentifiable
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType: Deprecated.
you should never use this property, rely instead on the actual type via Object.getClass().
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getId() - Method in class ubic.gemma.model.common.description.BibliographicReference
getId() - Method in class ubic.gemma.model.common.description.BibRefAnnotation
getId() - Method in class ubic.gemma.model.common.description.Characteristic
getId() - Method in class ubic.gemma.model.common.description.CitationValueObject: The ID of the BibliographicReference being represented.
getId() - Method in class ubic.gemma.model.common.description.DatabaseEntry
getId() - Method in interface ubic.gemma.model.common.GemmaSessionBackedValueObject
getId() - Method in interface ubic.gemma.model.common.Identifiable: Obtain the identifier of the object.
getId() - Method in class ubic.gemma.model.common.IdentifiableValueObject
getId() - Method in class ubic.gemma.model.expression.arrayDesign.AlternateName
getId() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getId() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: Gemma-internal platform id, suitable for GET /platforms/{id}.
getId() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getId() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getId() - Method in class ubic.gemma.model.expression.biomaterial.Compound
getId() - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
getId() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef
getId() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef
getId() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef
getId() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getId() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
getId() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getId() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getId() - Method in record class ubic.gemma.model.expression.experiment.ExpressionExperimentIdAndShortName
getId() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject: Gemma-internal dataset id, suitable for GET /datasets/{id}.
getId() - Method in class ubic.gemma.model.expression.experiment.FactorValue
getId() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
getId() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getId() - Method in class ubic.gemma.model.genome.gene.GeneAlias
getId() - Method in class ubic.gemma.model.genome.gene.GeneProduct
getId() - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject: Gemma-internal gene id, suitable for GET /genes/{id}.
getId() - Method in class ubic.gemma.model.genome.gene.GeneSet
getId() - Method in class ubic.gemma.model.genome.gene.GeneSetMember
getId() - Method in class ubic.gemma.model.genome.Gene
getId() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
getId() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getId() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject
getId() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetGroupValueObject
getId() - Method in class ubic.gemma.rest.GroupsWebService.GroupMemberValueObject
getId() - Method in class ubic.gemma.rest.GroupsWebService.GroupSummaryValueObject
getId() - Method in class ubic.gemma.rest.GroupsWebService.GroupValueObject
getId() - Method in class ubic.gemma.rest.HeatmapDataValueObject.GeneRef
getIdColumnName() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getIdentifier() - Method in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType: Identifier of the series type as it appears in the GEO SOFT files.
getIdentifier() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getIdentifier() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getIdentifier() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getIdentifier() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain a stable identifier for this ontology, suitable for a URL path segment, a CLI argument or a configuration key.
getIdentifier() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
getIdentifier() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterService.LintResult
getIdentifier() - Method in class ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject: The authority's accession, e.g.
getIdentifier(BioSequence) - Static method in class ubic.gemma.core.analysis.sequence.SequenceWriter: Modify the identifier for the purposes of using in temporary Fasta files.
getIdentifier(Gene) - Method in class ubic.gemma.core.loader.util.mapper.AbstractGeneIdentifierBasedDesignElementMapper: Extract an identifier from the gene.
getIdentifier(Gene) - Method in class ubic.gemma.core.loader.util.mapper.EnsemblIdDesignElementMapper
getIdentifier(Gene) - Method in class ubic.gemma.core.loader.util.mapper.GeneNameDesignElementMapper
getIdentifier(Gene) - Method in class ubic.gemma.core.loader.util.mapper.NcbiIdDesignElementMapper
getIdentifier(Gene) - Method in class ubic.gemma.core.loader.util.mapper.OfficialSymbolDesignElementMapper
getIdentifierPropertyName() - Method in class ubic.gemma.persistence.service.AbstractDao
getIdentifiers() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
getIdentifiers() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
getIdentifiers() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getIdentifiers() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
getIdentity() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getIdentity() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getIdentityThreshold() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getIdMap() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getIdMap(Collection) - Static method in class ubic.gemma.persistence.util.IdentifiableUtils: Given a set of entities, create a map of their ids to the entities.
getIds(Collection) - Static method in class ubic.gemma.persistence.util.IdentifiableUtils: Convert a collection of identifiable to their IDs.
getIdsForSearchQuery(QueryArg, Collection) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Shortcut for extracting the result IDs from DatasetArgService.getResultsForSearchQuery(QueryArg, Highlighter, Collection).
getIdsForSearchQuery(QueryArg, Map, Collection) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Shortcut for extracting the result IDs and scores from DatasetArgService.getResultsForSearchQuery(QueryArg, Highlighter, Collection).
getIdsHavingEvent(Class, Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the ids of every auditable of a class whose trail carries at least one event of any of the given types.
getIdsHavingEvent(Class, Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getIdsHavingEvent(Class, Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService: Obtain the ids of every auditable of a class whose trail carries at least one event of any of the given types.
getIdsHavingEvent(Class, Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getImmobilizedCharacteristic() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getImpliedAnnotations(String, String, String, String, Long, int, boolean, int) - Method in class ubic.gemma.rest.AnnotationsWebService: Is a term already implied by the terms an experiment carries?
getImpliedObject() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getImpliedObject() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getImpliedObjectUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getImpliedObjectUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getImpliedPredicate() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getImpliedPredicate() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getImpliedPredicateUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getImpliedPredicateUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getImpliedSubject() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary: The claim this relation licenses, as a triple in its own right — not the stored row read backwards.
getImpliedSubject() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: The claim the relation licenses, phrased as its own triple rather than left as the stored row for a client to invert.
getImpliedSubjectUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getImpliedSubjectUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getImpliedTripleKey() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary: Identity of the CLAIM this row licenses, as opposed to AnnotationRelationDao.RelationSummary.getTripleKey(), which is the identity of the row as stored.
getImpliedTripleKey() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: Identity of the CLAIM, for deduplicating a card.
getImportantFactors(ExpressionExperiment, Collection, Double) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService
getImportantFactors(ExpressionExperiment, Collection, Double) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
getInCategory() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getIncludedResultSetsInfo() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
getIncludeGeneCount() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getIncludeGenes() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getIncludeInteractions() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialAnalysisRunRequest
getIncompleteRecords() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.DryRunResult: Deprecated.

Accessions examined on degraded information: GEO served invalid MINiML, so the record was kept with whatever the summary gave rather than failing the batch.
getIndex() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
getIndex() - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
getIndex() - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain the index column.
getIndex(Class) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain the index column.
getIndexColumn() - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain the name of the column used as an index.
getIndices() - Method in class ubic.gemma.core.loader.util.anndata.SparseMatrix
getIndices() - Method in interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics: Each entry indicate which characteristic from CellLevelCharacteristics.getCharacteristics() is applicable for a given cell.
getIndices() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Deprecated.
Use CellTypeAssignment.getCellTypeIndices() instead.
getIndices() - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
getIndices(GeoPlatform, List, int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: Get the indices of the data for a set of samples - this can be used to get a slice of the data.
getIndividual(String) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyService: Obtain an individual from the ontology by URI.
getIndividual(String) - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl
getIndividuals() - Method in interface ubic.gemma.core.ontology.model.OntologyTerm
getIndividuals(boolean) - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
getIndividuals(boolean) - Method in interface ubic.gemma.core.ontology.model.OntologyTerm
getIndividuals(boolean) - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getIndptr() - Method in class ubic.gemma.core.loader.util.anndata.SparseMatrix
getInferenceDirection() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary: Which end of this relation licenses an inference about the other.
getInferenceDirection() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: SUBJECT_IMPLIES_OBJECT, OBJECT_IMPLIES_SUBJECT or NEITHER.
getInferenceMode() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getInferenceMode() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getInferenceMode() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getInferenceMode() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain the inference mode used for this ontology.
getInferredQuantitationType() - Method in exception class ubic.gemma.core.analysis.preprocess.detect.InferredQuantitationMismatchException
getInferredTerms() - Method in class ubic.gemma.rest.DatasetsWebService.FilteredAndInferredAndCursorPaginatedResponseDataObject
getInferredTerms() - Method in class ubic.gemma.rest.DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject
getInferredTerms() - Method in class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObject
getInferredTerms() - Method in class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject
getInferredTerms() - Method in class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject
getInferredTerms() - Method in class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredResponseDataObject
getInfo() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getInfo() - Method in class ubic.gemma.rest.monitoring.InfoWebService
getInitializationTime(String, TimeUnit) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor: Obtain the time spent initializing a bean.
getInObject() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getInode() - Method in class ubic.gemma.core.util.runtime.FileLockInfo
getInPredicate() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getInputStream() - Method in interface ubic.gemma.cli.util.CLIContext
getInputStream() - Method in class ubic.gemma.cli.util.SystemCLIContext
getInputStreamFromPlainOrCompressedFile(String) - Static method in class ubic.gemma.core.util.FileTools: Open a non-compressed, zipped, or gzipped file.
getInstance() - Static method in class ubic.gemma.persistence.util.DescribableComparator
getInstance() - Static method in class ubic.gemma.persistence.util.FactorValueComparator
getInstanceOf() - Method in interface ubic.gemma.core.ontology.model.OntologyIndividual: Return the term that this is an instance of.
getInstanceOf() - Method in class ubic.gemma.core.ontology.simple.OntologyIndividualSimple
getInstantiationTime(String, TimeUnit) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor: Obtain the time spent instantiating a bean.
getInstitute() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getInstrumentModel() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: Verbatim !Sample_instrument_model, e.g.
getInstrumentModel() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPlatform
getInstrumentPlatform() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPlatform
getInt(int) - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
getInt(int) - Method in class ubic.gemma.core.loader.util.anndata.EnumArray
getInt(String) - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getInt(String, int) - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getInt(K) - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
getInteger(long) - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset: Obtain a single integer value.
getIntensities(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper
getIntensity() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getInteractionDof() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getInteractionEffectDof() - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult: Obtain the degrees of freedom for the interaction effects, if any.
getInteractionEffectDof(String...) - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult
getInteractionEffectFactorNames() - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult: Obtain all the combinations of factor names that have interaction effects.
getInteractionEffectFStat() - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult: Obtain the F statistic for the interaction effects, if any.
getInteractionEffectFStat(String...) - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult
getInteractionEffectPValue() - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult: Obtain the p-value for the interaction effects, if any.
getInteractionEffectPValue(String...) - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult
getInteractionFStat() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getInteractionPValue() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getInteractionsToInclude() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getInteractionTerms() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
getInterceptCoefficient() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getInterceptPValue() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getInterceptTStat() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getInvalidatedBy() - Method in class ubic.gemma.rest.DatasetsWebService.StaleDatasetValueObject
getInvalidatedOn() - Method in class ubic.gemma.rest.DatasetsWebService.StaleDatasetValueObject
getInValue() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getInvestigation() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getInvestigation() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
getInvestigation() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
getInvestigation() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getInvestigationId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getInvestigationId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
getIri() - Method in class ubic.gemma.core.ontology.ols.OlsTerm
getIsAffymetrixAltCdf() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getIsAggregated() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsApproximateLength() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getIsArrayExpress() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getIsBackground() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsBackground() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getIsBackgroundSubtracted() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsBackgroundSubtracted() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getIsBaseline() - Method in class ubic.gemma.model.expression.experiment.FactorValue: Indicate if this factor value is a "forced" baseline or non-baseline condition.
getIsBatchCorrected() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
getIsBatchCorrected() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsBatchCorrected() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getIsCircular() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getIsGenesUsable() - Method in class ubic.gemma.model.genome.Taxon
getIsGenesUsable() - Method in class ubic.gemma.model.genome.TaxonValueObject: Whether Gemma has gene records loaded for this taxon — a loader-maintained capability bit, written false at creation and flipped by NcbiGeneLoader.updateTaxaWithGenesUsable once genes actually land.
getIsGroup() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getIsMajorTopic() - Method in class ubic.gemma.model.common.description.BibRefAnnotation
getIsMaskedPreferred() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType: Deprecated.
getIsMaskedPreferred() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject: Deprecated.
getIsMerged() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Indicates this array design is the merger of other array designs.
getIsMergee() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Indicates that this array design has been merged into another.
getIsNormalized() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsNormalized() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getIsOutlier() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getIsPaired() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata: Whether the reads are paired.
getIsPreferred() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
getIsPreferred() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsPreferred() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getIsProbeMissing() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getIsProbeOmitted() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getIsPublic() - Method in interface ubic.gemma.core.security.model.SecureValueObject: Indicate if the object is public.
getIsPublic() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getIsPublic() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getIsPublic() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getIsPublic() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getIsPublic() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getIsPublic() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetPermissionsValueObject
getIsPublic() - Method in class ubic.gemma.rest.DatasetsWebService.PermissionsUpdateRequest
getIsPublic() - Method in class ubic.gemma.rest.PipelineStatusValueObject
getIsQuery() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Was this gene directly used in a query? Or is it inferred somehow.
getIsRatio() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
getIsRatio() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsRatio() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getIsRecomputedFromRawData() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsRecomputedFromRawData() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getIsRNASeq() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getIsSelected() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getIsSelected() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
getIsShared() - Method in interface ubic.gemma.core.security.model.SecureValueObject: Indicate if the object is shared.
getIsShared() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getIsShared() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getIsShared() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getIsShared() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getIsShared() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getIsShared() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetPermissionsValueObject
getIsSingleCell() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Lombok would name these isSingleCell / setSingleCell; the wire name and the convention these flags follow in this class is getIsX / setIsX (see ExpressionExperimentValueObject.getIsPublic()).
getIsSingleCellPreferred() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsSingleCellPreferred() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getIsSpecies() - Method in class ubic.gemma.model.genome.TaxonValueObject
getIsSubset() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getIsSubset() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
getIsSubsumed() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Indicate if this array design is subsumed by some other array design.
getIsSubsumer() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Indicates if this array design subsumes some other array design(s)
getIssue() - Method in class ubic.gemma.model.common.description.BibliographicReference
getIssue() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getIssueReporter() - Method in class ubic.gemma.core.search.SearchContext
getItem(NodeList, int) - Static method in class ubic.gemma.core.util.XMLUtils: Obtain an item from a NodeList at a given index.
getItems() - Method in class ubic.gemma.rest.DatasetsWebService.Section
getJava() - Method in class ubic.gemma.rest.monitoring.InfoWebService.InfoValueObject
getJavaClass() - Method in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType: Obtain the Java class that corresponds to this primitive type.
getJdbcTemplate() - Method in class ubic.gemma.core.goldenpath.GoldenPath
getJob() - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
getJobs() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getJobs() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
getJobs() - Method in class ubic.gemma.rest.AdminWebService: Aggregated admin view of the in-memory background task queue.
getJudgedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
getJudgedBy() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
getJudgeKind() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
getJudgeKind() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
getJudgeKind() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
getKey() - Method in class ubic.gemma.cli.logging.log4j.UserDetailsThreadContextPopulator
getKey() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.RunMetrics: The report's own row key, e.g.
getKey() - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Stable lowercase-snake-case label used in byAnnotationCategory (e.g.
getKey() - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Stable lowercase-snake-case identifier the frontend matches in code — e.g.
getKey() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Stable lowercase-snake-case identifier the frontend matches in code.
getKey() - Method in class ubic.gemma.core.logging.log4j.BuildInfoThreadContextPopulator
getKey() - Method in interface ubic.gemma.core.logging.log4j.ThreadContextPopulator: Key in the ThreadContext this populator is responsible for.
getKey() - Method in interface ubic.gemma.core.util.math.linearmodels.AnovaResult
getKey() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getKey() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition: Obtain the key that is locked.
getKey() - Method in class ubic.gemma.rest.DatasetsWebService.RunQcMetricsValueObject: The report's own row key, e.g.
getKey(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
getKey(Collection) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
getKey(T) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
getKey(T) - Method in class ubic.gemma.core.loader.util.parser.LineMapParser
getKey(Reporter) - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
getKey(NcbiGeneHistory) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
getKey(NCBIGeneInfo) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
getKey(BioSequence) - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParser
getKey(Taxon) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParser
getKeys() - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getKeys() - Method in class ubic.gemma.core.loader.util.anndata.Mapping
getKeys(Cache) - Static method in class ubic.gemma.persistence.cache.CacheUtils
getKeySet() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
getKeySet() - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
getKeySet() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
getKeySet() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
getKeySet() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
getKeySet() - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParser
getKeySet() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParser
getKeySet() - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser: Getter for values in map that is BioMartEnsembleNcbi value objects associated with the parsing of this file
getKeySet() - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
getKeysInternal() - Method in class ubic.gemma.core.config.PropertySourcesConfiguration: Deprecated.
getKeyTuple() - Method in class ubic.gemma.persistence.util.Cursor
getKeywords() - Method in class ubic.gemma.model.common.description.BibliographicReference
getKeyWords() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getKillRequestedAt() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
getKind() - Method in class ubic.gemma.core.pipeline.SchedulerHandle
getKind() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getKind() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getKind() - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
getKindCV() - Method in class ubic.gemma.model.common.measurement.Measurement
getLabel() - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat: Curator-visible label (the Characteristic.value).
getLabel() - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Visitor-facing label with the canonical phrasing.
getLabel() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Visitor-facing label (canonical phrasing).
getLabel() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
getLabel() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getLabel() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
getLabel() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.Annotation
getLabel() - Method in interface ubic.gemma.core.ontology.model.OntologyResource: A label, if known, otherwise null.
getLabel() - Method in class ubic.gemma.core.ontology.model.OntologyTerm.TaxonConstraint
getLabel() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
getLabel() - Method in class ubic.gemma.core.ontology.ols.OlsTerm: The term's canonical label, or null when OlsTerm.isFound() is false.
getLabel() - Method in class ubic.gemma.core.ontology.search.OntologySearchService.Result
getLabel() - Method in class ubic.gemma.core.ontology.simple.AbstractOntologyResourceSimple
getLabel() - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject: A label for display purposes.
getLabel() - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
getLabel() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationCategoryValueObject
getLabel() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSimpleValueObject
getLabel() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject
getLabel() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonConstraintValueObject: Scientific name when the loaded model carries one, e.g.
getLabel() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonValueObject: The source's own rendering, e.g.
getLabel() - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermRef
getLabel() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject
getLabel(DatabaseEntry) - Static method in class ubic.gemma.core.loader.util.ExternalDatabaseUtils: Obtain a label for a given database entry.
getLabelField() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getLabelMd5() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getLabelProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getLabName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
getLaboratory() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getLane() - Method in class ubic.gemma.rest.AnnotationsWebService.CanonicalUriValueObject: malformed (the stored URI is wrong on its face) or clo_twin (two live Cell Line Ontology classes for one cell line).
getLanguageLevel() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getLanguageLevel() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getLanguageLevel() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getLanguageLevel() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain the OWL language level supported by this ontology.
getLastArrayDesignUpdate(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getLastArrayDesignUpdate(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getLastArrayDesignUpdate(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getLastArrayDesignUpdate(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getLastArrayDesignUpdate(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getLastArrayDesignUpdate(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getLastArrayDesignUpdate(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getLastArrayDesignUpdate(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getLastArrayDesignUpdate(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getLastArrayDesignUpdate(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getLastArrayDesignUpdate(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getLastArrayDesignUpdate(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getLastArrayDesignUpdateDate() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getLastBuildTime() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getLastComputed() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getLastEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
getLastEvent(Auditable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the latest event for a given auditable.
getLastEvent(Auditable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getLastEvent(Auditable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getLastEvent(Auditable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getLastEvent(Auditable, Class) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the latest event of a given type for a given auditable.
getLastEvent(Auditable, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getLastEvent(Auditable, Class) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getLastEvent(Auditable, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getLastEvent(Auditable, Class, Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the latest event of a given type, excluding a certain number of types.
getLastEvent(Auditable, Class, Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getLastEvent(Auditable, Class, Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getLastEvent(Auditable, Class, Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getLastEventAt() - Method in class ubic.gemma.model.pipeline.PipelineJob
getLastEventKind() - Method in class ubic.gemma.model.pipeline.PipelineJob
getLastEvents(Class, Class) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the latest events of a specified type for all auditable of a given type.
getLastEvents(Class, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getLastEvents(Class, Class) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getLastEvents(Class, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getLastEvents(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the latest event of any type for all given auditables — the batch counterpart of AuditEventDao.getLastEvent(Auditable).
getLastEvents(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getLastEvents(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService: Obtain the latest typed event for each of the given auditables, whatever its type.
getLastEvents(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getLastEvents(Collection, Class) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the latest events of a specified type for all given auditables.
getLastEvents(Collection, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getLastEvents(Collection, Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService: Fast method to retrieve auditEventTypes of multiple classes.
getLastEvents(Collection, Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getLastGeneMapping() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getLastGeneMapping(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getLastGeneMapping(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getLastGeneMapping(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Gets the AuditEvents of the latest gene mapping for the specified array design ids.
getLastGeneMapping(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getLastGeneMappingEvent(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getLastGeneMappingEvent(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
getLastGeoScrape() - Method in class ubic.gemma.rest.AdminWebService: Deprecated.
Reads the watermark written by the deprecated in-Gemma scrape. An agent that scrapes on its own side is the author of its own run records; this only ever sees runs Gemma performed.
getLastLinkAnalysis(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getLastLinkAnalysis(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getLastLinkAnalysis(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getLastLinkAnalysis(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getLastMissingValueAnalysis(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getLastMissingValueAnalysis(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getLastMissingValueAnalysis(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getLastMissingValueAnalysis(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getLastModified() - Method in class ubic.gemma.rest.DatasetsWebService.CurationBaseline
getLastName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
getLastName() - Method in class ubic.gemma.model.common.auditAndSecurity.Person: Deprecated.
getLastNeedsAttentionEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getLastNeedsAttentionEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getLastNeedsAttentionEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
getLastNoteUpdateEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getLastNoteUpdateEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getLastNoteUpdateEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
getLastOccurrence() - Method in class ubic.gemma.rest.CompactAuditEventValueObject
getLastProcessedDataUpdate(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getLastProcessedDataUpdate(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getLastProcessedDataUpdate(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getLastProcessedDataUpdate(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getLastProgressJson() - Method in class ubic.gemma.model.pipeline.PipelineJob
getLastProgressUpdates() - Method in interface ubic.gemma.core.job.SubmittedTask
getLastRepeatAnalysis(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getLastRepeatAnalysis(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getLastRepeatAnalysis(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getLastRepeatAnalysis(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getLastRepeatMask() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getLastRepeatMaskEvent(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getLastRepeatMaskEvent(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
getLastRun() - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject
getLastScannedAccession() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.DryRunResult: Deprecated.

The last record the scan actually LOOKED at, matched or not.
getLastScannedDate() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.DryRunResult: Deprecated.

Release date of GeoScrapeService.DryRunResult.getLastScannedAccession(), so a caller can step `until` without a lookup.
getLastSequenceAnalysis() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getLastSequenceAnalysis(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getLastSequenceAnalysis(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getLastSequenceAnalysis(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Gets the AuditEvents of the latest sequence analyses for the specified array design ids.
getLastSequenceAnalysis(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getLastSequenceAnalysisEvent(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getLastSequenceAnalysisEvent(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
getLastSequenceUpdate() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getLastSequenceUpdate(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getLastSequenceUpdate(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getLastSequenceUpdate(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Gets the AuditEvents of the latest sequence update for the specified array design ids.
getLastSequenceUpdate(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getLastSequenceUpdateEvent(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getLastSequenceUpdateEvent(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
getLastTroubledEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getLastTroubledEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getLastTroubledEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
getLastUpdate() - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
getLastUpdate() - Method in class ubic.gemma.rest.PipelineStatusValueObject: What changed here most recently, as a short label plus its date and performer — the thing curationDetails.lastUpdated leaves out.
getLastUpdated() - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
getLastUpdated() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getLastUpdated() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getLastUpdated() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
getLastUpdated() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getLastUpdated() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
getLastUpdated() - Method in interface ubic.gemma.model.common.description.Versioned: The last updated date, if known.
getLastUpdateDate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getLastUpdateDate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getLastUpdateDate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getLastWatermark() - Method in interface ubic.gemma.core.geoscrape.GeoScrapeService: Deprecated.
getLastWatermark() - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImpl
getLayer(String) - Method in class ubic.gemma.core.loader.util.anndata.AnnData: Obtain a layer by name.
getLayers() - Method in class ubic.gemma.core.loader.util.anndata.AnnData: Obtain all the layer names under layers/ path.
getLayout() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
getLength() - Method in class ubic.gemma.core.util.runtime.FileLockInfo
getLength() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getLength() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getLevel() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getLevel() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getLevelsForFactors() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
getLibraryDescriptor() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
getLibrarySelection() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: Verbatim !Sample_library_selection, e.g.
getLibrarySelection() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getLibrarySelection() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: How the library was selected — GEO's library_selection (polyA, cDNA, RANDOM, …), verbatim.
getLibrarySize() - Method in class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator
getLibrarySource() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getLibraryStrategy() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getLibraryStrategy() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getLibraryStrategy() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: What kind of library — GEO's library_strategy (RNA-Seq, scRNA-seq, Ribo-Seq, ATAC-seq, …).
getLibSource() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getLibStrategy() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getLimit() - Method in class ubic.gemma.persistence.util.CursorPage
getLimit() - Method in class ubic.gemma.persistence.util.Slice
getLimit() - Method in class ubic.gemma.rest.AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
getLimit() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getLimit() - Method in class ubic.gemma.rest.util.CursorPaginatedResponseDataObject
getLimit() - Method in class ubic.gemma.rest.util.FilteredAndLimitedResponseDataObject
getLimit() - Method in class ubic.gemma.rest.util.PaginatedResponseDataObject
getLimitingDate() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Obtain the limiting date (i.e.
getLinkAnalysisEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getLinkName() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
getLinks() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
getLinkType() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
getLinkUrl() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
getLiteratureSources() - Method in class ubic.gemma.model.genome.gene.GeneSet
getLo() - Method in class ubic.gemma.rest.PvalueDistributionValueObject.Bin
getLoadedGeneCount() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
getLoader() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI
getLoading() - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
getLoading() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject.Row
getLoadingRank() - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
getLoadPlatformOnly() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getLocalBasePath() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
getLocalInstallDbName() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getLocalName() - Method in interface ubic.gemma.core.ontology.model.OntologyResource: A local name for this resource.
getLocalName() - Method in class ubic.gemma.core.ontology.simple.AbstractOntologyResourceSimple
getLocalName() - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
getLocation() - Method in class ubic.gemma.rest.DatasetsWebService.Canonicalization: Request-body path to the rewritten slot, e.g.
getLocation() - Method in class ubic.gemma.rest.util.OntologyTermValidationException.Located
getLocation() - Method in class ubic.gemma.rest.util.WellComposedError
getLocation() - Method in class ubic.gemma.rest.util.WellComposedWarning
getLocationType() - Method in class ubic.gemma.rest.util.WellComposedError
getLocationType() - Method in class ubic.gemma.rest.util.WellComposedWarning
getLockedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
getLockedBy() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
getLockfilePath() - Method in class ubic.gemma.core.util.locking.FileLockInfo: Path being locked, which is usually FileLockInfo.getPath() with a .lock suffix.
getLockInfo(Path) - Method in interface ubic.gemma.core.util.locking.FileLockManager: Get the lock info for a given path.
getLockInfo(Path) - Method in class ubic.gemma.core.util.locking.FileLockManagerImpl
getLocusTag() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getLoess() - Method in class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator
getLog2FoldChange() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject: Log2 fold change for the primary contrast of the represented result-set.
getLogFoldChange() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getLogFoldChange() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getLogFoldChange() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
getLogFoldChange() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
getLostFactorValueIds() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef
getLowDistinctValueCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Minimum fraction of distinct values for a design element to be retained.
getLowExpressionCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Low cut for expression.
getLowVarianceCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: This threshold applies on the variance of the row.
getMageMlFile(Collection) - Method in class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
getMainEffectADof() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getMainEffectAFStat() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getMainEffectAPValue() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getMainEffectBDof() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getMainEffectBFStat() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getMainEffectBPValue() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
getMainEffectDof() - Method in interface ubic.gemma.core.util.math.linearmodels.OneWayAnovaResult
getMainEffectDof(String) - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult
getMainEffectFactorNames() - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult
getMainEffectFStat() - Method in interface ubic.gemma.core.util.math.linearmodels.OneWayAnovaResult
getMainEffectFStat(String) - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult
getMainEffectPValue() - Method in interface ubic.gemma.core.util.math.linearmodels.OneWayAnovaResult
getMainEffectPValue(String) - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult
getMajorDevice() - Method in class ubic.gemma.core.util.runtime.FileLockInfo
getManualQualityScore() - Method in class ubic.gemma.model.expression.experiment.Geeq
getManualQualityScore() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
getManufactureProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getManufacturer() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getMap() - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
getMapLocation() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getMappedDataVectorType(Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
getMappedDataVectorType(Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
getMappedDataVectorType(Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService: Infer all the mapped vector types that are subclasses of the given vector type.
getMappedDataVectorType(Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
getMappedDataVectorTypes(Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Obtain the vector types that are mapped and subclass of the given vector type.
getMappedDataVectorTypes(Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
getMappingStatistics(Collection) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper.StatefulEntityMapper: Calculate mapping statistics for a set of gene identifiers.
getMappingStatistics(Collection, Collection) - Method in class ubic.gemma.core.loader.util.mapper.ChainedEntityMapper
getMappingStatistics(Collection, Collection) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper: Calculate mapping statistics for a set of gene identifiers and candidates.
getMarkers() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getMask() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig: Categorical mask to use on data.
getMask() - Method in class ubic.gemma.core.security.acl.domain.AclEntry
getMatchedCriteria() - Method in class ubic.gemma.model.expression.experiment.PreboardedExperiment
getMatchedSynonym() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound: The synonym string that actually matched, which is the evidence for the identification.
getMatchedSynonym() - Method in class ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject: The synonym string that matched — the evidence for the identification, not decoration.
getMatchedText() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: The actual label or synonym text that scored the match — surfaced so the UI can render "↪ matches synonym 'Ammon's horn'" beneath the preferred label.
getMatchedVia() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Which Lucene field most likely produced this hit: preferred_label, exact_synonym, narrow_synonym, related_synonym, broad_synonym, alt_label (all equality tiers), or label_prefix, label_tokens, synonym_tokens (neighbourhood tiers).
getMatchedVia() - Method in class ubic.gemma.rest.AnnotationsWebService.RuledOutTermValueObject: Why it came back at all — label_prefix, label_tokens, … Never one of the equality tiers; those are exactly the rows that were kept.
getMatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getMatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getMatchKind() - Method in class ubic.gemma.model.common.search.SearchResult: How this result matched the query (exact symbol, alias, prefix look-alike, …), or null when the producing source did not classify it.
getMatchType() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: How this gene matched the search query (e.g.
getMatchType() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject: How the result matched the query (e.g.
getMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getMatrix() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix: Obtain the sparse matrix underlying this.
getMatrix() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix: Obtain the sparse matrix underlying this.
getMatrix() - Method in class ubic.gemma.core.loader.util.anndata.Layer: Obtain the matrix encoded in this layer.
getMatrix() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getMatrix() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getMatrix() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
getMatrix() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject: Which stored matrix this is: "regressed" (major factors regressed out) or "full" (none regressed).
getMatrix() - Method in class ubic.gemma.rest.HeatmapDataValueObject: The numeric matrix; row-major (one row per probe).
getMatrix(Collection) - Static method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix: Create a bulk expression data matrix from a collection of vectors.
getMatrix(Collection) - Static method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix: Create a matrix using all the vectors, which are assumed to share the same representation.
getMatrix(List) - Static method in interface ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix
getMatrixFile() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
getMax() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition: Upper end of MultiQC's plotting range, when it declares one.
getMax() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getMax() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getMax() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject: Upper end of MultiQC's plotting range, when it declares one.
getMaxAnalysisTimeMillis() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Maximum time to spend on the analysis, in milliseconds.
getMaxColumnLength() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getMaximumObjectBreadth() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getMaximumRepeatFraction() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getMaximumSubjectBreadth() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getMaximumXValue() - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
getMaximumYValue() - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
getMaxNumProbesPerComponent() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getMaxQueueMillis() - Method in class ubic.gemma.core.job.TaskCommand: How long we will allow this task to be queued before giving up, or -1 for no limit.
getMaxRecords() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
getMaxRecords() - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
getMaxResults() - Method in class ubic.gemma.model.common.search.SearchSettings: Limit for the number of results per result type.
getMaxResults() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getMaxResults() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getMaxResults() - Method in class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject: The maximum number of results, of null if unlimited.
getMaxRetries() - Method in class ubic.gemma.core.util.SimpleRetryPolicy
getMaxRuntimeMillis() - Method in class ubic.gemma.core.job.TaskCommand: How long we will allow this task to run before giving up, or -1 for no limit.
getMaxSize() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
getMaxTerms() - Method in class ubic.gemma.rest.GoTermsWebService.GoTermGeneCountValueObject
getMaxtrix() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getMaxX() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getMaxY() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getMd5() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getMd5() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getMd5() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getMd5() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
getMd5() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
getMeanGenesPerCell() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getMeanLogFoldChange() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getMeans() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
getMeans() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject: Means (typically log-CPM or normalized intensity), one per surviving point.
getMeanSq() - Method in class ubic.gemma.core.util.math.linearmodels.AnovaEffect
getMeanVariance() - Method in class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator
getMeanVarianceRelation() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getMeanVarianceRelationFilename(ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
getMeasurement() - Method in class ubic.gemma.model.expression.experiment.FactorValue: If this is a continuous factor, a measurement representing its value.
getMeasurement() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit
getMeasurementObject() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The measurement associated with this factor value.
getMeasurements() - Method in class ubic.gemma.rest.HeatmapDataValueObject.FactorEntry: bioAssayId -> measurement value.
getMedianCorrelation() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
getMemberCount() - Method in class ubic.gemma.rest.GroupsWebService.GroupSummaryValueObject
getMemberCount() - Method in class ubic.gemma.rest.GroupsWebService.GroupValueObject
getMemberIds() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getMemberNames() - Method in class ubic.gemma.core.loader.util.hdf5.H5Type
getMembers() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPool
getMembers() - Method in class ubic.gemma.model.genome.gene.GeneSet
getMembers() - Method in class ubic.gemma.rest.GroupsWebService.GroupWithMembersValueObject
getMemInfo() - Method in class ubic.gemma.core.util.runtime.ExtendedRuntime
getMerged() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
getMergedInto() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getMergedInto() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The platform this one was merged into, or null when it was not merged.
getMergees() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getMergees() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The platforms merged INTO this one — the inverse of ArrayDesignValueObject.mergedInto, empty when there are none.
getMeshHeadings() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord: MeSh headings, collected from PubMed.
getMeshTerms() - Method in class ubic.gemma.model.common.description.BibliographicReference
getMeshTerms() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getMessage() - Method in class ubic.gemma.cli.batch.BatchTaskProcessingResult
getMessage() - Method in class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult: Message explaining why the value is suspicious.
getMessage() - Method in class ubic.gemma.core.pipeline.JobSnapshot
getMessage() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterService.LintResult
getMessage() - Method in interface ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse.Error
getMessage() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
getMessage() - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: Note attached to the latest audit event, when present.
getMessage() - Method in class ubic.gemma.rest.TaskStatusValueObject: Last progress update emitted by the task.
getMessage() - Method in class ubic.gemma.rest.TaskStatusValueObject.TaskError: Human-readable description of the failure.
getMessage() - Method in class ubic.gemma.rest.util.WellComposedError
getMessage() - Method in class ubic.gemma.rest.util.WellComposedErrorBody
getMessage() - Method in class ubic.gemma.rest.util.WellComposedWarning
getMessages() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getMetadata() - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm: Descriptive metadata from the source vocabulary — species, cell-line type, donor sex, strain type, and any problematic-entry flag.
getMetadata() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getMetadata() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getMetadata() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getMetadata() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getMetadataFile(ExpressionExperiment, String, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
getMetadataFile(ExpressionExperiment, String, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getMetadataFile(ExpressionExperiment, String, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
getMetadataFile(ExpressionExperiment, String, boolean, long, TimeUnit) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getMetadataFile(ExpressionExperiment, ExpressionExperimentMetaFileType, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate a metadata file.
getMetadataFile(ExpressionExperiment, ExpressionExperimentMetaFileType, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getMetadataOutputFilename(ExpressionExperiment, QuantitationType, String) - Static method in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
getMetaFields() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getMetaPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getMetaPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getMetaPvalueRank() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getMetaQvalue() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getMetaQvalue() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getMethod() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject: Currently always "pearson" — Gemma's only supported correlation method here.
getMethods() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
getMetrics() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics: Definitions for the metric names appearing in SequencingQcMetrics.SampleMetrics.getValues(), in the order MultiQC lists them.
getMetrics() - Method in class ubic.gemma.rest.DatasetsWebService.SequencingQcMetricsValueObject: One entry per metric name appearing in DatasetsWebService.SampleQcMetricsValueObject.getValues() or in a sample's runs, in the order MultiQC lists them.
getMetThreshold() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getMicroRnaByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
getMicroRnaByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getMin() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition: Lower end of MultiQC's plotting range, when it declares one.
getMin() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getMin() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getMin() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject: Lower end of MultiQC's plotting range, when it declares one.
getMinimumExonOverlapFraction() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getMinimumFractionOfUniqueValues() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum number of unique values (as a fraction of the number of assays) for a particular design element to be included in the analysis.
getMinimumNumberOfCellsPerGene() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum number of cells for a particular gene to be included in the analysis.
getMinimumNumberOfCellsPerSample() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum number of cells for a particular sample to be included in the analysis.
getMinimumNumberOfSamplesToApplyRepetitiveValuesFilter() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum number of samples to apply the repetitive value filter.
getMinimumSpecificity() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getMinimumSupport() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getMinimumVariance() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum variance for a particular design element to be included in the analysis.
getMinimumXValue() - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
getMinimumYValue() - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
getMinorDevice() - Method in class ubic.gemma.core.util.runtime.FileLockInfo
getMinPresentCount() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Minimum number of samples for keeping rows when min-present filtering.
getMinPresentFraction() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Minimum fraction of samples that must have a value (or a present call if a present/absent boolean matrix is provided) for the design element to be retained.
getMinPvalue() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getMinPvalue() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getMinutesElapsed(StopWatch) - Static method in class ubic.gemma.core.profiling.StopWatchUtils
getMinX() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getMinY() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getMismatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getMismatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getMissingColor() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getMissingColor() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getMissingSeedCount() - Method in class ubic.gemma.core.ontology.providers.OntologySlimExtractor.ExtractResult
getMissingValueAnalysisEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getMissingValueData() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getMissingValueQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getMissingValuesVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the missing value vectors for a given experiment.
getMissingValuesVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getMissingValuesVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
getMissingValuesVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
getMissingValuesVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getMissingValuesVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getMode() - Method in class ubic.gemma.core.tasks.analysis.expression.GeeqTaskCommand
getMode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getMode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: How the ticket advances between actions.
getMode() - Method in class ubic.gemma.model.common.search.SearchSettings: Indicate the search mode to use.
getMode() - Method in class ubic.gemma.rest.DatasetsWebService.GeeqRecomputeRequest
getMode() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
getMode() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getMode() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getModel() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getModel() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getModel() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.RunProvenance
getModel() - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
getModeNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getMolecule() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getMoleculeAsCharacteristic() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel: Convert the molecule into a MGED Ontology-based MaterialType Characteristic.
getMouseSensitiveServerPort() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getMouseSeqFiles() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getMouseServerPort() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getMultifunctionality() - Method in class ubic.gemma.model.genome.Gene
getMultifunctionalityRank() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getMultiQCDataFileType() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getMultiqcDataTypeId() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getMultiQCLogFileType() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getMultiqcLogTypeId() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
getMyQueue(int, int) - Method in class ubic.gemma.rest.TicketsWebService: Calling admin's own ticket queue: assigned-to-me + the few cheap counters that back a "My Queue" card in the curation-UI.
getMyQueueSummary() - Method in class ubic.gemma.rest.TicketsWebService: Lightweight counters about the calling admin's ticket workload.
getMyself() - Method in class ubic.gemma.rest.RootWebService: Retrieve user information for the current user.
getN() - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
getN() - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
getN() - Method in class ubic.gemma.rest.PvalueDistributionValueObject
getName() - Method in class ubic.gemma.cli.completion.CompletionSource.Completion
getName() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition: Key used in SequencingQcMetrics.SampleMetrics.getValues(), e.g.
getName() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics: The assay's name, for axis labels.
getName() - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
getName() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
getName() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getName() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getName() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoBioAssayMapper
getName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
getName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
getName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
getName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
getName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata: Taxon name, either common or scientific.
getName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
getName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
getName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
getName() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getName() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getName() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
getName() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
getName() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
getName() - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
getName() - Method in class ubic.gemma.core.loader.util.mapper.ChainedEntityMapper
getName() - Method in class ubic.gemma.core.loader.util.mapper.EnsemblIdDesignElementMapper
getName() - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper: Obtain the name of the mapping strategy.
getName() - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper.StatefulEntityMapper
getName() - Method in class ubic.gemma.core.loader.util.mapper.GeneNameDesignElementMapper
getName() - Method in class ubic.gemma.core.loader.util.mapper.MapBasedEntityMapper
getName() - Method in class ubic.gemma.core.loader.util.mapper.NcbiIdDesignElementMapper
getName() - Method in class ubic.gemma.core.loader.util.mapper.OfficialSymbolDesignElementMapper
getName() - Method in class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper
getName() - Method in class ubic.gemma.core.loader.util.mapper.SimpleBioAssayMapper
getName() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getName() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getName() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getName() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain the name of this ontology if available.
getName() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getName() - Method in interface ubic.gemma.core.security.model.UserGroup: A unique name to identify the group.
getName() - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
getName() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
getName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
getName() - Method in class ubic.gemma.core.util.math.distribution.Histogram: The name of the histogram.
getName() - Method in class ubic.gemma.model.analysis.Analysis: Obtain the name of the object.
getName() - Method in class ubic.gemma.model.analysis.AnalysisValueObject
getName() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getName() - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
getName() - Method in class ubic.gemma.model.analysis.ProtocolValueObject
getName() - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
getName() - Method in class ubic.gemma.model.common.AbstractDescribable
getName() - Method in interface ubic.gemma.model.common.Describable: Obtain the name of the object.
getName() - Method in class ubic.gemma.model.common.description.BibliographicReference
getName() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
getName() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getName() - Method in class ubic.gemma.model.expression.arrayDesign.AlternateName
getName() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getName() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: Full name, e.g.
getName() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getName() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getName() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getName() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject: Deprecated.
getName() - Method in interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics: Obtain the name of the object.
getName() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getName() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
getName() - Method in class ubic.gemma.model.expression.biomaterial.Compound
getName() - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
getName() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
getName() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef
getName() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef
getName() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef
getName() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getName() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
getName() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
getName() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getName() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
getName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject: Full title.
getName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getName() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getName() - Method in class ubic.gemma.model.genome.Chromosome
getName() - Method in class ubic.gemma.model.genome.gene.GeneProduct
getName() - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
getName() - Method in class ubic.gemma.model.genome.gene.GeneSet
getName() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getName() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getName() - Method in class ubic.gemma.model.genome.Gene
getName() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getName() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getName() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
getName() - Method in class ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject: The authority's preferred name, e.g.
getName() - Method in class ubic.gemma.rest.DatasetsWebService.CurationBasics
getName() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetBasicsResponse
getName() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetBasicsUpdateRequest
getName() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject
getName() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetGroupValueObject
getName() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
getName() - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
getName() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject: Key this metric appears under in a sample's values, e.g.
getName() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getName() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject: The assay's name, for axis labels.
getName() - Method in class ubic.gemma.rest.GroupsWebService.GroupCreateRequest
getName() - Method in class ubic.gemma.rest.GroupsWebService.GroupSummaryValueObject
getName() - Method in class ubic.gemma.rest.GroupsWebService.GroupUpdateRequest
getName() - Method in class ubic.gemma.rest.GroupsWebService.GroupValueObject
getName() - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta
getName() - Method in class ubic.gemma.rest.HeatmapDataValueObject.GeneRef: Full gene name, e.g.
getName() - Method in class ubic.gemma.rest.monitoring.health.CacheHealthIndicator
getName() - Method in class ubic.gemma.rest.monitoring.health.DbHealthIndicator
getName() - Method in class ubic.gemma.rest.monitoring.health.DiskSpaceHealthIndicator
getName() - Method in interface ubic.gemma.rest.monitoring.health.HealthIndicator: Stable identifier for this component in the aggregated response (e.g.
getName() - Method in class ubic.gemma.rest.monitoring.InfoWebService.OsBlock
getName() - Method in interface ubic.gemma.rest.ranking.AnnotationSearchRankingStrategy: Short stable name used as the value of the ?rank= query parameter and as the bean name in the strategy registry.
getName() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategy
getName() - Method in class ubic.gemma.rest.ranking.CompositeRankingStrategy
getName() - Method in class ubic.gemma.rest.ranking.LuceneOrderRankingStrategy
getName() - Method in class ubic.gemma.rest.ranking.TokenCoverageRankingStrategy
getName() - Method in class ubic.gemma.rest.ranking.UsageWeightedRankingStrategy
getNames(Collection) - Static method in class ubic.gemma.model.common.DescribableUtils: Create a set of names from a collection of Describable objects.
getNames(OntologyService) - Static method in class ubic.gemma.core.ontology.providers.OntologyServiceResolver: Obtain every spelling OntologyServiceResolver.resolve(Collection, String) accepts for an ontology, most human-friendly first.
getNamespace() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition: Module the metric came from, e.g.
getNamespace() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExternalId
getNamespace() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
getNamespace() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
getNamespace() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject: Module that produced the metric, e.g.
getNcbiGeneId() - Method in class ubic.gemma.model.genome.Gene
getNCBIGeneIdsInGroup(long) - Method in interface ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService
getNCBIGeneIdsInGroup(long) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl: Given an NCBI Homologene Group ID returns a list of all the NCBI Gene Ids in the given group
getNcbiGi() - Method in class ubic.gemma.model.genome.gene.GeneProduct
getNcbiId() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
getNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
getNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject: NCBI gene id.
getNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getNcbiId() - Method in class ubic.gemma.model.genome.Taxon
getNcbiId() - Method in class ubic.gemma.model.genome.TaxonValueObject
getNcbiId() - Method in class ubic.gemma.rest.HeatmapDataValueObject.GeneRef: NCBI (Entrez) gene ID.
getNcbiTaxonId() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getNcbiTaxonId() - Method in class ubic.gemma.core.ontology.model.OntologyTerm.TaxonConstraint
getNcbiTaxonId() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonConstraintValueObject: NCBI taxon id, e.g.
getNcbiTaxonId() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonValueObject: NCBI taxonomy id.
getNcbiUri() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Synthetic ontology-style URI for this gene, derived from its NCBI gene ID (e.g.
getNeedsAttention() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getNeedsAttention() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getNeedsAttention() - Method in class ubic.gemma.model.expression.experiment.FactorValue: Indicate if this factor value needs attention.
getNeedsAttention() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getNeedsAttention() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
getNeedsAttention() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsUpdateRequest
getNegativeEvidence() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchResultValueObject
getNegativeEvidence() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResponseDataObject
getNetDataSourceUtil() - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
getNewArrayDesigns() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getNewBaseline() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getNewBioMaterialCount() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getNewEEIdsPerTaxon() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getNewExpressionExperiments() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getNewFactorClientRefs() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
getNewFactorValueClientRefsByParentKey() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
getNewLastUpdated() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getNewObjects() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getNewPassword() - Method in class ubic.gemma.rest.RootWebService.ChangePasswordRequest
getNewSinceDate(Class, Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Get auditables that have been created since the given date.
getNewSinceDate(Class, Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getNewSinceDate(Class, Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getNewSinceDate(Class, Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getNextAvailableName(Collection, String) - Static method in class ubic.gemma.model.common.DescribableUtils: Generate the next available name by appending a number to the given string.
getNextCursor() - Method in class ubic.gemma.persistence.util.CursorPage
getNextCursor() - Method in class ubic.gemma.rest.util.CursorPaginatedResponseDataObject
getNextOffset() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.DryRunResult: Deprecated.

Absolute offset into the resolved window where this scan stopped — feed straight back as skip alongside the same startAt to continue at record level rather than restarting that day.
getNodeDegreeNegRanks() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getNodeDegreePosRanks() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getNodeDegreesNeg() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Array containing number of links supported by 0,1,2, ....
getNodeDegreesPos() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Array containing number of links supported by 0,1,2, ....
getNomenclatureStatus() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getNonBlacklistedExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
getNonBlacklistedExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
getNonEmptyColumns(Path) - Static method in class ubic.gemma.core.loader.util.MatrixMarketUtils: Obtain the position of non-empty columns for a given matrix.
getNonRepeatNonSpecificSiteCountThreshold() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getNonSpecificSiteCountThreshold() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getNormalizationDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getNormalizationDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
getNormalized() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getNormalizedValue() - Method in class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator
getNormalizedValue(Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils
getNote() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getNote() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
getNote() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
getNote() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsUpdateRequest
getNote() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueNeedsAttentionRequest
getNs() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getNs() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getNthQuantitationType(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: Given a column number (count starts from zero) get the name of the corresponding quantitation type for this sample.
getNucleotide() - Method in class ubic.gemma.model.genome.PhysicalLocation
getNucleotide() - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
getNucleotideEnd() - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject: Deprecated.
getNucleotideLength() - Method in class ubic.gemma.model.genome.PhysicalLocation
getNucleotideLength() - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
getNucleotideStart() - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
getNullableBooleanArrayColumn(String) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain a nullable boolean array column.
getNullableIntegerArrayColumn(String) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain a nullable integer array column.
getNullMode() - Method in class ubic.gemma.persistence.util.Sort: Indicate if null values should appear last when sorting.
getNullMode() - Method in class ubic.gemma.rest.util.args.SortArg.Sort
getNumAnnotations() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: The number of terms (Characteristics) the experiment has to describe it.
getNumBatches() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound: Number of batches.
getNumberDiffExpressedProbes() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getNumberDiffExpressedProbesDown() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getNumberDiffExpressedProbesUp() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getNumberOfAnnotations(QueryArg, FilterArg, String, Integer, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getNumberOfAssignedCells() - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: Indicate how many cells have an assigned cell type, or null if this information is not available.
getNumberOfAssignedCells() - Method in interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics: Obtain the number of cells assigned with a characteristic.
getNumberOfAssignedCells() - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject: Indicate how many cells have an assigned characteristic, or null if this information is not available.
getNumberOfAssignedCells() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment
getNumberOfAssignedCells() - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
getNumberOfAssignedCellsByCellType() - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: How many cells carry each cell type, keyed by the id of the entry in CellTypeAssignmentValueObject.cellTypes.
getNumberOfBatches() - Method in class ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
getNumberOfBioAssays() - Method in interface ubic.gemma.model.expression.experiment.BioAssaySetValueObject: Obtain the number of assays in this set.
getNumberOfBioAssays() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getNumberOfBioAssays() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getNumberOfBoxplots() - Method in class ubic.gemma.core.visualization.SingleCellDataBoxplot: Obtain the number of boxplots that would be displayed.
getNumberOfCellIds() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Number of cell IDs.
getNumberOfCellIds() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: Number of cells.
getNumberOfCellIds() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Number of cell IDs in the preferred single-cell dimension, or null when there is none.
getNumberOfCellIdsBySample(int) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Obtain the number for cells for the given sample.
getNumberOfCells() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getNumberOfCells() - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellDerivedBulkExpressionDataMatrix
getNumberOfCells() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getNumberOfCells() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getNumberOfCells() - Method in class ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector: Obtain the number of cells that were used to compute each value in this data vector, or null if now known/available.
getNumberOfCells() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
getNumberOfCells() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
getNumberOfCells() - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
getNumberOfCells() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: Deprecated.
use SingleCellDimensionValueObject.getNumberOfCellIds() instead
getNumberOfCells() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getNumberOfCells() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Total number of cells, or null when this is not a single-cell experiment or the count has not been computed.
getNumberOfCells(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getNumberOfCells(int, int) - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellDerivedBulkExpressionDataMatrix
getNumberOfCells(Collection, int, CellLevelCharacteristics, int, boolean[]) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics: Calculate the number of cells with at least one gene expressed.
getNumberOfCellsByDesignElements() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getNumberOfCellsByDesignElements() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getNumberOfCellsByDesignElements(Collection, int, CellLevelCharacteristics, int, boolean[]) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics: Calculate the number of expressed cell by gene pairs.
getNumberOfCellsByDesignElements(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int, boolean[]) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics
getNumberOfCellsForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getNumberOfCellsForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellDerivedBulkExpressionDataMatrix
getNumberOfCellsForColumn(BioMaterial) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getNumberOfCellsForColumn(BioMaterial) - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellDerivedBulkExpressionDataMatrix
getNumberOfCellsForRow(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getNumberOfCellsForRow(int) - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellDerivedBulkExpressionDataMatrix
getNumberOfCellsForRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getNumberOfCellsForRow(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellDerivedBulkExpressionDataMatrix
getNumberOfCellTypes() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Number of cell types.
getNumberOfCharacteristics() - Method in interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics: The number of characteristics in CellLevelCharacteristics.getCharacteristics().
getNumberOfCharacteristics() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Deprecated.
Use CellTypeAssignment.getNumberOfCellTypes() instead.
getNumberOfCharacteristics() - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
getNumberOfDatasets(QueryArg, FilterArg) - Method in class ubic.gemma.rest.DatasetsWebService
getNumberOfDataVectors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getNumberOfDesignElements() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getNumberOfDesignElements() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getNumberOfDesignElements(Collection, int, CellLevelCharacteristics, int, boolean[]) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics: Calculate the number of genes expressed in at least one cell.
getNumberOfDesignElements(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int, boolean[]) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics
getNumberOfDesignElementsPerSample(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getNumberOfDesignElementsPerSample(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getNumberOfDesignElementsPerSample(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getNumberOfDesignElementsPerSample(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getNumberOfDesignElementsPerSample(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain the number of design elements for the platform of each bioassay in the given experiment.
getNumberOfDesignElementsPerSample(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getNumberOfDiffExpressedProbes() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Number of diffex probes in the Direction.EITHER hit list if available.
getNumberOfDiffExpressedProbes() - Method in class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
getNumberOfDistinctFactorValues() - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat: Diversity metric: distinct factor values existing under this category across the corpus.
getNumberOfDistinctTerms() - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Annotation-diversity metric: number of distinct ontology-backed terms in use under this category (free-text excluded).
getNumberOfDownregulatedProbes() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getNumberOfElementsAnalyzed() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis
getNumberOfExperiments() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getNumberOfExperiments() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getNumberOfExperimentsAtBioMaterial() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getNumberOfExperimentsAtBioMaterial() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getNumberOfExperimentsAtFactorValue() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getNumberOfExperimentsAtFactorValue() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getNumberOfExperimentsAtTag() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getNumberOfExperimentsAtTag() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getNumberOfExperimentsWithSubject() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getNumberOfExperimentsWithSubject() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getNumberOfExpressionExperiments() - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Annotation-burden metric: number of public experiments carrying at least one annotation in this category.
getNumberOfExpressionExperiments() - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat: Burden metric: distinct experiments carrying at least one factor under this category.
getNumberOfExpressionExperiments() - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat: Distinct public experiments carrying this gene as a perturbation target.
getNumberOfExpressionExperiments() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getNumberOfExpressionExperiments() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm: The number of associated ExpressionExperiment.
getNumberOfExpressionExperiments() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject: Number of times the characteristic is mentioned among matching datasets.
getNumberOfExpressionExperiments() - Method in class ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject
getNumberOfExpressionExperiments() - Method in class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject
getNumberOfExpressionExperiments() - Method in interface ubic.gemma.rest.DatasetsWebService.UsageStatistics
getNumberOfExpressionExperimentsForTechnologyType() - Method in class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
getNumberOfGenes() - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
getNumberOfGenes() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Distinct genes the platform's elements map to, or null when the caller did not ask.
getNumberOfGenesAnalyzed() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getNumberOfGenesAnalyzed() - Method in class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
getNumberOfGenesDiffExpressed() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getNumberOfGenesTested() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getNumberOfGenesTested() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getNumberOfMappedElements() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Elements on the platform that map to at least one gene, or null when the caller did not ask.
getNumberOfNonZeroes(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the number of non-zeroes.
getNumberOfNonZeroes(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getNumberOfNonZeroes(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getNumberOfNonZeroes(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getNumberOfNonZeroesBySample(ExpressionExperiment, QuantitationType, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the number of non-zeroes by sample.
getNumberOfNonZeroesBySample(ExpressionExperiment, QuantitationType, int, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getNumberOfNonZeroesBySample(ExpressionExperiment, QuantitationType, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getNumberOfNonZeroesBySample(ExpressionExperiment, QuantitationType, int, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getNumberOfPlatforms(FilterArg) - Method in class ubic.gemma.rest.PlatformsWebService
getNumberOfProbes() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getNumberOfProbes() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getNumberOfProbes() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getNumberOfProbes() - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
getNumberOfProbesAnalyzed() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getNumberOfProbesAnalyzed() - Method in class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
getNumberOfProbesDiffExpressed() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getNumberOfProbesDiffExpressed() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getNumberOfProbesDiffExpressed() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getNumberOfProbesDownRegulated() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getNumberOfProbesOnArray() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getNumberOfProbesTested() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getNumberOfProbesTotal() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getNumberOfProbesUpRegulated() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getNumberOfReads() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics: Usually a number, but can take the value "variable".
getNumberOfResultSets(FilterArg) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService
getNumberOfSamples() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getNumberOfSamples(FilterArg) - Method in class ubic.gemma.rest.DatasetsWebService
getNumberOfSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the number of single-cell vectors for a given QT.
getNumberOfSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getNumberOfSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain the number of single-cell vectors for a given quantitation type.
getNumberOfSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getNumberOfSingleCellDataVectors(ExpressionExperiment, SingleCellDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the number of single-cell vectors for a given single-cell dimension.
getNumberOfSingleCellDataVectors(ExpressionExperiment, SingleCellDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getNumberOfSpots() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics: Might be missing if SraRunStatistics.numberOfReads is "variable".
getNumberOfStatements() - Method in class ubic.gemma.model.expression.experiment.Statement
getNumberOfUpregulatedProbes() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getNumBins() - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
getNumBlatHits() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getNumBlatHits() - Method in class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject
getNumChannels() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getNumComponentsStored() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getNumeratorDof() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getNumExperimentsInScope() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getNumGenes() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The number of unique genes that this array design maps to.
getNumGenes() - Method in class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject
getNumGenesAnalyzed() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
getNumGenesAnalyzed() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
getNumGenesAnalyzed() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getNumGoTerms() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Number of GO terms associated with this gene.
getNumGoTerms() - Method in class ubic.gemma.model.genome.gene.Multifunctionality
getNumMetThreshold() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getNumMissingValues(QuantitationType) - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getNumPopulatedFactors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: The number of experimental factors the experiment has (counting those that are populated with biomaterials).
getNumProbeAlignments() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The number of probes that have BLAT alignments.
getNumProbes() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getNumProbeSequences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The number of probes that map to bioSequences.
getNumProbesToGenes() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The number of probes that map to genes.
getNumResults() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getNumResultSetsIncluded() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getNumSamples() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getNumSamples() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getNumSearchedExperiments() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getNumSkipped() - Method in class ubic.gemma.core.loader.genome.BlatResultParser
getNumThreads() - Method in class ubic.gemma.cli.util.AbstractCLI
getNumTimesUsed() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
getNumValues() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject: Number of factor values.
getNumVariables() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getNumWithCoexpressionAnalysis() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getNumWithDifferentialExpressionAnalysis() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getObject() - Method in class ubic.gemma.core.context.AbstractAsyncFactoryBean
getObject() - Method in interface ubic.gemma.core.context.AsyncFactoryBean: Obtain a bean asynchronously.
getObject() - Method in interface ubic.gemma.core.ontology.model.OntologyStatement
getObject() - Method in class ubic.gemma.core.ontology.simple.OntologyStatementSimple
getObject() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getObject() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getObject() - Method in class ubic.gemma.model.expression.experiment.Statement
getObject() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getObject() - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
getObject() - Method in class ubic.gemma.persistence.initialization.BootstrappedDataSourceFactory
getObject() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getObject() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getObject() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getObject() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getObject() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
getObject(int) - Method in class ubic.gemma.model.expression.experiment.Statement
getObject(int, int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
getObject(int, int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix: Converts to a String that can be read by read.table in R, using default parameters
getObject(int, int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
getObject(int, int) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
getObject(int, int) - Method in interface ubic.gemma.core.util.matrix.PrimitiveMatrix
getObject(int, int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
getObject(int, int) - Method in class ubic.gemma.core.util.matrix.StringMatrix
getObject(Matrix2D, int, int) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
getObjectAlias() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
getObjectAlias() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getObjectAlias() - Method in class ubic.gemma.persistence.util.Filter
getObjectAlias() - Method in interface ubic.gemma.persistence.util.PropertyMapping: Alias in the query/criteria space, if applicable.
getObjectAlias() - Method in class ubic.gemma.persistence.util.Sort
getObjectAlias() - Method in class ubic.gemma.persistence.util.Subquery.Alias
getObjectBreadth() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getObjectBreadth() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: How many distinct subjects this object relates to.
getObjectCategory() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getObjectCategory() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getObjectCategory() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getObjectCategoryUri() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getObjectCategoryUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getObjectCategoryUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getObjectCategoryUris() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getObjectClass() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getObjectId() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
getObjectId() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: A unique ontology identifier (i.e.
getObjectIdClass() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
getObjectIdentities(List) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
getObjectIdentities(List) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCollectionFilteringProvider
getObjectIdentity() - Method in class ubic.gemma.core.security.acl.domain.AclImpl
getObjectIdentity(Object) - Method in class ubic.gemma.core.security.acl.ObjectIdentityRetrievalStrategyImpl
getObjectType() - Method in class ubic.gemma.core.context.AbstractAsyncFactoryBean
getObjectType() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory
getObjectType() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceBasedSecurityContextFactory
getObjectType() - Method in class ubic.gemma.core.util.TextResourceToSetOfLinesFactoryBean
getObjectType() - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
getObjectType() - Method in class ubic.gemma.persistence.initialization.BootstrappedDataSourceFactory
getObjectUri() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getObjectUri() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getObjectUri() - Method in class ubic.gemma.model.expression.experiment.Statement
getObjectUri() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getObjectUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getObjectUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getObjectUri() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getObjectUri() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getObjectUri(int) - Method in class ubic.gemma.model.expression.experiment.Statement
getObjectValue() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getObjectValue() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getObjectValues() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getObjectValueUri() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getObjectValueUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getObjectValueUris() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getObs() - Method in class ubic.gemma.core.loader.util.anndata.AnnData
getObs(Class) - Method in class ubic.gemma.core.loader.util.anndata.AnnData
getObsoletedInVersion() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: Ontology release that retired this term, e.g.
getObsoleteTerms(Integer) - Method in class ubic.gemma.rest.AdminWebService: In-application port of FindObsoleteTermsCli: which obsolete ontology terms do Gemma's annotations still use, and what does each owning ontology say should replace them.
getOccurredAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
getOccurredAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
getOccurredAt() - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
getOfficialName() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getOfficialName() - Method in class ubic.gemma.model.genome.Gene
getOfficialSymbol() - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject: Official gene symbol, e.g.
getOfficialSymbol() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getOfficialSymbol() - Method in class ubic.gemma.model.genome.Gene
getOfficialSymbol() - Method in class ubic.gemma.rest.HeatmapDataValueObject.GeneRef
getOffset() - Method in class ubic.gemma.persistence.util.Slice
getOffset() - Method in class ubic.gemma.rest.AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
getOffset() - Method in class ubic.gemma.rest.util.PaginatedResponseDataObject
getOldStyleCharacteristics() - Method in class ubic.gemma.model.expression.experiment.FactorValue: Deprecated.
getOnBehalfOf() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getOnBehalfOf() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject: The curator an agent acted for, when the credential that authenticated the write is not the person who asked for it.
getOntologies(boolean) - Method in class ubic.gemma.rest.AdminWebService: Per-ontology load status.
getOntologyEntry() - Method in class ubic.gemma.model.association.Gene2GOAssociation
getOntologyId() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: A unique ontology identifier (i.e.
getOntologyName() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getOntologyTermCompletions(String, int) - Method in class ubic.gemma.rest.CompletionsWebService
getOntologyTermCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Total distinct ontology-backed annotation terms in use across all public datasets.
getOntologyTermFormatter - Interface in ubic.gemma.core.search
getOntologyTermId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
getOntologyUrl() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getOntologyUrl() - Method in class ubic.gemma.core.ontology.providers.GemmaOntologyService
getOntologyUsed() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: what Ontology uses this term
getOntologyVersion() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: Version (release) of the ontology this term came from — owl:versionInfo (often a release date), falling back to owl:versionIRI.
getOpenApi(String, String) - Method in class ubic.gemma.rest.OpenApiWebService: Retrieve the specification as JSON or YAML, depending on the extension used in the request path.
getOpenTicketSummary() - Method in class ubic.gemma.rest.TicketsWebService: Global open-ticket roll-up for the admin dashboard's TicketsSection.
getOperator() - Method in class ubic.gemma.persistence.service.FilteringDao.ConjunctSpec
getOperator() - Method in class ubic.gemma.persistence.util.Filter
getOptions() - Method in class ubic.gemma.cli.util.AbstractCLI
getOptions() - Method in interface ubic.gemma.cli.util.CLI: Obtain the options for the CLI.
getOptionValue(CommandLine, String, Predicate) - Static method in class ubic.gemma.cli.util.OptionsUtils: Obtain the value of an option and if present, make sure that it satisfies a predicate.
getOptionValues(CommandLine, String, Predicate) - Static method in class ubic.gemma.cli.util.OptionsUtils
getOrCreateScratchpad(Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Return the curator's scratchpad, provisioning it on first call.
getOrCreateScratchpad(Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
getOrder() - Method in class ubic.gemma.core.context.LazyInitByDefaultPostProcessor
getOrder() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getOrder() - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
getOrderApplied() - Method in class ubic.gemma.model.expression.biomaterial.Treatment
getOrderBy() - Method in class ubic.gemma.rest.util.args.SortArg.Sort
getOrderBy() - Method in class ubic.gemma.rest.util.SortValueObject
getOrganism() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getOrganism() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getOrganism() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getOrganism() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getOrganism() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
getOrganisms() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getOrganisms() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getOrganisms() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getOrganisms() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
getOrganization() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
getOrganization() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
getOrientation() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getOriginalDesignElement() - Method in class ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector: Bulk data vectors are never mapped from an external source, so this is always null.
getOriginalDesignElement() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector: The original design element that was used to create this vector.
getOriginalDesignElement() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
getOriginalParseException() - Method in exception class ubic.gemma.core.search.ParseSearchException: The original ParseException if this query was reattempted.
getOriginalPlatform() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getOriginalPlatform() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: The platform this assay was originally run on before a platform switch, or null if it was never switched.
getOriginalPlatforms() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: The platforms this dataset's assays were run on BEFORE a platform switch, when one happened.
getOriginalPlatforms(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService: The platforms the dataset was originally submitted on, before any switch — empty when it was never switched.
getOriginalPlatformsUsageFrequency(int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain dataset usage frequency by original platforms.
getOriginalPlatformsUsageFrequency(int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getOriginalPlatformsUsageFrequency(Collection, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain dataset usage frequency by platform currently for the given dataset IDs.
getOriginalPlatformsUsageFrequency(Collection, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getOriginalProperty() - Method in class ubic.gemma.persistence.util.Filter: The origin, if known.
getOriginalProperty() - Method in interface ubic.gemma.persistence.util.PropertyMapping: Obtain the original property, if available.
getOriginalProperty() - Method in class ubic.gemma.persistence.util.Sort: Indicate the original property from which this sort originates.
getOriginalQuery() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getOriginalValue() - Method in class ubic.gemma.model.common.description.Characteristic
getOriginalValue() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: The submitter's own wording, as it arrived — before curation replaced CharacteristicValueObject.value with an ontology label, and before a compound field was split.
getOs() - Method in class ubic.gemma.rest.monitoring.InfoWebService.InfoValueObject
getOtherCellLevelCharacteristics(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractDelegatingSingleCellDataLoader
getOtherCellLevelCharacteristics(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getOtherCellLevelCharacteristics(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
getOtherCellLevelCharacteristics(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
getOtherCellLevelCharacteristics(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getOtherCellLevelCharacteristics(SingleCellDimension) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader: Load cell-level characteristics that are not cell type assignments present in the data.
getOtherCellLevelCharacteristicsDefaultValues() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Default values to use for the cell-level characteristics.
getOtherCellLevelCharacteristicsDefaultValueUris() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Default value URIs to use for the cell-level characteristics.
getOtherCellLevelCharacteristicsFile() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: A location where additional cell-level characteristics can be loaded.
getOtherCellLevelCharacteristicsNames() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Name to use for the cell-level characteristics.
getOtherIssues() - Method in class ubic.gemma.model.expression.experiment.Geeq
getOtherIssues() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
getOtherKind() - Method in class ubic.gemma.model.common.measurement.Measurement
getOtherParts() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getOtherParts() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: The other parts of the study this dataset was split off from, empty when it was not split.
getOtherRelevant() - Method in class ubic.gemma.rest.DatasetsWebService.CurationPublications
getOtherRelevantPublications() - Method in class ubic.gemma.model.analysis.Investigation
getOtherRelevantPublications() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getOtherRelevantPublications() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getOtherRelevantPublications() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationsUpdateRequest
getOutlier() - Method in class ubic.gemma.rest.DatasetsWebService.SampleOutlierRequest
getOutlier() - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta: Tri-state outlier flag — boxed so the producer can leave it null when unknown.
getOutlierDetails(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.OutlierDetectionService: Obtain existing outlier details from a previous OutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment) invocation.
getOutlierDetails(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceImpl
getOutputDir() - Method in class ubic.gemma.cli.options.DataFileOptionValue: Write the file to the given output directory.
getOutputFile() - Method in class ubic.gemma.cli.options.DataFileOptionValue: Write the file to the given output file.
getOutputFile(String) - Method in class ubic.gemma.cli.options.DataFileOptionValue
getOutputMatrix(M, int, int) - Method in class ubic.gemma.core.util.matrix.datafilter.AbstractFilter
getOutputStream() - Method in interface ubic.gemma.cli.util.CLIContext
getOutputStream() - Method in class ubic.gemma.cli.util.SystemCLIContext
getOverallDesign() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getOverallDesign() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getOverallPValue() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary: Overall p value for F stat of model fit (upper tail probability)
getOverlap() - Method in class ubic.gemma.core.loader.util.mapper.EntityMapper.MappingStatistics: Proportion of the identifiers that were mapped to a candidate.
getOverlap() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getOwner() - Method in class ubic.gemma.core.security.acl.domain.AclImpl
getOwner() - Method in class ubic.gemma.model.analysis.Investigation
getOwner(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Obtain the owner of a given object.
getOwner(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
getOwners(Collection) - Method in interface ubic.gemma.core.security.SecurityService: Obtain the owners of a collection of objects.
getOwners(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
getOwnerSid() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
getOwningDataset() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
getP() - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
getP() - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
getP() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getPages() - Method in class ubic.gemma.model.common.description.BibliographicReference
getPages() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getPaired() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
getPalette() - Method in class ubic.gemma.core.util.graphics.ColorMap
getPaletteSize() - Method in class ubic.gemma.core.util.graphics.ColorMap
getPaperUrl() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
getParamsJson() - Method in class ubic.gemma.core.pipeline.SubmitRequest
getParamsJson() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
getParent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getParentAcl() - Method in class ubic.gemma.core.security.acl.domain.AclImpl
getParentClasses() - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Obtain the classes of entities can can own a Characteristic.
getParentClasses() - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
getParentDescription() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getParentId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getParentIdentity(Object) - Method in interface ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategy: Obtain the parent ACL identity for the given ACL identity.
getParentIdentity(Object) - Method in class ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategyImpl
getParentLink() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getParentName() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getParentName() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getParentObject() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
getParentOfParentDescription() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getParentOfParentLink() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getParentOfParentName() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getParentOfParentName() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getParentOfParentUri() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getParents() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getParents() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Nearest is_a OR part_of parents of this term, if enriched.
getParents() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: Nearest is_a OR part_of parents of this term.
getParents(boolean) - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Note that any restriction superclasses are not returned, unless they are has_proper_part
getParents(boolean, boolean) - Method in interface ubic.gemma.core.ontology.model.OntologyTerm
getParents(boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
getParents(boolean, boolean, boolean) - Method in interface ubic.gemma.core.ontology.model.OntologyTerm
getParents(boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getParents(Collection, boolean, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain all the parents of a given set of terms, excluding obsolete terms.
getParents(Collection, boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getParents(Collection, boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getParents(Collection, boolean, boolean, boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getParents(Collection, boolean, boolean, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain all the parents of a given set of terms.
getParents(Collection, boolean, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain the parents of a collection of terms.
getParents(Collection, boolean, boolean, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getParents(Collection, Collection, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Obtain the parents (i.e.
getParents(Collection, Collection, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
getParents(Collection, Collection, boolean, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicReadService
getParents(Collection, Collection, boolean, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl
getParents(Collection, Collection, boolean, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
getParents(Collection, Collection, boolean, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
getParentSubtreeUris() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Ontology parent URIs; expanded via OntologyService.getChildren into a full subClassOf descendant set.
getParentTerms() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject: URIs of parent terms, or null if excluded.
getParentTerms() - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
getParkedElements() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getParsedOptionValue(CommandLine, String, Predicate) - Static method in class ubic.gemma.cli.util.OptionsUtils
getPassword() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
getPassword() - Method in interface ubic.gemma.core.security.model.User
getPassword() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getPassword() - Method in class ubic.gemma.rest.AuthWebService.LoginRequest
getPasswordHint() - Method in interface ubic.gemma.core.security.model.User
getPasswordHint() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getPath() - Method in class ubic.gemma.core.loader.util.anndata.Layer: Indicate where this layer is located relative to the H5 file.
getPath() - Method in class ubic.gemma.core.loader.util.hdf5.H5File
getPath() - Method in class ubic.gemma.core.util.locking.FileLockInfo: Path subject to locking.
getPath() - Method in interface ubic.gemma.core.util.locking.LockedPath: Retrieve the path being locked.
getPath() - Method in class ubic.gemma.rest.util.Sendfile: File path to send.
getPayload() - Method in class ubic.gemma.core.security.audit.AuditedEvent
getPayload() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getPayload() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getPayload() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
getPayload() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
getPayload() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: What the screen that produced this ticket asked, verbatim and opaque.
getPayload() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getPayloadJson() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getPayloadJson() - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
getPayloadSchemaVersion() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getPayloadSchemaVersion() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: Which schema TicketValueObject.payload follows; null when the writer declared none.
getPayloadSchemaVersion() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getPayloadSize() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: Size of the omitted payloadJson in characters.
getPc() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject: 1-indexed principal component number this payload is for.
getPcaAnalysisEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getPendingAssignments() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
getPercent() - Method in class ubic.gemma.core.job.progress.ProgressData
getPerformer() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getPerformer() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
getPerformer() - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject: Username of whoever performed the change, or null when the row has no performer — which is what an unattended batch job leaves behind.
getPermission() - Method in class ubic.gemma.core.security.acl.domain.AclEntry
getPermissions(AclObjectIdentity) - Static method in class ubic.gemma.persistence.util.SecurityUtils: Checks ACL related properties from the AclObjectIdentity.
getPersistJobDetails() - Method in class ubic.gemma.core.job.TaskCommand: If true, the jobDetails associated with this task will be persisted in the database.
getPerTaxonCount() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
getPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getPerTaxonCount() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getPerTaxonCount() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getPerTaxonCount() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the count of distinct experiments per taxon.
getPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPerTaxonCount() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getPerTaxonCount() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getPerTaxonCount(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the count of distinct experiments per taxon for experiments with the given IDs.
getPerTaxonCount(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPhases() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getPhone() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getPhysicalLocation() - Method in class ubic.gemma.model.genome.ChromosomeFeature
getPhysicalLocationsValueObjects(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
getPhysicalLocationsValueObjects(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
getPhysicalLocationsValueObjects(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
getPhysicalLocationsValueObjects(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
getPid() - Method in class ubic.gemma.core.util.runtime.ExtendedRuntime
getPid() - Method in class ubic.gemma.core.util.runtime.FileLockInfo: PID of the process holding the lock.
getPipeline() - Method in class ubic.gemma.core.pipeline.SubmitRequest
getPipeline() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
getPipelineJobReporter() - Method in class ubic.gemma.cli.util.AbstractCLI: Obtain the pipeline-job progress reporter for this run.
getPivotOrder() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition
getPlatform() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getPlatform() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getPlatform() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
getPlatform() - Method in class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
getPlatformAnnotations(PlatformArg, String, Boolean, Boolean) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the annotation file for the given platform.
getPlatformCompletions(String, int, boolean) - Method in class ubic.gemma.rest.CompletionsWebService
getPlatformConstraint() - Method in class ubic.gemma.model.common.search.SearchSettings: Constraint results to be related to the given platform.
getPlatformConstraint() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getPlatformCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Total public platforms (array designs).
getPlatformCount() - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Number of platforms carrying at least one probe for this gene.
getPlatformCountById(Long, boolean) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
getPlatformCountById(Long, boolean) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getPlatformData() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getPlatformDatasets(PlatformArg, OffsetArg, LimitArg, CursorArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves experiments in the given platform.
getPlatformElement(PlatformArg, CompositeSequenceArrayArg, OffsetArg, LimitArg, CursorArg, boolean, boolean) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves composite sequences (elements) of the given platform.
getPlatformElementGenes(PlatformArg, CompositeSequenceArg, OffsetArg, LimitArg, CursorArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the genes on the given platform element.
getPlatformElementMappingSummary(PlatformArg, CompositeSequenceArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the per-probe gene-mapping summary (BLAT alignments + biological-sequence metadata + supported genes) for a single probe on a given platform.
getPlatformElementPslTrack(PlatformArg, CompositeSequenceArg, Boolean) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the BLAT alignments of a single probe as a UCSC Genome Browser custom track, in PSL format.
getPlatformElements(PlatformArg, OffsetArg, LimitArg, CursorArg, boolean, boolean, QueryArg, FilterArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the composite sequences (elements) for the given platform.
getPlatformFilter() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg
getPlatformId() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getPlatformInformation() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getPlatformMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getPlatforms() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getPlatforms() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getPlatforms() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: The platforms this dataset's assays were run on, as accession + full name.
getPlatforms(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Retrieves the Platforms of the Dataset that this argument represents.
getPlatforms(FilterArg, OffsetArg, LimitArg, SortArg, CursorArg, boolean) - Method in class ubic.gemma.rest.PlatformsWebService
getPlatformSampleMap(GeoSeries) - Static method in class ubic.gemma.core.loader.expression.geo.DatasetCombiner
getPlatformsByCursor(Filters, Cursor, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Cursor-mode counterpart to SecurableFilteringVoEnabledService.loadValueObjects(Filters, Sort, int, int).
getPlatformsByIds(PlatformArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg, boolean) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves all datasets matching the given identifiers.
getPlatformTickets(PlatformArg, CursorArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the open curation tickets for a given platform.
getPlatformTroubled() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getPlatformType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getPlatformUsed() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
getPmid() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
getPolymerType() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getPool() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getPopulatedFactorCounts(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getPopulatedFactorCounts(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPopulatedFactorCounts(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getPopulatedFactorCounts(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getPopulatedFactorCounts(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getPopulatedFactorCounts(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getPopulatedFactorCountsExcludeBatch(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getPopulatedFactorCountsExcludeBatch(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPopulatedFactorCountsExcludeBatch(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getPopulatedFactorCountsExcludeBatch(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getPopulatedFactorCountsExcludeBatch(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getPopulatedFactorCountsExcludeBatch(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getPossibleIdentifiers(Collection, EntityMapper) - Static method in class ubic.gemma.core.loader.util.mapper.EntityMapperUtils: Render a breakdown of possible BioAssay -> sample identifier associations.
getPossibleValues() - Method in class ubic.gemma.cli.util.EnumConverter
getPossibleValues() - Method in interface ubic.gemma.cli.util.EnumeratedConverter: Obtain a list of possible values that the converter can convert to T.
getPossibleValues() - Method in class ubic.gemma.cli.util.EnumeratedStringConverter
getPossibleValuesCommand() - Method in interface ubic.gemma.cli.util.EnumeratedByCommandConverter: Command that can be used to get possible values.
getPossibleValuesCommand() - Method in class ubic.gemma.cli.util.EnumeratedByCommandStringConverter
getPostCode() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getPreboarded(Long) - Method in class ubic.gemma.rest.PreboardedWebService: Fetch a preboarded by id + its latest annotation set (proposal role).
getPreboardedId() - Method in exception class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PreboardedAlreadyPromotedException
getPreboardedId() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PromotionResult
getPredicate() - Method in interface ubic.gemma.core.ontology.model.OntologyStatement
getPredicate() - Method in class ubic.gemma.core.ontology.simple.OntologyStatementSimple
getPredicate() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getPredicate() - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Predicate label for Statement-backed annotations (e.g.
getPredicate() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getPredicate() - Method in class ubic.gemma.model.expression.experiment.Statement
getPredicate() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: The predicate and object halves are absent rather than null when nothing was said.
getPredicate() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getPredicate() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getPredicate() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getPredicate() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getPredicate() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getPredicate() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
getPredicate(int) - Method in class ubic.gemma.model.expression.experiment.Statement
getPredicateUri() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getPredicateUri() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getPredicateUri() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getPredicateUri() - Method in class ubic.gemma.model.expression.experiment.Statement
getPredicateUri() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getPredicateUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getPredicateUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getPredicateUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getPredicateUri() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getPredicateUri() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getPredicateUri(int) - Method in class ubic.gemma.model.expression.experiment.Statement
getPredicateUris() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getPredictedOutlier() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: Whether the median-correlation algorithm flags this assay as a possible outlier.
getPredictedOutlierBioAssayIds() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject: BioAssay ids the median-correlation algorithm flags as outliers (OutlierDetectionService.getOutlierDetails(ExpressionExperiment)).
getPreExistingFactorIds() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
getPreExistingFactorValueIds() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
getPreferred() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getPreferred() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePreferredRequest
getPreferredAndMissingQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getPreferredCellTypeAssignment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain the preferred cell type labelling from the preferred single-cell vectors.
getPreferredCellTypeAssignment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPreferredCellTypeAssignment(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the preferred assignment for the given quantitation type.
getPreferredCellTypeAssignment(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPreferredCellTypeAssignment(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getPreferredCellTypeAssignment(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPreferredCellTypeAssignmentName() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Name of the CTA to mark as preferred, or null to ignore.
getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the preferred assignment for the given quantitation type without loading the indices.
getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPreferredData() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getPreferredDataChangedEventForVectorType(Class) - Static method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl: Resolve the concrete PreferredDataChangedEvent subclass that matches a data-vector type, or null if no event is emitted for that vector type (currently: processed data — multiple processed sets are not allowed so a "preference change" has no meaning).
getPreferredName() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound: ChEMBL's preferred name, e.g.
getPreferredName(OntologyService) - Static method in class ubic.gemma.core.ontology.providers.OntologyServiceResolver: The abbreviation to lead with when naming an ontology to a human, falling back to the identifier.
getPreferredPrefixes() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationCategoryValueObject
getPreferredQTypes() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getPreferredQuantitationType(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the preferred quantitation type for the raw vectors, if available.
getPreferredQuantitationType(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPreferredQuantitationType(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Iterates over the quantitation types for a given expression experiment and returns the preferred quantitation types.
getPreferredQuantitationType(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getPreferredQuantitationType(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getPreferredQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getPreferredRawDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the preferred raw data vectors for a given experiment.
getPreferredRawDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPreferredRawDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
getPreferredRawDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
getPreferredRawDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getPreferredRawDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getPreferredSingleCellDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain preferred single-cell vectors.
getPreferredSingleCellDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPreferredSingleCellDimension(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the preferred single-cell dimension, that is the dimension associated to the preferred set of single-cell vectors.
getPreferredSingleCellDimension(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPreferredSingleCellDimension(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain the preferred single-cell dimension.
getPreferredSingleCellDimension(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment, boolean, boolean, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain the preferred single-cell dimension.
getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Load a single-cell dimension without its cell IDs.
getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain the preferred single-cell dimension without its cell IDs.
getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPreferredSingleCellQuantitationType(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the preferred quantitation type for single-cell data, if available.
getPreferredSingleCellQuantitationType(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPreferredSingleCellQuantitationType(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain the preferred single-cell quantitation type.
getPreferredSingleCellQuantitationType(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getPrefetchForVo(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Batch-fetch the experimentalFactors + baselineGroup associations of the given result sets in two queries (one per association, to avoid MultipleBagFetchException and Cartesian explosion on a multi-row join), and return a map keyed by result-set id.
getPrefetchForVo(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
getPrefix() - Method in class ubic.gemma.core.ontology.model.OntologyXref: The prefix of OntologyXref.getCurie() — DOID, NCIT, UMLS, … — upper-cased.
getPrefixes() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getPreflightAtApply() - Method in class ubic.gemma.model.expression.experiment.DesignApplyOutcome
getPrevCursor() - Method in class ubic.gemma.persistence.util.CursorPage
getPrevCursor() - Method in class ubic.gemma.rest.util.CursorPaginatedResponseDataObject
getPreviousClicks() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord: How many times a curator has already looked at the details.
getPreviousId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory: If the id was ever changed, give the previous id from the current.
getPreviousIds() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
getPreviousNcbiGeneId() - Method in class ubic.gemma.model.genome.Gene
getPreviousState() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowTransition
getPrimary() - Method in class ubic.gemma.rest.DatasetsWebService.CurationPublications
getPrimaryArrayTaxon(Collection, Collection) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
getPrimaryArrayTaxon(Collection, Collection) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl: This method determines the primary taxon on the array: There are 4 main branches of logic.
getPrimaryCitation() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getPrimaryId() - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
getPrimaryPublication() - Method in class ubic.gemma.model.analysis.Investigation
getPrimaryPublication() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getPrimaryPublication() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest: The paper to attach as primary, with the basis for attaching it.
getPrimaryPublication() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationsUpdateRequest
getPrimaryTaxon() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getPrincipal() - Method in class ubic.gemma.core.security.acl.domain.AclPrincipalSid
getPriorCategories() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Distinct-experiment counts grouped by the category that prior curators applied when tagging this URI on an experiment — e.g.
getPriorCuration() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResponseDataObject: What prior curators chose when they met this string, most used first.
getPriorCurationCount() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Distinct experiments on which a prior curator annotated this term after being given the query string itself — the evidence ?rank=commonality orders by.
getPriorDof() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getPriority() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getPriority() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject: The ticket's priority.
getPriority() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getPriority() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
getPriority() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getPriority() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getPrivateGeneCount() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
getProbe() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getProbe() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getProbe() - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
getProbe() - Method in class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject
getProbeId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
getProbeId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getProbeLoadings() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getProbeName() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
getProbeNamesInGemma() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getProbeResults() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getProblematic() - Method in class ubic.gemma.rest.AnnotationsWebService.LexicalTermMetadataValueObject: Non-null iff the source flags this entry as problematic, carrying the reason — most often Misidentified/contaminated.
getProcessDomainObjectClass() - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCompositeSequenceByArrayDesignFilteringProvider
getProcessDomainObjectClass() - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCompositeSequenceCollectionByArrayDesignFilteringProvider
getProcessedBioAssayDimension(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Retrieve the dimension associated to the procesed data vectors.
getProcessedBioAssayDimension(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getProcessedBioAssayDimension(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain the dimension associated to the processed data for the given experiment.
getProcessedBioAssayDimension(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getProcessedBioAssayDimensions(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Batched variant of ExpressionExperimentDao.getProcessedBioAssayDimensions(ExpressionExperiment) — one HQL with an IN clause for the supplied experiments.
getProcessedBioAssayDimensions(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getProcessedBioAssayDimensions(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getProcessedBioAssayDimensions(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getProcessedBioAssayDimensionsWithAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain the dimension associated to the processed data for the given experiment.
getProcessedBioAssayDimensionsWithAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getProcessedData() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getProcessedDataArrays(Collection, Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataArrays(Collection, Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataArrays(BioAssaySet, Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataArrays(BioAssaySet, Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataArrays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataArrays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataArraysByProbe(Collection, Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataArraysByProbe(Collection, Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataArraysByProbe(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataArraysByProbe(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataVectorComputationEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Retrieve the processed vector for an experiment.
getProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
getProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
getProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getProcessedDataVectors(ExpressionExperiment, List) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Retrieve a slice of processed vectors for an experiment.
getProcessedDataVectors(ExpressionExperiment, List) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getProcessedDataVectors(ExpressionExperiment, List) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
getProcessedDataVectors(ExpressionExperiment, List) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
getProcessedDataVectors(ExpressionExperiment, List) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getProcessedDataVectors(ExpressionExperiment, List) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getProcessedDataVectors(ExpressionExperiment, BioAssayDimension, int, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataVectors(ExpressionExperiment, BioAssayDimension, int, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataVectorsAndThaw(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Retrieve and thaw a collection of vectors for a given experiment.
getProcessedDataVectorsAndThaw(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataVectorsDesignElements(ExpressionExperiment, BioAssayDimension, int, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataVectorsDesignElements(ExpressionExperiment, BioAssayDimension, int, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedExpressionDataMatrix(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService: Obtain the processed expression data matrix for a given experiment.
getProcessedExpressionDataMatrix(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getProcessedExpressionDataMatrix(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService
getProcessedExpressionDataMatrix(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getProcessedExpressionDataMatrix(ExpressionExperiment, List) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService
getProcessedExpressionDataMatrix(ExpressionExperiment, List) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getProcessedExpressionDataVectors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getProcessedExpressionVectorCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getProcessedQuantitationType(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the quantitation type for the processed vectors, if available.
getProcessedQuantitationType(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getProcessedQuantitationType(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getProcessedQuantitationType(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getProcessedVectors() - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: What the processed-vector creation did to the data: which raw quantitation type it started from, which one it produced, how many cells were masked for missing values and for outliers, and whether the result was quantile-normalized.
getProcessedVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getProcessedVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessedVectors(ExpressionExperiment, BioAssayDimension, int, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao: Retrieve a slice of processed vectors.
getProcessedVectors(ExpressionExperiment, BioAssayDimension, int, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessedVectorsAndGenes(Collection, Map) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao: Obtain processed expression vectors with their associated genes.
getProcessedVectorsAndGenes(Collection, Map) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessedVectorsDesignElements(ExpressionExperiment, BioAssayDimension, int, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao: Only retrieve the design elements for a slice of vectors.
getProcessedVectorsDesignElements(ExpressionExperiment, BioAssayDimension, int, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessImports() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getProcessImports() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getProcessImports() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getProcessImports() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Check if this ontology will process imports.
getProcessingDate() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getProcessingDate() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getProcInfo() - Method in class ubic.gemma.core.util.locking.FileLockInfo: Process-level information about the file lock.
getProducts() - Method in class ubic.gemma.model.genome.Gene
getProducts(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
getProducts(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
getProducts(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
getProducts(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
getProgressReporter() - Method in class ubic.gemma.cli.batch.BatchTaskExecutorService
getProgressReporterFactory() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector
getProgressUpdates() - Method in interface ubic.gemma.core.job.SubmittedTask: Returns queue of log statements from the running task.
getProjectedAccessions(String) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator: Determine the set of external accession values that will be generated during parsing.
getProperty() - Method in class ubic.gemma.core.ontology.lexical.LexicalAnnotationProperty
getProperty() - Method in interface ubic.gemma.core.ontology.model.AnnotationProperty: A label for the property of this annotation.
getProperty() - Method in class ubic.gemma.persistence.service.FilteringDao.ConjunctSpec
getProperty(String) - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getPropertyInternal(String) - Method in class ubic.gemma.core.config.PropertySourcesConfiguration: Deprecated.
getPropertyName() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
getPropertyName() - Method in class ubic.gemma.persistence.util.Filter
getPropertyName() - Method in interface ubic.gemma.persistence.util.PropertyMapping: Property name in the query/criteria space.
getPropertyName() - Method in class ubic.gemma.persistence.util.Sort
getPropertyName() - Method in class ubic.gemma.persistence.util.Subquery.Alias
getPropertyName() - Method in class ubic.gemma.persistence.util.Subquery: The property name being queried.
getPropertyType() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
getPropertyType() - Method in class ubic.gemma.persistence.util.Filter
getProposalSetId() - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
getProposedDesign() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getProteinAccession() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getProteinAccessionVersion() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getProteinGI() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getProtocol() - Method in class ubic.gemma.model.analysis.Analysis
getProtocol() - Method in class ubic.gemma.model.analysis.AnalysisValueObject
getProtocolCompletions(String, int) - Method in class ubic.gemma.rest.CompletionsWebService
getPubAccession() - Method in class ubic.gemma.model.common.description.BibliographicReference
getPubAccession() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getPublication() - Method in class ubic.gemma.model.common.description.BibliographicReference
getPublication() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getPublication() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getPublication() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssertion
getPublicationDate() - Method in class ubic.gemma.model.common.description.BibliographicReference
getPublicationDate() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getPublications() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getPublications(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getPublications(DatasetArg, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService: A dataset's publications, each carrying the evidenced claim that attaches it.
getPublicationsCreated() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getPublicationsDeleted() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getPublicationsUnchanged() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getPublicGeneCount() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: number of occurrences in all genes
getPublicQualityScore() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getPublished() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getPublishedAt() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata: Publication timestamp (seconds since the epoch), or null if not provided.
getPublisher() - Method in class ubic.gemma.model.common.description.BibliographicReference
getPublisher() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getPubmedAccession() - Method in class ubic.gemma.model.common.description.CitationValueObject
getPubmedId() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getPubmedId() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
getPubmedId() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: PubMed ID of the primary publication, when it is indexed by PubMed.
getPubMedId() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: PubMed identifier.
getPubMedId() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
getPubMedId() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
getPubmedIds() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getPubMedIds() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getPubMedIds() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getPubmedURL() - Method in class ubic.gemma.model.common.description.CitationValueObject
getpValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getPvalue() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails.BatchEffectStatistics: A P-value statistic for that component.
getPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject: The four contrast statistics are rounded to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits on the way out; see DifferentialExpressionAnalysisResultValueObject for why significant digits and why at serialization time rather than in the constructor.
getPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
getPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getPvalue() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: If this vector is associated to a statistical test (i.e.
getPvalue() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject: Uncorrected p-value for the contrast represented by the result-set used to populate this VO.
getPvalue() - Method in class ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
getPvalue() - Method in class ubic.gemma.rest.DatasetsWebService.BatchEffectStatisticsValueObject
getPvalue() - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta: Differential-expression p-value, or any single per-row numeric statistic the producer wants the client to know.
getPValue() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
getPValue() - Method in class ubic.gemma.core.util.math.linearmodels.AnovaEffect
getPValue() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject: Rounded to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits on the way out.
getPvalueDistribution() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getPvalueDistribution(ExpressionAnalysisResultSetArg, int, String) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService: Histogram-binned p-values for a differential-expression result set.
getPythonExecutable() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation: Obtain a path to the Python executable from the Cell Ranger Anaconda environment.
getQ() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition: Generates and returns the (economy-sized - first p columns only) orthogonal factor Q.
getQ() - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
getQ() - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
getQChtml() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getQR() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition: For testing.
getQraux() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition
getqScoreBatchConfound() - Method in class ubic.gemma.model.expression.experiment.Geeq
getQScoreBatchConfound() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
getqScoreBatchEffect() - Method in class ubic.gemma.model.expression.experiment.Geeq
getQScoreBatchEffect() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
getqScoreBatchInfo() - Method in class ubic.gemma.model.expression.experiment.Geeq
getqScoreBatchInfo() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getqScoreOutliers() - Method in class ubic.gemma.model.expression.experiment.Geeq
getqScoreOutliers() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getqScorePlatformsTech() - Method in class ubic.gemma.model.expression.experiment.Geeq
getqScorePlatformsTech() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getqScorePublicBatchConfound() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getqScorePublicBatchEffect() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getqScoreReplicates() - Method in class ubic.gemma.model.expression.experiment.Geeq
getqScoreReplicates() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getqScoreSampleCorrelationVariance() - Method in class ubic.gemma.model.expression.experiment.Geeq
getqScoreSampleCorrelationVariance() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getqScoreSampleMeanCorrelation() - Method in class ubic.gemma.model.expression.experiment.Geeq
getqScoreSampleMeanCorrelation() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getqScoreSampleMedianCorrelation() - Method in class ubic.gemma.model.expression.experiment.Geeq
getqScoreSampleMedianCorrelation() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getQualifiers() - Method in class ubic.gemma.model.common.description.MedicalSubjectHeading
getQualityControlDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getQualityControlDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
getQualityScoreArray() - Method in class ubic.gemma.model.expression.experiment.Geeq
getQualityScoreWeightsArray() - Method in class ubic.gemma.model.expression.experiment.Geeq
getQuantitationType() - Method in exception class ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException: Quantitation type for the data.
getQuantitationType() - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getQuantitationType() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getQuantitationType() - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getQuantitationType() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Obtain the quantitation type for this matrix.
getQuantitationType() - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getQuantitationType() - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix: Obtain the quantitation type for this matrix.
getQuantitationType() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getQuantitationType() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getQuantitationType() - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix: Return the quantitation type for this matrix.
getQuantitationType() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: Required if data is provided.
getQuantitationType() - Method in class ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector
getQuantitationType() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector: Owning QuantitationType.
getQuantitationType() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
getQuantitationType() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
getQuantitationType() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
getQuantitationType() - Method in class ubic.gemma.rest.HeatmapDataValueObject: The quantitation type the matrix is in.
getQuantitationType() - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection
getQuantitationType(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getQuantitationType(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix: Return the quantitation type used for data from the given design element.
getQuantitationTypeCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getQuantitationTypeCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getQuantitationTypeCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getQuantitationTypeCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getQuantitationTypeIndex(GeoPlatform, String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
getQuantitationTypeName() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig: Name of the QT to use if more than one is present in the data as per DataLoader.getQuantitationTypes().
getQuantitationTypeNewName() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig: Override the name of the resulting QT.
getQuantitationTypeNewScaleType() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig: Override the scale type of the resulting QT.
getQuantitationTypeNewType() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig: Override the type of the resulting QT.
getQuantitationTypes() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getQuantitationTypes() - Method in interface ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix: Return the quantitation types for this matrix.
getQuantitationTypes() - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
getQuantitationTypes() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoader
getQuantitationTypes() - Method in interface ubic.gemma.core.loader.expression.DataLoader: Load quantitation types present in the data.
getQuantitationTypes() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getQuantitationTypes() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
getQuantitationTypes() - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getQuantitationTypes() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getQuantitationTypes() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetGroupValueObject
getQuantitationTypes(GeoPlatform) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
getQuantitationTypes(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Retrieve all the quantitation types used by the given expression experiment.
getQuantitationTypes(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getQuantitationTypes(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Retrieve all the quantitation types used by the given experiment and dimension.
getQuantitationTypes(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getQuantitationTypes(ExpressionExperiment, BioAssayDimension, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getQuantitationTypes(ExpressionExperiment, BioAssayDimension, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getQuantitationTypes(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Retrieve a dataset with quantitation type initialized.
getQuantitationTypesByVectorType(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getQuantitationTypesByVectorType(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getQuantitationTypeValueObjects(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load all QuantitationType associated to an expression experiment as VOs.
getQuantitationTypeValueObjects(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getQuantityValuedPredicateLabels() - Static method in enum class ubic.gemma.model.common.description.RelationTopicality
getQuantityValuedPredicateUris() - Static method in enum class ubic.gemma.model.common.description.RelationTopicality
getQueries() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getQuery() - Method in exception class ubic.gemma.core.ontology.search.OntologySearchException
getQuery() - Method in exception class ubic.gemma.core.search.ParseSearchException
getQuery() - Method in class ubic.gemma.model.common.search.SearchSettings: Processed query for performing a search.
getQuery() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getQuery() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest.Item
getQuery() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchResultValueObject
getQuery() - Method in class ubic.gemma.rest.AnnotationsWebService.NegativeEvidenceValueObject: The designation that was identity-matched.
getQuery() - Method in class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
getQuery() - Method in class ubic.gemma.rest.util.QueriedAndFilteredAndCursorPaginatedResponseDataObject
getQuery() - Method in class ubic.gemma.rest.util.QueriedAndFilteredAndLimitedResponseDataObject
getQuery() - Method in class ubic.gemma.rest.util.QueriedAndFilteredAndPaginatedResponseDataObject
getQuery() - Method in class ubic.gemma.rest.util.QueriedAndFilteredResponseDataObject
getQuery(Document) - Static method in class ubic.gemma.core.loader.entrez.EntrezXmlUtils
getQueryCacheRegion() - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao: Name of the Hibernate L2 query-cache region to use for filtered-VO queries from this DAO, or null to use Hibernate's default StandardQueryCache region.
getQueryCacheRegion() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl: Shard the abstract filtered-VO query path (load / loadValueObjects / count / countWithCache via AbstractQueryFilteringVoEnabledDao) into ExpressionExperimentDaoImpl.FILTERED_VO_CACHE_REGION rather than the shared StandardQueryCache.
getQueryEnd() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getQueryEnd() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getQueryGapBases() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getQueryGapBases() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getQueryGapCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getQueryGapCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getQueryId() - Method in class ubic.gemma.core.loader.entrez.EntrezQuery
getQueryId(Document) - Static method in class ubic.gemma.core.loader.entrez.EntrezXmlUtils
getQuerySequence() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getQuerySequence() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
getQueryStart() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getQueryStart() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getQueryStarts() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getQueryStarts() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getQueryString() - Method in class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
getQueryString() - Method in class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject
getQueued() - Method in class ubic.gemma.rest.AdminWebService.ReindexAcceptedResponse
getQuick(int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix1D: This is an optimized version of getQuick.
getQuickGenes() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getqValues() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getQvalueThresholdForStorage() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
getR() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition: Returns the upper triangular factor, R.
getRanAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getRanAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getRanAt() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.RunProvenance
getRanAt() - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDao: Pick a random experimental design that needs attention.
getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl
getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignReadService
getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignReadServiceImpl
getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService: Obtain a random experimental design that needs attention.
getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignServiceImpl
getRandomProcessedDataArrays(ExpressionExperiment, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getRandomProcessedDataArrays(ExpressionExperiment, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getRandomProcessedVectors(ExpressionExperiment, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getRandomProcessedVectors(ExpressionExperiment, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl: Obtain a random sample of processed vectors for the given experiment.
getRandomRawVectors(QuantitationType, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao: Fetch up to limit raw vectors for the given quantitation type, chosen uniformly at random.
getRandomRawVectors(QuantitationType, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl
getRandomRawVectors(QuantitationType, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService: Fetch up to limit raw vectors for the given quantitation type, chosen uniformly at random.
getRandomRawVectors(QuantitationType, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorServiceImpl
getRange() - Method in interface ubic.gemma.core.ontology.model.ObjectProperty
getRank() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition
getRank() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getRank() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
getRank() - Method in enum class ubic.gemma.model.common.description.AnnotationRelationBasis: Higher wins.
getRank() - Method in enum class ubic.gemma.model.common.description.PublicationAssociationSource
getRank() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
getRank() - Method in class ubic.gemma.model.genome.gene.Multifunctionality
getRank() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getRankByMax() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
getRankByMax() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector: The relative expression level of this vector in the study.
getRankByMean() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
getRankByMean() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector: Relative expression level of this vector in the study.
getRankMatrix(Collection, Collection, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService
getRankMatrix(Collection, Collection, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getRanks(Collection, Collection, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getRanks(Collection, Collection, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getRanks(Collection, Collection, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getRanks(Collection, Collection, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getRanks(ExpressionExperiment, Collection, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getRanks(ExpressionExperiment, Collection, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getRanksByMean() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRanksByMean() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getRatio() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getRatSensitiveServerPort() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getRatSeqFiles() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getRatServerPort() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getRaw() - Method in class ubic.gemma.core.pipeline.JobSnapshot
getRawDataVectorCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getRawDataVectorCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getRawDataVectorCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getRawDataVectorCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getRawDataVectorCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getRawDataVectorCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getRawDataVectorCount(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getRawDataVectorCount(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getRawDataVectors(ExpressionExperiment, List, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a slice of the raw vectors for a given experiment and QT.
getRawDataVectors(ExpressionExperiment, List, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getRawDataVectors(ExpressionExperiment, List, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
getRawDataVectors(ExpressionExperiment, List, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
getRawDataVectors(ExpressionExperiment, List, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getRawDataVectors(ExpressionExperiment, List, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getRawDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain raw vectors for a given experiment and QT.
getRawDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getRawDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
getRawDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
getRawDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getRawDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getRawExpressionDataMatrix(ExpressionExperiment, List, QuantitationType) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService
getRawExpressionDataMatrix(ExpressionExperiment, List, QuantitationType) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getRawExpressionDataMatrix(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService: Obtain a raw expression data matrix for a given quantitation type
getRawExpressionDataMatrix(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getRawExpressionDataVectors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getRawMatrix() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
getRawMatrix() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
getRawMatrix() - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix: Access the entire matrix.
getRawMatrix() - Method in class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
getRawMatrix() - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
getRawMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
getRawMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRawMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getRawMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
getRawMatrix() - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getRawMatrixAsDoubles() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
getRawMatrixAsDoubles() - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveDoubleMatrix: Obtain the raw matrix as a double array.
getRawMatrixAsDoubles() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Obtain the raw matrix without boxing.
getRawMatrixAsInts() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
getRawMatrixAsInts() - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveIntMatrix: Obtain the raw matrix as a int array.
getRawSummary(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
getRawSummary(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getRawSummary(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
getRawSummary(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
getRawSummary(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getRawSummary(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getRawSummary(ArrayDesign, int) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
getRawSummary(ArrayDesign, int) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getRawSummary(ArrayDesign, int) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
getRawSummary(ArrayDesign, int) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
getRawSummary(ArrayDesign, int) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getRawSummary(ArrayDesign, int) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getRawValue(int, int) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getRawVar() - Method in class ubic.gemma.core.loader.util.anndata.AnnData: Obtain the raw var dataframe if this AnnData object has been filtered.
getRawVar(Class) - Method in class ubic.gemma.core.loader.util.anndata.AnnData: Obtain the raw var dataframe if this AnnData object has been filtered.
getRawX() - Method in class ubic.gemma.core.loader.util.anndata.AnnData: Obtain the raw X layer if this AnnData object has been filtered.
getReadCount() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics: Sequencing depth for the assay.
getReadCount() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata: The number of reads in the library.
getReadCount() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject: Sequencing depth, from the report's total_reads where present and from BioAssay.getSequenceReadCount() otherwise.
getReadCountSource() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics: Where SequencingQcMetrics.SampleMetrics.getReadCount() came from: "report", "bioAssay", or null when there is no read count.
getReadCountSource() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject: Where DatasetsWebService.SampleQcMetricsValueObject.getReadCount() came from: report, bioAssay, or null.
getReadHoldCount() - Method in class ubic.gemma.core.util.locking.FileLockInfo
getReadLength() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata: The length of the reads.
getReadLockCount() - Method in class ubic.gemma.core.util.locking.FileLockInfo
getReadStatistics() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics: Might be missing if SraRunStatistics.numberOfReads is "variable".
getReason() - Method in class ubic.gemma.core.geoscrape.GeoRecordMatcher.MatchResult
getReason() - Method in class ubic.gemma.core.ontology.TermViolation
getReason() - Method in class ubic.gemma.model.blacklist.BlacklistedEntity
getReason() - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
getReason() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
getReason() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
getReason() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getReason() - Method in class ubic.gemma.rest.AnnotationsWebService.RuledOutTermValueObject: Why this term is not the answer: near_match (lexically close, different entity) or out_of_category (right name, impossible namespace for the category).
getReason() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getReason() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getReason() - Method in exception class ubic.gemma.rest.util.CurationCommitConflictException
getReason() - Method in class ubic.gemma.rest.util.WellComposedError
getReason() - Method in class ubic.gemma.rest.util.WellComposedWarning
getReason() - Method in class ubic.gemma.rest.WorkflowWebService.AdvanceWorkflowRequest
getReasonCode() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getReasonCode() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getRecentExperiments() - Method in class ubic.gemma.core.analysis.report.HomeStats: Most-recently curated public experiments, for the scrolling-names widget.
getRecomputedFromRawData() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getRecordedBeans() - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
getRecordsMatched() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
getRecordsScanned() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
getRecordType() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoQuery: Type of record being queried.
getReferencedDatabaseEntry() - Method in class ubic.gemma.model.association.ReferenceAssociation
getRegistryNumber() - Method in class ubic.gemma.model.expression.biomaterial.Compound
getRegressedCoexpressionMatrix() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis: Note that since you get a full square matrix, all correlations are represented twice, and values on the main diagonal will always be 1.
getReidentified() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getRejectedPublications() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationsUpdateRequest
getRelatedDesigns(ArrayDesign) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli: Mergees or subsumees of the platform.
getRelatedExperiments(int, int) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao: Get a slice of the references that are linked to experiments.
getRelatedExperiments(int, int) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
getRelatedExperiments(int, int) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
getRelatedExperiments(int, int) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
getRelatedExperiments(int, int) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService: Return all the BibRefs that are linked to ExpressionExperiments.
getRelatedExperiments(int, int) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
getRelatedExperiments(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao: Get the related experiments for the given references.
getRelatedExperiments(Collection) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
getRelatedExperiments(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
getRelatedExperiments(Collection) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
getRelatedExperiments(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
getRelatedExperiments(Collection) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
getRelations() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
getRelationTerms() - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain terms allowed for the predicate (relationship) in a Statement.
getRelationTerms() - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getRelativeDate(Date, String) - Static method in class ubic.gemma.core.util.DateUtil: Turn a string like '-7d' into the date equivalent to "seven days ago".
getRelease() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound: ChEMBL release the identification was read from, e.g.
getReleaseDate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getReleaseUrl() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getReleaseUrl() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
getReleaseUrl() - Method in interface ubic.gemma.model.common.description.Versioned: External URL to the release, if applicable.
getReleaseUrl() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getReleaseVersion() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getReleaseVersion() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
getReleaseVersion() - Method in interface ubic.gemma.model.common.description.Versioned: The version of the release, if applicable.
getReleaseVersion() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getRemainingTasks() - Method in class ubic.gemma.cli.batch.BatchTaskExecutorService: Obtain the number of completed batch tasks.
getRemoved() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport
getRenamingFile() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig: A file containing a mapping of sample names to bioassay names.
getRepetitiveValuesFilterMode() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the default mode of operation for the RepetitiveValuesFilter.
getReplacedByLabel() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
getReplacedByUri() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
getReplacementHops() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
getReplicateDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getReplicateDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
getReplicates() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getReplicates() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getReplicatesIssues() - Method in class ubic.gemma.model.expression.experiment.Geeq
getReplicatesIssues() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getRepMatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getRepMatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getReport(Date) - Method in interface ubic.gemma.core.analysis.report.WhatsNewService: Generate the report covering everything that changed since a given date.
getReport(Date) - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
getReportDir() - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService: Absolute directory the cached platform reports are read from and written to.
getReportDir() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
getReporter() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getReporterId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getReporterName() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getRepresentation() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
getRepresentation() - Method in class ubic.gemma.model.common.measurement.Measurement
getRepresentation() - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
getRepresentation() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getRepresentation() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getRepresentation() - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
getRepresentation() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getReprocessedFromRawData() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getRequiredId(Identifiable) - Static method in class ubic.gemma.persistence.util.IdentifiableUtils: Obtain the identifier of the object, throwing a NullPointerException if it is null.
getRequiredValue() - Method in class ubic.gemma.persistence.util.Filter
getResidualDof() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
getResidualDofs() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
getResiduals() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
getResiduals() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getResidualsDof() - Method in interface ubic.gemma.core.util.math.linearmodels.AnovaResult
getResidualsDof() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getResidualsFStat() - Method in interface ubic.gemma.core.util.math.linearmodels.AnovaResult
getResidualsPValue() - Method in interface ubic.gemma.core.util.math.linearmodels.AnovaResult
getResolvedLabel() - Method in class ubic.gemma.core.ontology.TermViolation: The canonical label the URI actually resolves to; set for TermViolation.Reason.LABEL_MISMATCH, null otherwise (there is nothing to resolve to).
getResolvedVia() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getResolvedVia() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage: Which mechanical rule produced ObsoleteTermUsage.replacedByUri.
getResource() - Method in class ubic.gemma.core.ontology.search.OntologySearchService.Result
getResource(String) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getResource(String) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getResource(String) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getResource(String) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Retrieve a GO resource by ID or URI.
getResource(String) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getResource(String) - Method in class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService
getResource(String) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Looks through both Terms and Individuals for a OntologyResource that has a uri matching the uri given.
getResponseBuilder(ContainerRequest, E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper
getResponseBuilder(ContainerRequest, WebApplicationException) - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapper
getRestrictedTo() - Method in interface ubic.gemma.core.ontology.model.OntologyClassRestriction
getRestrictedTo() - Method in interface ubic.gemma.core.ontology.model.OntologyDatatypeRestriction
getRestrictionOn() - Method in interface ubic.gemma.core.ontology.model.OntologyRestriction
getRestrictions() - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
getRestrictions() - Method in interface ubic.gemma.core.ontology.model.OntologyTerm
getRestrictions() - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getResult() - Method in exception class ubic.gemma.core.analysis.expression.diff.FilteringRelatedAnalysisException
getResult() - Method in interface ubic.gemma.core.job.SubmittedTask: Get the result of the task.
getResult() - Method in class ubic.gemma.core.ontology.search.OntologySearchResult
getResultClass() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getResultClass() - Method in class ubic.gemma.model.common.search.SearchResultValueObject
getResultId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
getResultId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getResultId() - Method in class ubic.gemma.model.common.search.SearchResult: Obtain the result ID.
getResultId() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
getResultObject() - Method in class ubic.gemma.model.common.search.SearchResult: Result object this search result is referring to.
getResultObject() - Method in class ubic.gemma.model.common.search.SearchResultValueObject
getResultObject() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
getResultObjectUrl() - Method in class ubic.gemma.model.common.search.SearchResultValueObject: A URL for the result.
getResultObjectUrl() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
getResults() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
getResults() - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
getResults() - Method in class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
getResults() - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
getResults() - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParser
getResults() - Method in class ubic.gemma.core.loader.genome.BlatResultParser
getResults() - Method in class ubic.gemma.core.loader.genome.FastaParser
getResults() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
getResults() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
getResults() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
getResults() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
getResults() - Method in class ubic.gemma.core.loader.genome.gene.SwissProtParser
getResults() - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParser
getResults() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParser
getResults() - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser: Getter for values in map that is BioMartEnsembleNcbi value objects associated with the parsing of this file
getResults() - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
getResults() - Method in class ubic.gemma.core.loader.util.parser.BasicLineParser
getResults() - Method in interface ubic.gemma.core.loader.util.parser.Parser
getResults() - Method in class ubic.gemma.core.loader.util.parser.RecordParser
getResults() - Method in class ubic.gemma.model.analysis.AnalysisResultSetValueObject: Obtain the VO of the associated analysis result to this result set.
getResults() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject: Related analysis results.
getResults() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getResults() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
getResults() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
getResults() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchResultValueObject
getResults() - Method in class ubic.gemma.rest.GeneWebService.GeneDifferentialExpressionGroupValueObject
getResultSet() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getResultSet(ExpressionAnalysisResultSetArg, Double, OffsetArg, LimitArg, Boolean, Boolean, Boolean, HttpHeaders) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService: Retrieve a AnalysisResultSet given its identifier.
getResultSetCounts(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache: Retrieve cached per-result-set hit-list counts (the inputs to DiffExResultSetSummaryValueObject's numberOfDiffExpressedProbes / up / down counts).
getResultSetCounts(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
getResultSetId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getResultSetId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getResultSetId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
getResultSetId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getResultSetId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getResultSetId() - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
getResultSetId() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject: The result set ID to which this result belong.
getResultSetId() - Method in class ubic.gemma.rest.PvalueDistributionValueObject
getResultSets() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis: Groups of results produced by this differential expression analysis.
getResultSets() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
getResultSets(DatasetArrayArg, DatabaseEntryArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService: Retrieve all AnalysisResultSet matching a set of criteria.
getResultSetsByCursor(Collection, Collection, Filters, Cursor, int) - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgService: Cursor-mode counterpart to ExpressionAnalysisResultSetService.findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort).
getResultSetsIncluded() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
getResultsForSearchQuery(QueryArg, Highlighter, Collection) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Obtain the search results for a given query and highlighter.
getResultsUsed() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getResultType() - Method in class ubic.gemma.cli.batch.BatchTaskProcessingResult
getResultType() - Method in class ubic.gemma.model.common.search.SearchResult: Type of search result, immutable.
getResultType() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
getResultTypes() - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap
getResultTypes() - Method in class ubic.gemma.model.common.search.SearchSettings: Entities to retrieve.
getResultTypes() - Method in class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
getResultValueObject() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getResync() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
getResyncFailures() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync
getRetracted() - Method in class ubic.gemma.model.common.description.BibliographicReference
getRetryDelayMillis() - Method in class ubic.gemma.core.util.SimpleRetryPolicy
getRnaNucleotideAccession() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getRnaNucleotideAccessionVersion() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getRnaNucleotideGI() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getRole() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getRole() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getRole() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getRole() - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
getRootAlias() - Method in class ubic.gemma.persistence.util.Subquery: Root alias of this subquery.
getRow() - Method in class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult: Affected row or -1 if all rows are affected.
getRow() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getRow(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a single row of the matrix, by index.
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getRow(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getRow(int) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getRow(int) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getRow(int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix: Return a reference to a specific row.
getRow(int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix: Return a reference to a specific row.
getRow(int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getRow(int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
getRow(int) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
getRow(int) - Method in interface ubic.gemma.core.util.matrix.ObjectMatrix
getRow(int) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
getRow(int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix: Return a reference to a specific row.
getRow(int) - Method in class ubic.gemma.core.util.matrix.StringMatrix
getRow(Matrix2D, int) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getRow(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Return a row that 'came from' the given design element.
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getRowArrayList(int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
getRowArrayList(int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
getRowArrayList(int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getRowArrayList(int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
getRowArrayList(int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
getRowAsDoubles(int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
getRowAsDoubles(int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRowAsDoubles(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveDoubleMatrix: Retrieve a row without boxing.
getRowAsDoubles(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getRowAsDoubles(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
getRowAsDoubles(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRowAsDoubles(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveDoubleMatrix: Retrieve the row for the given design element without boxing.
getRowAsDoubles(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getRowAsInts(int) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
getRowAsInts(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveIntMatrix: Retrieve a row without boxing.
getRowAsInts(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getRowAsInts(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
getRowAsInts(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveIntMatrix: Retrieve the row for the given design element without boxing.
getRowAsInts(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getRowByName(A) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getRowByName(R) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getRowByName(R) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
getRowByName(R) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix: Return a reference to a specific row.
getRowByName(R) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getRowByName(R) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
getRowCount() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getRowCount() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getRowElement(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getRowElement(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getRowElement(int) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getRowElement(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Deprecated.
use ExpressionDataMatrix.getDesignElementForRow(int) instead
getRowElement(int) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix: Deprecated.
getRowElement(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getRowElement(int) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getRowElements() - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getRowElements() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getRowElements() - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getRowElements() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Deprecated.
use ExpressionDataMatrix.getDesignElements() instead
getRowElements() - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix: Deprecated.
getRowElements() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getRowElements() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getRowHeight() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getRowIndex(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getRowIndex(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getRowIndex(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getRowIndex(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
getRowIndex(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getRowIndex(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getRowIndex(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getRowIndexByName(A) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getRowIndexByName(R) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getRowIndexByName(R) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
getRowIndexByName(R) - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Get the index of a row by name..
getRowIndices(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getRowIndices(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getRowIndices(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getRowIndices(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Obtain all the rows that correspond to the given design element, or null if the design element is not found.
getRowIndices(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getRowIndices(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getRowIndices(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getRowLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
getRowLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix: Obtain a label suitable for describing a row of the matrix.
getRowLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
getRowLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.AbstractSingleCellExpressionDataMatrix
getRowLabel(int) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
getRowName() - Method in class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult: Affected row name, if known.
getRowName(int) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getRowName(int) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getRowName(int) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
getRowName(int) - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Get the row name for an index
getRowNameMapIterator() - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
getRowNameMapIterator() - Method in interface ubic.gemma.core.util.matrix.Matrix2D
getRowNames() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRowNames() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getRowNames() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getRowNames() - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
getRowNames() - Method in interface ubic.gemma.core.util.matrix.Matrix2D
getRowObj(int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
getRowObj(int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
getRowObj(int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
getRowObj(int) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
getRowObj(int) - Method in interface ubic.gemma.core.util.matrix.PrimitiveMatrix
getRowObj(int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
getRowRange(int, int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
getRowRange(int, int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
getRowRange(int, int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
getRowRange(int, int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
getRowRange(int, int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
getRows() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject: Top-N probe loadings, sorted by |loading| desc (direction=both), descending loading (positive), or ascending loading (negative).
getRows() - Method in class ubic.gemma.rest.HeatmapDataValueObject: Optional.
getRowsCount() - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection
getRSquared() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
getRuledOut() - Method in class ubic.gemma.rest.AnnotationsWebService.NegativeEvidenceValueObject: Terms that came back for the query and are NOT it.
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.QuantifierContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
getRuleNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getRuleNames() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getRun() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getRunId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getRunId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getRunId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
getRunId() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest: The producing side's run identifier, if this commit is being applied by an agent run.
getRunId() - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
getRunningStatus() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getRunParentProposal() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest: The PROPOSAL annotation set this commit applies, if it applies one.
getRunProvenance() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest: Which build produced the run named by CurationCommitRequest.getRunId().
getRuns() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics: Rows whose key merely STARTS with this assay's accession — one per sequencing run or per mate of a paired run, which is how the FASTQ-level modules key their output.
getRuns() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
getRuns() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject: Rows below the sample level — one per sequencing run, or per mate of a paired run.
getRunSets() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
getRunSha() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getRunSha() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getRunSha() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.RunProvenance
getRunSha() - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
getRuntime() - Static method in class ubic.gemma.core.util.runtime.ExtendedRuntime
gets - Variable in class ubic.gemma.rest.AdminWebService.CacheStatRow: Total gets — hits + misses; some providers report it directly.
getS() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getS() - Method in class ubic.gemma.core.util.math.linalg.SingularValueDecomposition
getS2n() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
getSample() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getSample() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getSampleCharacteristics() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getSampleCharacteristics(DatasetArg, Long) - Method in class ubic.gemma.rest.DatasetsWebService
getSampleCharsCreated() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getSampleCharsDeleted() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getSampleCharsIdMap() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getSampleCharsToAdd() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getSampleCharsToDelete() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getSampleCharsUnchanged() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getSampleCharsUnchanged() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getSampleCorrespondence() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSampleCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Total distinct biomaterials across all public experiments.
getSampleCount() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getSampleDataAsDoubles(SingleCellExpressionDataVector, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils: Obtain the data of a sample.
getSampleDataAsDoubles(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsDoubles(SingleCellExpressionDataVector, DoubleBuffer, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsDoubles(SingleCellExpressionDataVector, DoubleBuffer, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils: Obtain the data of a sample.
getSampleDataAsDoubles(SingleCellExpressionDataVector, BioAssay) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsFloats(SingleCellExpressionDataVector, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils: Obtain the data of a sample.
getSampleDataAsFloats(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsFloats(SingleCellExpressionDataVector, FloatBuffer, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsFloats(SingleCellExpressionDataVector, FloatBuffer, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils: Obtain the data of a sample.
getSampleDataAsInts(SingleCellExpressionDataVector, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsInts(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsInts(SingleCellExpressionDataVector, IntBuffer, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsInts(SingleCellExpressionDataVector, IntBuffer, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsLongs(SingleCellExpressionDataVector, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsLongs(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsLongs(SingleCellExpressionDataVector, LongBuffer, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataAsLongs(SingleCellExpressionDataVector, LongBuffer, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleDataProcessing() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleDescriptions() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleDetails() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleDirs() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurer
getSampleDirs() - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer
getSampleDirs() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer
getSampleEnd(SingleCellDimension, int[], int, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils: Only exposed for internal use, prefer SingleCellExpressionDataVectorUtils.getSampleEnd(SingleCellExpressionDataVector, int, int).
getSampleEnd(SingleCellExpressionDataVector, int, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils: Get the *exclusive* index of the last cell for a given sample.
getSampleEnd(SingleCellExpressionDataVector, BioAssay) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleEnd(SingleCellExpressionDataVector, BioAssay, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleExtractProtocols() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleFactorName() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
getSampleGEOAccessions() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleLabelProtocols() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleLabels() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getSampleMolecules() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
getSampleNames() - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
getSampleNames() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoader
getSampleNames() - Method in interface ubic.gemma.core.loader.expression.DataLoader: Obtain the sample names present in the data.
getSampleNames() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurer
getSampleNames() - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer
getSampleNames() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getSampleNames() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
getSampleNames() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer
getSampleNames() - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getSampleRemovalEvents(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSampleRemovalEvents(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSampleRemovalEvents(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getSampleRemovalEvents(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getSampleRemovalEvents(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getSampleRemovalEvents(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSampleRemovedFlags() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Details of samples that were removed (or marked as outliers).
getSamples() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics: One entry per BioAssay of the experiment, ordered by bioAssay id.
getSamples() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getSamples() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
getSamples() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSamples() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
getSamples() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
getSamples() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: Samples to be associated with this experiment.
getSamples() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getSamples() - Method in class ubic.gemma.rest.DatasetsWebService.SequencingQcMetricsValueObject: One entry per bioAssay of the dataset, ordered by bioAssay id, including assays the report says nothing about.
getSamples(DatasetArg, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getSamples(DatasetArg, QuantitationType, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Obtain a collection of BioAssays that represent the experiments samples for a particular quantitation type.
getSamplesAfterMinimumCells() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Number of samples left after filtering for minimum number of cells.
getSamplesAfterOutliers() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
getSamplesByCursor(DatasetArg, Cursor, int, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Cursor-mode counterpart to DatasetArgService.getSamples(DatasetArg, boolean) for the GET /datasets/{dataset}/samples endpoint — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
getSamplesByTech() - Method in class ubic.gemma.core.analysis.report.HomeStats: Sample (biomaterial) counts broken down by technology bucket — companion to HomeStats.sampleCount.
getSamplesCharacteristics(Collection) - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
getSamplesCharacteristics(Collection) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoader
getSamplesCharacteristics(Collection) - Method in interface ubic.gemma.core.loader.expression.DataLoader: Load samples characteristics present in the data.
getSamplesCharacteristics(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getSamplesCharacteristics(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader: MEX does not provide sample characteristics.
getSamplesCharacteristics(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getSampleStart(SingleCellExpressionDataVector, int, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils: Get the index of the first cell for a given sample.
getSampleStart(SingleCellExpressionDataVector, BioAssay) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSampleStart(SingleCellExpressionDataVector, BioAssay, int) - Static method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
getSamplesWithData(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilterUtils: Obtain the set of samples (columns) with data.
getSampleTitle() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
getSampleType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getSampleUsed() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getScale() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
getScale() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getScale() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getScale() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getScaleType() - Method in class ubic.gemma.cli.options.ExpressionDataFileOptionValue
getScanDateExtractor() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
getScanFrom() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark: Inclusive lower bound of the scrape window; null if the first scrape ever.
getScannedAt() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark: When the scrape started (or was last updated).
getScanProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getScanTo() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark: Exclusive upper bound of the scrape window; null while IN_PROGRESS.
getSchedulerHandle() - Method in class ubic.gemma.model.pipeline.PipelineJob
getSchedulerKind() - Method in class ubic.gemma.model.pipeline.PipelineJob
getScientificName() - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
getScientificName() - Method in class ubic.gemma.model.genome.Taxon
getScientificName() - Method in class ubic.gemma.model.genome.TaxonValueObject
getScope() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
getScore() - Method in class ubic.gemma.core.ontology.search.OntologySearchResult
getScore() - Method in class ubic.gemma.core.ontology.search.OntologySearchService.Result
getScore() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getScore() - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
getScore() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getScore() - Method in class ubic.gemma.model.common.search.SearchResult: Score for ranking this result among other results.
getScore() - Method in class ubic.gemma.model.common.search.SearchResultValueObject
getScore() - Method in class ubic.gemma.model.genome.gene.GeneSetMember
getScore() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getScore() - Method in class ubic.gemma.model.genome.gene.Multifunctionality
getScore() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getScore() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary: Ranking score, highest first: the basis rank dominates, and support x specificity orders within a basis.
getScore() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject: Search relevance score; higher is better.
getScore() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
getScratchpad() - Method in class ubic.gemma.rest.TicketsWebService: The calling curator's scratchpad, provisioned on first access.
getScreeningResult() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
getScreeningResult() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
getScreeningResult() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTargetStatusRequest
getScreeningResultReason() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
getScreeningResultReason() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
getScreeningResultReason() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTargetStatusRequest
getSearchableName() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound: The name to hand back to Gemma's ontology search.
getSearchedDatabase() - Method in class ubic.gemma.core.goldenpath.GoldenPath
getSearchedDatabase() - Method in class ubic.gemma.core.loader.genome.BlatResultParser
getSearchedDatabase() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
getSearchedGenome(Taxon) - Static method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getSearchIndices() - Method in class ubic.gemma.rest.AdminWebService: Per-@Indexed-entity Hibernate Search 7 index status.
getSearchResult() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
getSearchSettings() - Method in class ubic.gemma.rest.SearchWebService.SearchResultsResponseDataObject
getSearchTerm() - Method in class ubic.gemma.model.genome.gene.GOGroupValueObject
getSecondaryAccession() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Identifier in a second database, if available.
getSecondaryExternalDatabase() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getSecondaryExternalUri() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getSecondaryNcbiId() - Method in class ubic.gemma.model.genome.Taxon
getSecondBaseline() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
getSecondBaselineGroup() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
getSecondFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.Baseline
getSecondFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.Contrast
getSecondFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getSecondFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
getSecondFactorValueId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
getSecondFactorValueId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
getSecondGene() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
getSecondObject() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getSecondObject() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getSecondObject() - Method in class ubic.gemma.model.expression.experiment.Statement
getSecondObject() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getSecondObject() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getSecondObject() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getSecondObject() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getSecondObject() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
getSecondObjectId() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
getSecondObjectUri() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getSecondObjectUri() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getSecondObjectUri() - Method in class ubic.gemma.model.expression.experiment.Statement
getSecondObjectUri() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getSecondObjectUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getSecondObjectUri() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getSecondObjectUri() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getSecondPredicate() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getSecondPredicate() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getSecondPredicate() - Method in class ubic.gemma.model.expression.experiment.Statement
getSecondPredicate() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: The second clause of a compound statement (e.g.
getSecondPredicate() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getSecondPredicate() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getSecondPredicate() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getSecondPredicate() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit: The second predicate-object pair, for a statement that makes two claims about one subject.
getSecondPredicateUri() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
getSecondPredicateUri() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getSecondPredicateUri() - Method in class ubic.gemma.model.expression.experiment.Statement
getSecondPredicateUri() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getSecondPredicateUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getSecondPredicateUri() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getSecondPredicateUri() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getSecurableClass() - Method in interface ubic.gemma.core.security.model.SecureValueObject
getSecurableClass() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getSecurableClass() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getSecurableClass() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getSecurableClass() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getSecurableClass() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getSecurityContext() - Method in class ubic.gemma.core.job.TaskCommand: Used to propagate security to grid workers.
getSecurityOwner() - Method in interface ubic.gemma.core.security.model.SecuredChild
getSecurityOwner() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getSecurityOwner() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis: Experiment analysis are always owned by the experiment (or source experiment, if a subset).
getSecurityOwner() - Method in interface ubic.gemma.model.common.auditAndSecurity.SecuredChild: Obtain the security owner of this secured child.
getSecurityOwner() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getSecurityOwner() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
getSecurityOwner() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getSecurityOwner() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getSecurityOwner() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getSecurityOwner() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
getSecurityOwner() - Method in class ubic.gemma.model.expression.experiment.FactorValue
getSecurityOwnerClass(Class) - Method in class ubic.gemma.core.security.authorization.acl.AclClassMetadata: Obtain the parent class for a given secured child.
getSecurityOwnerIdQueries(Class, String) - Method in class ubic.gemma.core.security.authorization.acl.AclClassMetadata: Obtain the parent ID query(ies) for a given secured child.
getSeedDirection() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getSeedFromExperimentId() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getSelection() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
getSemanticName() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getSeqDir() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getSequence() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Raw probe sequence from the associated BioSequence.sequence.
getSequence() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getSequence() - Method in class ubic.gemma.model.genome.Chromosome
getSequence() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getSequenceData(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: Batch-fetch the probe-sequence projection for the supplied composite-sequence ids.
getSequenceData(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getSequenceData(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
getSequenceData(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
getSequenceData(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getSequenceData(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getSequenceDatabaseEntry() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getSequenceDatabaseEntry() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getSequenceLength() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Pre-computed length from BioSequence.length, exposed alongside sequence.
getSequencePairedReads() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getSequencePairedReads() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getSequenceReadCount() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getSequenceReadCount() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getSequenceReadLength() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getSequenceReadLength() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getSequences(ArrayDesign) - Static method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
getSequences(ArrayDesign, Taxon) - Static method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
getSequencingMetadata(Collection) - Method in class ubic.gemma.core.loader.expression.sequencing.AbstractDelegatingSequencingDataLoader
getSequencingMetadata(Collection) - Method in interface ubic.gemma.core.loader.expression.sequencing.SequencingDataLoader: Retrieve various sequencing metadata if counting data is present.
getSequencingMetadata(Collection) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadataFileDataLoader
getSequencingMetadata(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getSequencingMetadata(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
getSequencingMetadata(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getSequencingMetadata(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.SequencingMetadataFileSingleCellDataLoader
getSequencingMetadata(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractDelegatingSingleCellDataLoader
getSequencingMetadata(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getSequencingMetadata(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
getSequencingMetadata(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getSequencingMetadata(SingleCellDimension) - Method in class ubic.gemma.core.loader.expression.singleCell.SequencingMetadataFileSingleCellDataLoader
getSequencingMetadata(SingleCellDimension) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader
getSequencingMetadataFile() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig: File containing per-assay sequencing metadata.
getSequencingQcMetrics(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetricsService: Obtain the sequencing QC metrics for an experiment.
getSequencingQcMetrics(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetricsServiceImpl
getSerializedATN() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getSerializedATN() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getSeries() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getSeriesAppearsIn() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getSeriesId() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSeriesMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getSeriesType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSeriesTypes() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getServerHost() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getServerPort() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getServerProcess() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getSessionFactory() - Method in class ubic.gemma.persistence.persister.ArrayDesignPersister
getSessionFactory() - Method in class ubic.gemma.persistence.persister.CommonPersister
getSessionFactory() - Method in class ubic.gemma.persistence.persister.GenomePersister
getSessionFactory() - Method in class ubic.gemma.persistence.persister.RelationshipPersister
getSessionFactory() - Method in class ubic.gemma.persistence.service.AbstractDao
getSessions() - Method in class ubic.gemma.rest.AdminWebService: Authenticated session listing.
getSeuratDiskFile(ExpressionExperiment) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl
getSex() - Method in class ubic.gemma.rest.AnnotationsWebService.LexicalTermMetadataValueObject: Donor sex where stated.
getShape() - Method in class ubic.gemma.core.loader.util.anndata.DenseMatrix
getShape() - Method in interface ubic.gemma.core.loader.util.anndata.Matrix: Obtain the shape of this matrix.
getShape() - Method in class ubic.gemma.core.loader.util.anndata.SparseMatrix
getShape() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
getShortDesc() - Method in class ubic.gemma.apps.AffyDataFromCelCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignBlatCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignMergeCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignReportCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli
getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli
getShortDesc() - Method in class ubic.gemma.apps.BatchEffectPopulationCli
getShortDesc() - Method in class ubic.gemma.apps.BibRefUpdaterCli
getShortDesc() - Method in class ubic.gemma.apps.BioSequenceCleanupCli
getShortDesc() - Method in class ubic.gemma.apps.BlacklistCli
getShortDesc() - Method in class ubic.gemma.apps.CellXGeneDataAdderCli
getShortDesc() - Method in class ubic.gemma.apps.CompleteCli
getShortDesc() - Method in class ubic.gemma.apps.DeleteDiffExCli
getShortDesc() - Method in class ubic.gemma.apps.DeleteExperimentsCli
getShortDesc() - Method in class ubic.gemma.apps.DetectQuantitationTypeCli
getShortDesc() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli
getShortDesc() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisWriterCli
getShortDesc() - Method in class ubic.gemma.apps.ExperimentalDesignImportCli
getShortDesc() - Method in class ubic.gemma.apps.ExperimentalDesignViewCli
getShortDesc() - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI
getShortDesc() - Method in class ubic.gemma.apps.ExpressionDataCorrMatCli
getShortDesc() - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI
getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli
getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogViewerCli
getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli
getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli
getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli
getShortDesc() - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli
getShortDesc() - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli
getShortDesc() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli
getShortDesc() - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI
getShortDesc() - Method in class ubic.gemma.apps.FactorValueOntologyWriterCli
getShortDesc() - Method in class ubic.gemma.apps.FindObsoleteTermsCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli
getShortDesc() - Method in class ubic.gemma.apps.GeeqCli
getShortDesc() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli
getShortDesc() - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator
getShortDesc() - Method in class ubic.gemma.apps.GeoGrabberCli
getShortDesc() - Method in class ubic.gemma.apps.GeoSingleCellDataDownloaderCli
getShortDesc() - Method in class ubic.gemma.apps.IndexGemmaCLI
getShortDesc() - Method in class ubic.gemma.apps.InitializeDatabaseCli
getShortDesc() - Method in class ubic.gemma.apps.ListExpressionDataFIleLocksCli
getShortDesc() - Method in class ubic.gemma.apps.ListQuantitationTypesCli
getShortDesc() - Method in class ubic.gemma.apps.LoadExpressionDataCli
getShortDesc() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli
getShortDesc() - Method in class ubic.gemma.apps.LockExpressionDataFileCli
getShortDesc() - Method in class ubic.gemma.apps.MakeExperimentPrivateCli
getShortDesc() - Method in class ubic.gemma.apps.MakeExperimentsPublicCli
getShortDesc() - Method in class ubic.gemma.apps.MergeDuplicateBibRefsCli
getShortDesc() - Method in class ubic.gemma.apps.MultifunctionalityCli
getShortDesc() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI
getShortDesc() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI
getShortDesc() - Method in class ubic.gemma.apps.OrderVectorsByDesignCli
getShortDesc() - Method in class ubic.gemma.apps.ProcessedDataComputeCLI
getShortDesc() - Method in class ubic.gemma.apps.ProcessedDataDeleterCli
getShortDesc() - Method in class ubic.gemma.apps.ProtocolAdderCli
getShortDesc() - Method in class ubic.gemma.apps.ProtocolDeleterCli
getShortDesc() - Method in class ubic.gemma.apps.ProtocolListCli
getShortDesc() - Method in class ubic.gemma.apps.PubMedLoaderCli
getShortDesc() - Method in class ubic.gemma.apps.PubMedSearcher
getShortDesc() - Method in class ubic.gemma.apps.RawDataDeleterCli
getShortDesc() - Method in class ubic.gemma.apps.RawExpressionDataWriterCli
getShortDesc() - Method in class ubic.gemma.apps.RefreshExperimentCli
getShortDesc() - Method in class ubic.gemma.apps.ReplaceDataCli
getShortDesc() - Method in class ubic.gemma.apps.RNASeqDataAddCli
getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli
getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataDeleterCli
getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataLoaderCli
getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataTransformCli
getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataWriterCli
getShortDesc() - Method in class ubic.gemma.apps.SingleCellSparsityMetricsUpdaterCli
getShortDesc() - Method in class ubic.gemma.apps.SplitExperimentCli
getShortDesc() - Method in class ubic.gemma.apps.SVDCli
getShortDesc() - Method in class ubic.gemma.apps.TaxonLoaderCli
getShortDesc() - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli
getShortDesc() - Method in class ubic.gemma.apps.UpdateDatabaseCli
getShortDesc() - Method in class ubic.gemma.apps.UpdateEe2AdCli
getShortDesc() - Method in class ubic.gemma.apps.UpdateEE2CCli
getShortDesc() - Method in class ubic.gemma.apps.UpdateExternalRelationsCli
getShortDesc() - Method in class ubic.gemma.apps.UpdateGene2CsCli
getShortDesc() - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCli
getShortDesc() - Method in class ubic.gemma.apps.UpdateOntologyRelationsCli
getShortDesc() - Method in class ubic.gemma.apps.UpdatePubMedCli
getShortDesc() - Method in class ubic.gemma.apps.VectorMergingCli
getShortDesc() - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCli
getShortDesc() - Method in class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator.CommandMeta
getShortDesc() - Method in class ubic.gemma.cli.util.AbstractCLI
getShortDesc() - Method in interface ubic.gemma.cli.util.CLI: Obtain a short description for this command explaining what it does.
getShortLabel() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getShortLabel() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getShortLabel() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
getShortLabel() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
getShortName() - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
getShortName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
getShortName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
getShortName() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
getShortName() - Method in class ubic.gemma.model.blacklist.BlacklistedEntity
getShortName() - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
getShortName() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getShortName() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: Short name, e.g.
getShortName() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getShortName() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getShortName() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getShortName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getShortName() - Method in record class ubic.gemma.model.expression.experiment.ExpressionExperimentIdAndShortName
getShortName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject: Short name, e.g.
getShortName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getShortName() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getShortName() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
getShortName() - Method in class ubic.gemma.rest.DatasetsWebService.CurationBasics
getShortName() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject
getShortName() - Method in class ubic.gemma.rest.DatasetsWebService.RenameDatasetRequest
getShortName() - Method in class ubic.gemma.rest.DatasetsWebService.RenameDatasetResponse
getShortName() - Method in class ubic.gemma.rest.DatasetsWebService.StaleDatasetValueObject
getShouldSplitOnFactorId() - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit: Curator split advice (factor id, or -1 for "do not split"); recorded in the curation note.
getShouldSplitRationale() - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit
getSid() - Method in class ubic.gemma.core.security.acl.domain.AclEntry: Returns the stored sid as a Spring Security Sid (built via AclSid.toSid()).
getSidEntity() - Method in class ubic.gemma.core.security.acl.domain.AclEntry: Returns the underlying Hibernate-mapped acl_sid entity.
getSids(Authentication) - Method in class ubic.gemma.core.security.acl.AclSidRetrievalStrategyImpl
getSigma() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary: Residual standard deviation
getSignalChannelA() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getSignalChannelB() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getSignificantBatchConfounds(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService: Obtain the significant batch confounds for a dataset.
getSignificantBatchConfounds(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
getSignificantBatchConfoundsForSubsets(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService: Obtain the significant batch confounds for a dataset subsets.
getSignificantBatchConfoundsForSubsets(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
getSignupToken() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
getSignupToken() - Method in interface ubic.gemma.core.security.model.User
getSignupToken() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getSignupTokenDatestamp() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
getSignupTokenDatestamp() - Method in interface ubic.gemma.core.security.model.User
getSignupTokenDatestamp() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getSince() - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow: Resolved start of the window — generatedAt - days.
getSince() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
getSince() - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
getSingle() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
getSingleCellCount() - Method in class ubic.gemma.core.analysis.report.HomeStats: Number of public experiments that have at least one single-cell dimension recorded (orthogonal to platform-technology type — a single-cell experiment usually rides on a GENELIST platform).
getSingleCellDataLoader(GeoSeries, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AnnDataDetector
getSingleCellDataLoader(GeoSeries, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Obtain a single-cell data loader.
getSingleCellDataLoader(GeoSeries, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.LoomSingleCellDetector
getSingleCellDataLoader(GeoSeries, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
getSingleCellDataLoader(GeoSeries, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.SeuratDiskDetector
getSingleCellDataLoader(GeoSeries, SingleCellDataLoaderConfig) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Obtain a single cell data loader for the given GEO series based on previously downloading data.
getSingleCellDataType(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Determine the type of single-cell data a GEO series contains.
getSingleCellDataVectors(ExpressionExperiment, List, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain single-cell vectors for a particular sample.
getSingleCellDataVectors(ExpressionExperiment, List, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDataVectors(ExpressionExperiment, List, QuantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getSingleCellDataVectors(ExpressionExperiment, List, QuantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a set of single-cell data vectors for the given quantitation type.
getSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain single-cell vectors for a given quantitation type.
getSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDataVectors(ExpressionExperiment, QuantitationType, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a set of single-cell data vectors for the given quantitation type.
getSingleCellDataVectors(ExpressionExperiment, QuantitationType, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDataVectors(ExpressionExperiment, QuantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getSingleCellDataVectors(ExpressionExperiment, QuantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDataVectorWithoutCellIds(ExpressionExperiment, QuantitationType, CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSingleCellDataVectorWithoutCellIds(ExpressionExperiment, QuantitationType, CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDataVectorWithoutCellIds(ExpressionExperiment, QuantitationType, CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a single single-cell vector without initializing cell IDs.
getSingleCellDataVectorWithoutCellIds(ExpressionExperiment, QuantitationType, CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimension() - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
getSingleCellDimension() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
getSingleCellDimension() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
getSingleCellDimension() - Method in interface ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix: Return the single-cell dimension for this matrix.
getSingleCellDimension() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getSingleCellDimension() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
getSingleCellDimension() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
getSingleCellDimension(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractDelegatingSingleCellDataLoader
getSingleCellDimension(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
getSingleCellDimension(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
getSingleCellDimension(Collection) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
getSingleCellDimension(Collection) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader: Load the single-cell dimension present in the data.
getSingleCellDimension(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the single-cell dimension used by a specific QT.
getSingleCellDimension(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDimension(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a single-cell dimension used for a given dataset and QT.
getSingleCellDimension(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimensionById(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a single-cell dimension by ID.
getSingleCellDimensionById(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDimensionByIdWithoutCellIds(ExpressionExperiment, Long, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getSingleCellDimensionByIdWithoutCellIds(ExpressionExperiment, Long, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimensionForCellLevelCharacteristicsById(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSingleCellDimensionForCellLevelCharacteristicsById(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDimensionForCellTypeAssignmentById(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSingleCellDimensionForCellTypeAssignmentById(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDimensions(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.
getSingleCellDimensions(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDimensions(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain all the single-cell dimensions used by a given dataset.
getSingleCellDimensions(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimensionsWithoutCellIds(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.
getSingleCellDimensionsWithoutCellIds(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDimensionsWithoutCellIds(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getSingleCellDimensionsWithoutCellIds(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimensionsWithoutCellIds(ExpressionExperiment, boolean, boolean, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSingleCellDimensionsWithoutCellIds(ExpressionExperiment, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDimensionsWithoutCellIds(ExpressionExperiment, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getSingleCellDimensionsWithoutCellIds(ExpressionExperiment, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Retrieve a single-cell dimension with its bioassays and cell-level characteristics initialized.
getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Load a single-cell dimension used by a specific QT without its cell IDs.
getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType, boolean, boolean, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellDimensionWithoutCellIdsById(ExpressionExperiment, Long, boolean, boolean, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSingleCellDimensionWithoutCellIdsById(ExpressionExperiment, Long, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellExpressionDataFileOptionValue(CommandLine, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
getSingleCellExpressionDataFileOptionValue(CommandLine, boolean, String, boolean) - Static method in class ubic.gemma.cli.options.DataFileOptionsUtils
getSingleCellExpressionDataMatrix(ExpressionExperiment, List, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a single-cell expression data matrix for the given quantitation type.
getSingleCellExpressionDataMatrix(ExpressionExperiment, List, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellExpressionDataMatrix(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a single-cell expression data matrix for the given quantitation type.
getSingleCellExpressionDataMatrix(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellExpressionDataVectors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getSingleCellQuantitationType() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap: Quantitation type of the single-cell data this heatmap was generated from, if applicable.
getSingleCellQuantitationTypes(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a list of single-cell QTs.
getSingleCellQuantitationTypes(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellQuantitationTypes(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
getSingleCellQuantitationTypes(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingleCellQuantitationTypesBySingleCellDimensionWithoutCellIds(ExpressionExperiment, boolean, boolean, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSingleCellQuantitationTypesBySingleCellDimensionWithoutCellIds(ExpressionExperiment, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSingleCellQuantitationTypesBySingleCellDimensionWithoutCellIds(ExpressionExperiment, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain the single-cell quantitation types by single-cell dimension.
getSingleCellQuantitationTypesBySingleCellDimensionWithoutCellIds(ExpressionExperiment, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
getSingularValues() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getSingularValues() - Method in class ubic.gemma.core.util.math.linalg.SingularValueDecomposition
getSize() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getSize() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getSize() - Method in class ubic.gemma.core.loader.util.hdf5.H5Type: Obtain the size of the type in bytes.
getSize() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getSize() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getSize() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getSize(Path, Class, Type, Annotation[], MediaType) - Method in class ubic.gemma.rest.providers.MexBundlerProvider
getSize(Path, Class, Type, Annotation[], MediaType) - Method in class ubic.gemma.rest.providers.PathProvider
getSize(Cache) - Static method in class ubic.gemma.persistence.cache.CacheUtils
getSize(GeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
getSize(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
getSize(GeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
getSize(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
getSize(Sendfile, Class, Type, Annotation[], MediaType) - Method in class ubic.gemma.rest.providers.SendfileProvider
getSizeInBytes() - Method in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType
getSizeInBytes(String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector
getSkip() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
getSkip() - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.

Records to skip at the start of the resolved window; see ScrapeRequest.skip.
getSkippedDeferred() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
getSkippedNotCorrectable() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
getSlot() - Method in class ubic.gemma.core.ontology.TermCanonicalization: The slot that was rewritten: one of category, value, predicate, object, secondPredicate, secondObject.
getSlot() - Method in class ubic.gemma.core.ontology.TermViolation: The slot that failed: one of category, value, predicate, object, secondPredicate, secondObject.
getSnapshotAnnotationSetId() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getSnapshotAnnotationSetId() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
getSnapshotCreatedBy() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest: Who committed, recorded on the snapshot row so the displaced state names the commit that displaced it.
getSnapshotPayloadJson() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest: The dataset's current curation, serialized as the CurationDocument the commit itself accepts, to be stored as a SNAPSHOT AnnotationSet if this commit changes anything.
getSort() - Method in class ubic.gemma.persistence.util.CursorPage
getSort() - Method in class ubic.gemma.persistence.util.Slice
getSort() - Method in class ubic.gemma.rest.AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
getSort() - Method in class ubic.gemma.rest.util.CursorPaginatedResponseDataObject
getSort() - Method in class ubic.gemma.rest.util.FilteredResponseDataObject
getSort() - Method in class ubic.gemma.rest.util.PaginatedResponseDataObject
getSort(String, Sort.Direction, Sort.NullMode) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getSort(String, Sort.Direction, Sort.NullMode) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getSort(String, Sort.Direction, Sort.NullMode) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getSort(String, Sort.Direction, Sort.NullMode) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a Sort object for a property of the O.
getSort(String, Sort.Direction, Sort.NullMode) - Method in interface ubic.gemma.persistence.service.FilteringService
getSort(SortArg) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getSort(SortArg) - Method in interface ubic.gemma.rest.util.args.EntityArgService: Obtain a Sort from a sort argument.
getSortedMeans() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject.Fit
getSortKey() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getSortKey() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getSortSpec() - Method in class ubic.gemma.persistence.util.Cursor
getSource() - Method in class ubic.gemma.cli.batch.BatchTaskProcessingResult
getSource() - Method in class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat: External-database name (e.g.
getSource() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
getSource() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
getSource() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getSource() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getSource() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getSource() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getSource() - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
getSource() - Method in class ubic.gemma.model.common.search.SearchResult: Object representing the source of this result object.
getSource() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getSource() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getSource() - Method in class ubic.gemma.model.expression.experiment.PreboardedExperiment
getSource() - Method in class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
getSource() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getSource() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssertion
getSource() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getSource() - Method in class ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject: Which authority answered, e.g.
getSource() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject: Reserved — placeholder for the producing method (e.g.
getSource() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
getSource() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
getSourceAccession() - Method in class ubic.gemma.model.genome.gene.GeneSet
getSourceAnalysis() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getSourceBioAssayDimension() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject: If this is a subset, or a padded, BioAssayDimensionValueObject, the sourceBioAssayDimension is the original.
getSourceBioAssayId() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: If this BioAssay has a parent via BioMaterial.getSourceBioMaterial(), this is the ID.
getSourceBioMaterial() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial: Parent biomaterial or null if this is a top-level biomaterial.
getSourceBioMaterialId() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: The BioMaterial this one was derived from, or null if this is a sample in its own right.
getSourceCodeLocation(URL) - Static method in class ubic.gemma.core.util.ResourceUtils: Attempt to resolve a likely source code location for a given resource.
getSourceExperiment() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject: Deprecated.
use DifferentialExpressionAnalysisValueObject.getSourceExperimentId() instead
getSourceExperiment() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
getSourceExperimentId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
getSourceExperimentId() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject: The ID of the ExpressionExperiment this is a subset of.
getSourceExperimentId() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
getSourceExperimentId() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject: The ID of the source experiment, which differs only if this result is from a subset.
getSourceExperimentShortName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject: The short name of the ExpressionExperiment this is a subset of.
getSourceMetadata() - Method in class ubic.gemma.model.analysis.Investigation
getSourceMetadata() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Descriptive metadata for hits that came from a flat lexical source (Cellosaurus cell lines, MGI mouse strains): species, cell-line type, donor sex, strain type, and any problematic-entry flag.
getSourceMetadata() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: Descriptive metadata from a flat lexical source (Cellosaurus cell lines, MGI mouse strains) — species, cell-line type, donor sex, strain type, and any problematic-entry flag.
getSourceMetadata(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: The stored GEO source metadata document, or null when none has been harvested.
getSourceMetadata(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSourceMetadata(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getSourceMetadata(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSourceMetadataSchemaVersion() - Method in class ubic.gemma.model.analysis.Investigation
getSourceName() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getSourceRelease() - Method in class ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject: Release the identification was read from, e.g.
getSourceTaxon() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getSourceUrl() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound: Stable link to the compound record, for a curator who wants to check the claim.
getSourceUrl() - Method in class ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject: Link to the authority's record, for a curator who wants to check it.
getSourceVectorId() - Method in class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject: Obtain the ID of the vector from which this slice is derived from.
getSourceVersion() - Method in class ubic.gemma.core.ontology.providers.OntologySlimExtractor.ExtractResult: The release the source ontology declared, or null when it declares none.
getSourceVersion() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getSourceVersion() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getSourceVersion() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getSparseArrayElement(List, int[], int, int, T) - Static method in class ubic.gemma.core.datastructure.sparse.SparseListUtils: Get an element of a sparse array.
getSparseMatrix() - Method in class ubic.gemma.core.loader.util.anndata.Layer: Obtain the sparse matrix encoded in this layer.
getSparseRangeArrayElement(List, int[], int, int) - Static method in class ubic.gemma.core.datastructure.sparse.SparseListUtils: Get an element of a sparse range array.
getSpec(OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getSpecies() - Method in class ubic.gemma.rest.AnnotationsWebService.LexicalTermMetadataValueObject: Every organism the entry derives from, in source order.
getSpecificationUrl() - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject
getSpecificity() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getSpecificity() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary: The fraction of the subject's experiments this object accounts for, or 0 when there is no denominator to divide by.
getSpecificity() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getSpecificityScore() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
getSplitByPlatform() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getSplitOnFactorId() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getSplitRationale() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getSpots() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
getSpots() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
getSqlType() - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
getSqlType() - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
getSratoolkit() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getSsQ() - Method in class ubic.gemma.core.util.math.linearmodels.AnovaEffect
getStaleDatasets(OffsetArg, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService: The datasets that owe pipeline work: every dataset with at least one stale step, and which steps those are.
getStaleSteps() - Method in class ubic.gemma.rest.DatasetsWebService.StaleDatasetValueObject
getStandardizedEnabled() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getStanding() - Method in exception class ubic.gemma.persistence.service.common.description.PublicationAssociationConflictException
getStart() - Method in class ubic.gemma.core.util.runtime.FileLockInfo
getStartAt() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
getStartAt() - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.

GEO accession to resume from; see ScrapeRequest.startAt.
getStartedAt() - Method in class ubic.gemma.model.pipeline.PipelineJob
getStartedAt() - Method in class ubic.gemma.rest.TaskStatusValueObject
getStartInBioChar() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getStartingColumns() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getStartingDesignElements() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Starting number of design elements.
getStartingRows() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
getStartingSamples() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Starting set of samples prior to filtering.
getStartPosition() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getStartTime() - Method in interface ubic.gemma.core.job.SubmittedTask
getStartTime() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getStartTimeMillis() - Method in class ubic.gemma.rest.monitoring.InfoWebService.UptimeBlock
getState() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getState() - Method in class ubic.gemma.core.pipeline.JobSnapshot
getState() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getState() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
getState() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getState() - Method in class ubic.gemma.model.pipeline.PipelineJob
getState() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
getState() - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: One of PipelineStatusValueObject.PipelineStepValueObject.STATUS_OK, PipelineStatusValueObject.PipelineStepValueObject.STATUS_FAILED, PipelineStatusValueObject.PipelineStepValueObject.STATUS_NOT_RUN, PipelineStatusValueObject.PipelineStepValueObject.STATUS_NOT_APPLICABLE, PipelineStatusValueObject.PipelineStepValueObject.STATUS_STALE.
getState() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getStatementId() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
getStatements() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: The same annotations as BioMaterialValueObject.characteristics, as statements — carrying the predicate and object when a curator wrote one.
getStatements() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The statements associated with this factor value.
getStatements() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit
getStatements() - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
getStatistics() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getStatus() - Method in interface ubic.gemma.core.job.SubmittedTask
getStatus() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getStatus() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getStatus() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getStatus() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getStatus() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getStatus() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: Where a proposal stands with its reviewer.
getStatus() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
getStatus() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
getStatus() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getStatus() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getStatus() - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
getStatus() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
getStatus() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getStatus() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: ASSERTED or REFUTED — whether the source states this relation holds, or states that it does not.
getStatus() - Method in class ubic.gemma.rest.monitoring.health.HealthResult
getStatus() - Method in class ubic.gemma.rest.monitoring.HealthWebService.ComponentValueObject
getStatus() - Method in class ubic.gemma.rest.monitoring.HealthWebService.HealthValueObject
getStatus() - Method in class ubic.gemma.rest.TaskStatusValueObject: Lower-cased SubmittedTask.Status value: queued, running, completed, failed, cancelling, unknown.
getStatus() - Method in class ubic.gemma.rest.TicketsWebService.RemovedTargetResult
getStatus() - Method in class ubic.gemma.rest.TicketsWebService.TicketTargetRequest
getStatus() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTargetStatusRequest
getStatus(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper: Translate the exception to an HTTP Response.Status.
getStatus(NotFoundException) - Method in class ubic.gemma.rest.providers.NotFoundExceptionMapper
getStatus(WebApplicationException) - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapper
getStatus(Throwable) - Method in class ubic.gemma.rest.providers.UnhandledExceptionMapper
getStatus(AccessDeniedException) - Method in class ubic.gemma.rest.providers.AccessDeniedExceptionMapper
getStatus(AuthenticationException) - Method in class ubic.gemma.rest.providers.AuthenticationExceptionMapper
getStatus(CurationCommitConflictException) - Method in class ubic.gemma.rest.providers.CurationCommitConflictExceptionMapper
getStatus(MalformedArgException) - Method in class ubic.gemma.rest.providers.MalformedArgExceptionMapper
getStatus(OntologyTermValidationException) - Method in class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapper
getStatus(UnknownQueryParameterException) - Method in class ubic.gemma.rest.providers.UnknownQueryParameterExceptionMapper
getStdev() - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
getStdevUnscaled() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary: Unscaled standard deviations for the coefficient estimators in same order as coefficients.
getStep() - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: Which pipeline step.
getStep() - Method in class ubic.gemma.rest.TaskStatusValueObject: Pipeline step the task corresponds to: preprocess, pca, batchInfo, dea, deaRemove.
getSteps() - Method in class ubic.gemma.rest.PipelineStatusValueObject
getStepSize(int, int, int) - Method in class ubic.gemma.core.util.graphics.ColorMap: Calculate how fast we have to change color components.
getStolenAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
getStolenFrom() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
getStopWatch() - Method in class ubic.gemma.core.profiling.StopWatchUtils.StopWatchRegion
getStoredValue() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
getStrainType() - Method in class ubic.gemma.rest.AnnotationsWebService.LexicalTermMetadataValueObject: MGI strain category, e.g.
getStrand() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getStrand() - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
getStrand() - Method in class ubic.gemma.model.genome.PhysicalLocation
getStrand() - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
getStrand() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getStrand() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getStrategy() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
getStreet() - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
getStrength() - Method in class ubic.gemma.core.ontology.model.OntologyXref
getStrength(String, String) - Method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex: The qualifier a particular mapping carries, or null when there is no such mapping.
getString(String) - Static method in class ubic.gemma.core.config.Configuration: Obtain a configuration value by key.
getString(String) - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getString(String, String) - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getStringArray(String) - Static method in class ubic.gemma.core.config.Settings: Deprecated.
getStringArrayColumn(String) - Method in class ubic.gemma.core.loader.util.anndata.Dataframe: Obtain a string-array column.
getStringAttribute(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
getStringAttribute(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location
getStringAttribute(String, String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location: Obtain an attribute for a given path.
getStudentizedResiduals() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
getSubBuckets() - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Nested partition.
getSubBuckets() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Optional nested partition.
getSubject() - Method in interface ubic.gemma.core.ontology.model.OntologyStatement
getSubject() - Method in class ubic.gemma.core.ontology.simple.OntologyStatementSimple
getSubject() - Method in class ubic.gemma.model.expression.experiment.Statement: Obtain the subject of the statement.
getSubject() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getSubject() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getSubject() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
getSubject(int) - Method in class ubic.gemma.model.expression.experiment.Statement
getSubjectBreadth() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getSubjectBreadth() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: How many distinct objects this SUBJECT relates to UNDER THE SAME PREDICATE -- the mirror of AnnotationsWebService.AnnotationRelationValueObject.objectBreadth.
getSubjectCategory() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getSubjectCategory() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getSubjectCategory() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getSubjectCategoryUri() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getSubjectCategoryUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getSubjectCategoryUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getSubjectCategoryUris() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getSubjectId() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
getSubjectId() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: A unique ontology identifier (i.e.
getSubjectUri() - Method in class ubic.gemma.model.expression.experiment.Statement: Obtain the subject URI of the statement.
getSubjectUri() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
getSubjectUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getSubjectUri(int) - Method in class ubic.gemma.model.expression.experiment.Statement
getSubjectValue() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getSubjectValue() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getSubjectValues() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getSubjectValueUri() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getSubjectValueUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getSubjectValueUris() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getSubmission() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
getSubmissionComment() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
getSubmissionDate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getSubmissionDate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getSubmissionDate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSubmissionTime() - Method in interface ubic.gemma.core.job.SubmittedTask
getSubmittedAt() - Method in class ubic.gemma.model.pipeline.PipelineJob
getSubmittedAt() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
getSubmittedAt() - Method in class ubic.gemma.rest.TaskStatusValueObject
getSubmittedBy() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
getSubmittedLabel() - Method in class ubic.gemma.core.ontology.TermCanonicalization: The label as submitted; null/blank when a URI arrived with no label and one was filled in.
getSubmittedLabel() - Method in class ubic.gemma.core.ontology.TermViolation
getSubmittedLabel() - Method in class ubic.gemma.rest.DatasetsWebService.Canonicalization: The label as submitted; null when a URI arrived with no label and one was filled in.
getSubmittedTask(String) - Method in interface ubic.gemma.core.job.TaskRunningService
getSubmittedTask(String) - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
getSubmittedTasks() - Method in interface ubic.gemma.core.job.TaskRunningService
getSubmittedTasks() - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
getSubmittedUri() - Method in class ubic.gemma.core.ontology.TermCanonicalization: The URI as submitted.
getSubmittedUri() - Method in class ubic.gemma.core.ontology.TermViolation
getSubmittedUri() - Method in class ubic.gemma.rest.DatasetsWebService.Canonicalization: The URI as submitted (off-base when it differs from canonicalUri).
getSubmitter() - Method in class ubic.gemma.core.job.notification.EmailNotificationContext
getSubmitter() - Method in class ubic.gemma.core.job.TaskCommand: Task submitted, if known.
getSubmitterIds() - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
getSubSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSubSeriesOf() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSubSet(DatasetArg, Long) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getSubsetBatchConfounds() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
getSubSetById(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSubSetById(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSubSetByIdWithCharacteristics(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getSubSetByIdWithCharacteristics(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetByIdWithCharacteristics(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain a particular subset by ID, with characteristics initialized.
getSubSetByIdWithCharacteristics(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain a particular subset by ID.
getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain a particular subset by ID, with characteristics initialized and assays thawed.
getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubsetFactor() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Factor to subset the analysis on, if non-null.
getSubsetFactor() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
getSubsetFactor() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
getSubsetFactorId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
getSubsetFactorId() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialAnalysisRunRequest
getSubsetFactorValue() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: If this is non-null, this is a subset analysis for this factor value.
getSubsetFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis: If non-null, a factor value applicable to the ExpressionExperimentSubSet being analyzed.
getSubsetFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
getSubsetFactorValueId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
getSubsetFactorValueId() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef
getSubSetGroupIds() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject
getSubSetGroupIds(DatasetArg, ExpressionExperimentSubSet) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getSubsetMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getSubsetRelevance() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Curator/agent hint about whether a differential expression analysis should SUBSET by this factor.
getSubsetRelevance() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getSubsetRelevance() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Curator/agent hint about whether a differential expression analysis should SUBSET by this factor — the write side of ExperimentalFactorValueObject.subsetRelevance.
getSubsetRelevanceReason() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Free-text rationale paired with ExperimentalDesignValueObject.ExperimentalFactorEntry.subsetRelevance.
getSubsetRelevanceReason() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getSubsetRelevanceReason() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Free-text rationale paired with DatasetsWebService.FactorCommit.subsetRelevance.
getSubsets() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getSubSets() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getSubSets() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetGroupValueObject
getSubSets(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSubSets(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSubSets(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSubSets(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSubSets(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain the subsets for a particular dimension.
getSubSets(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSets(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain the subsets for a particular dimension.
getSubSets(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSets(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getSubSetSamples(DatasetArg, Long, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getSubSetSamplesByCursor(DatasetArg, Long, Cursor, int, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Cursor-mode counterpart to DatasetArgService.getSubSetSamples(DatasetArg, Long, boolean) for the GET /datasets/{dataset}/subSets/{subSet}/samples endpoint — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u (the subset-scoped twin of step 1k for GET /datasets/{dataset}/samples).
getSubSetsByDimension(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSubSetsByDimension(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSubSetsByDimension(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain all the subsets organized by dimension for a given dataset.
getSubSetsByDimension(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetsByDimension(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain all the subsets organized by dimension for a given dataset.
getSubSetsByDimension(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSetsByDimensionWithBioAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain all the subsets organized by dimension for a given dataset.
getSubSetsByDimensionWithBioAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetsByDimensionWithBioAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain all the subsets organized by dimension for a given dataset, with assays thawed.
getSubSetsByDimensionWithBioAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSetsByExpressionExperiments(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Batched variant of ExpressionExperimentDao.getSubSets(ExpressionExperiment): obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
getSubSetsByExpressionExperiments(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSubSetsByFactorValue(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Reconstitute the FV to subset mapping for a given experiment.
getSubSetsByFactorValue(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetsByFactorValue(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Reconstitute the FV-to-subset mapping for a given experiment along all separating factors.
getSubSetsByFactorValue(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSetsByFactorValue(ExpressionExperiment, ExperimentalFactor, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Reconstitute the FV to subset mapping for a given experiment and factor.
getSubSetsByFactorValue(ExpressionExperiment, ExperimentalFactor, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetsByFactorValue(ExpressionExperiment, ExperimentalFactor, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Reconstitute the FV-to-subset mapping for a given experiment and factor.
getSubSetsByFactorValue(ExpressionExperiment, ExperimentalFactor, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment, ExperimentalFactor, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Reconstitute the FV to subset mapping for a given experiment and factor.
getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment, ExperimentalFactor, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment, ExperimentalFactor, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Reconstitute the FV-to-subset mapping for a given experiment and factor, with subset characteristics initialized and assays thawed.
getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment, ExperimentalFactor, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSetsGroupIds(DatasetArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getSubSetsWithBioAssays(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Batched variant of ExpressionExperimentService.getSubSetsWithBioAssays(ExpressionExperiment): obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
getSubSetsWithBioAssays(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetsWithBioAssays(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Batched variant: obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
getSubSetsWithBioAssays(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSetsWithBioAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain all the subsets for a given dataset.
getSubSetsWithBioAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetsWithBioAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain all the subsets for a given dataset.
getSubSetsWithBioAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSetsWithBioAssays(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain the subsets for a particular dimension.
getSubSetsWithBioAssays(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetsWithBioAssays(ExpressionExperiment, BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain the subsets for a particular dimension, with assays lightly thawed.
getSubSetsWithBioAssays(ExpressionExperiment, BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubSetsWithCharacteristics(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain all the subsets for a given dataset.
getSubSetsWithCharacteristics(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubSetsWithCharacteristics(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Obtain all the subsets for a given dataset, with characteristics initialized.
getSubSetsWithCharacteristics(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
getSubsetsWithStaleAnchor() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport: Subsets whose definitional factor-value anchors would be deleted.
getSubsetsWithStaleAnchor() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
getSubsumedArrayDesigns() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getSubsumingArrayDesign() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getSuffix() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition: Unit suffix MultiQC appends when rendering, e.g.
getSuffix() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject: Unit suffix to render after the value, e.g.
getSuffix() - Method in enum class ubic.gemma.rest.PlatformsWebService.AnnotationFileType
getSuitableForDEA() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getSummaries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSummary() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSummary() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: Human-readable summary of the factor value.
getSummary() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport
getSummaryMapValueObjects(Collection) - Method in interface ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService: FIXME this is only public so we can use it in the DesignElementController; need refactoring (see CompositeSequenceService) Function to get a collection of CompositeSequenceMapValueObjects that contain information about a composite sequence and related tables.
getSummaryMapValueObjects(Collection) - Method in class ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl
getSummaryMapValueObjects(ArrayDesign) - Method in interface ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService
getSummaryMapValueObjects(ArrayDesign) - Method in class ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl
getSummaryObject() - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getSummaryObject() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl: Get the cached summary object that represents all platforms.
getSummaryObject(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getSummaryObject(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl: Get a specific cached summary object
getSummaryObject(Collection) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getSummaryObject(Collection) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl: Get the cached summary objects
getSummaryString(AbstractFactorValueValueObject) - Static method in class ubic.gemma.model.expression.experiment.FactorValueUtils
getSummaryString(FactorValue) - Static method in class ubic.gemma.model.expression.experiment.FactorValueUtils: Produce a summary string for this factor value.
getSummaryString(FactorValue, String) - Static method in class ubic.gemma.model.expression.experiment.FactorValueUtils
getSummaryString(FactorValue, Characteristic, String) - Static method in class ubic.gemma.model.expression.experiment.FactorValueUtils
getSupertype() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getSupplementaryFile() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getSupplementaryFiles() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getSupplementaryFiles() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSupport() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getSupportedResultTypes() - Method in interface ubic.gemma.core.search.SearchService: Returns a set of supported result types.
getSupportedResultTypes() - Method in class ubic.gemma.core.search.SearchServiceImpl
getSupportedSources() - Method in interface ubic.gemma.core.ontology.relation.OntologyRelationProducer: The sources this producer can read, in the order it reads them.
getSupportedSources() - Method in class ubic.gemma.core.ontology.relation.OntologyRelationProducerImpl
getSupportedTaxaWithNCBIGenes() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator: Those taxa that are supported by GEMMA and have genes in NCBI.
getSupportingEvidence() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getSupportingEvidence() - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Verbatim provenance backing a curated tag — a JSON array of {quote, source, location, ...} items the curation agents emitted (the agents-side FindingEvidence shape).
getSupportingEvidence() - Method in class ubic.gemma.model.common.description.Characteristic
getSupportingEvidence() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: Verbatim provenance backing a curated characteristic — a JSON array of {quote, source, location, …} items the curation agents emitted.
getSupportingEvidence() - Method in class ubic.gemma.model.common.description.PublicationAssociation
getSupportingEvidence() - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
getSupportingEvidence() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: Verbatim provenance backing this factor VALUE — a JSON array of {quote, source, location, …} items the curation agents emitted.
getSupportingEvidence() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Verbatim provenance backing this FACTOR — a JSON array of {quote, source, location, …} items the curation agents emitted, stored and served opaquely.
getSupportingEvidence() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getSupportingEvidence() - Method in class ubic.gemma.model.expression.experiment.FactorValue
getSupportingEvidence() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: Verbatim provenance backing this statement — a JSON array of {quote, source, location, …} items the curation agents emitted.
getSupportingEvidence() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssertion
getSupportingEvidence() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Verbatim provenance for this FACTOR — a JSON array of {quote, source, location, …} items.
getSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: Verbatim provenance for this factor VALUE — a JSON array of {quote, source, location, …} items.
getSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
getSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit: Verbatim provenance for this sample characteristic.
getSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit: Verbatim provenance for this statement — a JSON array of {quote, source, location, …} items.
getSupportingEvidence() - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit: Verbatim provenance for this tag.
getSuppressMatching() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getSuppressNearMatches() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getSuppressPostProcessing() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
getSuspiciousValues() - Method in exception class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException
getSvd(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService: Obtain the SVD analysis for the given experiment, if it exists.
getSvd(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl: Get the SVD information for experiment with id given.
getSvdFactorAnalysis(PrincipalComponentAnalysis) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService: Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
getSvdFactorAnalysis(PrincipalComponentAnalysis) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
getSvdFactorAnalysis(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService: Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
getSvdFactorAnalysis(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
getSwitchedExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getSwitchedExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getSwitchedExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.
getSwitchedExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getSwitchedExpressionExperimentCount() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getSwitchedExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Obtain a collection of ExpressionExperiment identifiers that have been switched from a given platform.
getSwitchedExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl: Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.
getSynonyms() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getSynonyms() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: Typed synonyms drawn from the OBO/IAO synonym predicates (exact / narrow / broad / related / alt_label).
getSystem() - Method in class ubic.gemma.rest.AdminWebService: Process-level memory / GC / thread / load snapshot.
getSystemWideSalt() - Method in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider
getTagCount() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getTagCount() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getTagCount() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCounts
getTagCount() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: Derived hint; null means unknown, never zero.
getTagLength() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getTags() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
getTagsCreated() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getTagsDeleted() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getTagsIdMap() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getTagsToAdd() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getTagsToDelete() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getTagsUnchanged() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
getTagsUnchanged() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
getTarget() - Method in class ubic.gemma.core.security.audit.AuditedEvent
getTargetAlignedRegion() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
getTargetArrayDesign() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskCommand
getTargetArrayDesignName() - Method in class ubic.gemma.rest.DatasetsWebService.PlatformSwitchRequest
getTargetChromosome() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
getTargetChromosomeName() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getTargetCount() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject: How many TicketTargets the ticket holds.
getTargetDatabase() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getTargetEnd() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getTargetEnd() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getTargetGapBases() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getTargetGapBases() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getTargetGapCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getTargetGapCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getTargetId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
getTargetId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
getTargetId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
getTargetId() - Method in class ubic.gemma.rest.TicketsWebService.AddTargetRequest.TargetRef
getTargetId() - Method in class ubic.gemma.rest.TicketsWebService.RemovedTargetResult
getTargetId() - Method in class ubic.gemma.rest.TicketsWebService.TicketTargetRequest
getTargetOntologiesFor(Collection) - Method in interface ubic.gemma.core.ontology.relation.OntologyRelationProducer: Tokens for the vocabularies the named sources point at but do NOT merge, and therefore cannot name a target out of.
getTargetOntologiesFor(Collection) - Method in class ubic.gemma.core.ontology.relation.OntologyRelationProducerImpl
getTargets() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getTargets() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getTargets() - Method in class ubic.gemma.rest.TicketsWebService.AddTargetRequest
getTargets() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getTargetSequence() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
getTargetStart() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getTargetStart() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getTargetStarts() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getTargetStarts() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getTargetState() - Method in exception class ubic.gemma.persistence.service.expression.experiment.DisallowedWorkflowTransitionException
getTargetState() - Method in class ubic.gemma.rest.WorkflowWebService.AdvanceWorkflowRequest
getTargetStatus() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject: This target's status on this ticket.
getTargetType() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
getTargetType() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
getTargetType() - Method in class ubic.gemma.rest.TicketsWebService.AddTargetRequest.TargetRef
getTargetType() - Method in class ubic.gemma.rest.TicketsWebService.RemovedTargetResult
getTargetType() - Method in class ubic.gemma.rest.TicketsWebService.TicketTargetRequest
getTaskClass() - Method in class ubic.gemma.core.job.TaskCommand: Obtain the class of the Task object that will be run for this command.
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.GeeqTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.MultifunctionalityTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
getTaskCommand() - Method in class ubic.gemma.core.job.AbstractTask
getTaskCommand() - Method in interface ubic.gemma.core.job.SubmittedTask
getTaskCommand() - Method in interface ubic.gemma.core.job.Task
getTaskId() - Method in class ubic.gemma.core.job.notification.EmailNotificationContext
getTaskId() - Method in class ubic.gemma.core.job.progress.ProgressData
getTaskId() - Method in interface ubic.gemma.core.job.SubmittedTask
getTaskId() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getTaskId() - Method in class ubic.gemma.rest.TaskStatusValueObject
getTaskName() - Method in class ubic.gemma.core.job.notification.EmailNotificationContext
getTaskStatus(String) - Method in class ubic.gemma.rest.TasksWebService
getTaxa() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject: When genes are included, this field is populated.
getTaxa() - Method in class ubic.gemma.rest.TaxaWebService: Lists all available taxa.
getTaxa(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getTaxa(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getTaxa(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Return the taxon for each of the given experiments.
getTaxa(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getTaxa(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao: Return all the taxa of the gene set members.
getTaxa(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
getTaxa(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
getTaxa(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
getTaxa(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Obtain all the taxa for the members of a given gene set.
getTaxa(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
getTaxaByIds(TaxonArrayArg) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves single taxon based on the given identifier.
getTaxaFromBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Obtain all the taxa associated to the BioSequence of the given platform.
getTaxaFromBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getTaxaFromBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
getTaxaFromBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
getTaxaFromBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Return the taxa for the array design.
getTaxaFromBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getTaxaUsageFrequency(Filters, Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getTaxaUsageFrequency(Filters, Set) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getTaxaUsageFrequency(Filters, Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Calculate the usage frequency of taxa by the datasets matching the provided filters.
getTaxaUsageFrequency(Filters, Set) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getTaxaWithArrays() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonReadService
getTaxaWithArrays() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonReadServiceImpl
getTaxaWithArrays() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
getTaxaWithArrays() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
getTaxaWithDatasets() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonReadService
getTaxaWithDatasets() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonReadServiceImpl
getTaxaWithDatasets() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
getTaxaWithDatasets() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
getTaxaWithGenes() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonReadService
getTaxaWithGenes() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonReadServiceImpl
getTaxaWithGenes() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
getTaxaWithGenes() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
getTaxId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getTaxId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getTaxon() - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat: Lowercase common name of the gene's taxon, matching HomeStats.TaxonStat.commonName.
getTaxon() - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
getTaxon() - Method in class ubic.gemma.core.goldenpath.GoldenPath
getTaxon() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
getTaxon() - Method in class ubic.gemma.core.loader.genome.BlatResultParser
getTaxon() - Method in class ubic.gemma.core.tasks.maintenance.MultifunctionalityTaskCommand
getTaxon() - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
getTaxon() - Method in class ubic.gemma.model.common.description.AnnotationRelation
getTaxon() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
getTaxon() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getTaxon() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment: Taxon of this dataset.
getTaxon() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getTaxon() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getTaxon() - Method in class ubic.gemma.model.genome.Chromosome
getTaxon() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getTaxon() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getTaxon() - Method in class ubic.gemma.model.genome.Gene
getTaxon() - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
getTaxon() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getTaxon() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getTaxon() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
getTaxon() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject: Common name of the taxon, suitable for a typeahead chip.
getTaxon() - Method in class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
getTaxon(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Determine the taxon for a given experiment or subset.
getTaxon(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getTaxon(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService: Included for cycle-break parity with the facade: the only read-method back-edge from ExpressionExperimentSetServiceImpl is getTaxon.
getTaxon(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getTaxon(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Returns the taxon of the given experiment.
getTaxon(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getTaxon(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao: Returns the taxon of an arbitrary member of the set.
getTaxon(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
getTaxon(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
getTaxon(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
getTaxon(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes
getTaxon(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
getTaxonCommonName() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getTaxonCommonName() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getTaxonCommonName() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Common name of a gene hit's taxon (e.g.
getTaxonCompletions(String, int) - Method in class ubic.gemma.rest.CompletionsWebService
getTaxonConstraint() - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: The taxon this term is restricted to, when the ontology declares one, else null.
getTaxonConstraint() - Method in class ubic.gemma.model.common.search.SearchSettings: Constraint results to to be related to the given taxon.
getTaxonConstraint() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getTaxonConstraint() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: The taxon this ONTOLOGY TERM is restricted to, when the ontology declares one — OBO's in_taxon.
getTaxonDatasets(TaxonArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves datasets for the given taxon.
getTaxonForGemmaRest() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getTaxonGeneGoTerms(TaxonArg, GeneArg) - Method in class ubic.gemma.rest.TaxaWebService
getTaxonGeneLocations(TaxonArg, GeneArg) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves gene location for the gene on the given taxon.
getTaxonGeneProbes(TaxonArg, GeneArg, OffsetArg, LimitArg, CursorArg) - Method in class ubic.gemma.rest.TaxaWebService
getTaxonGenes(TaxonArg, OffsetArg, LimitArg, CursorArg) - Method in class ubic.gemma.rest.TaxaWebService
getTaxonGenesByIds(TaxonArg, GeneArrayArg) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves genes matching the identifier on the given taxon.
getTaxonGenesOverlappingChromosome(TaxonArg, String, String, Long, Integer) - Method in class ubic.gemma.rest.TaxaWebService: Finds genes overlapping a given region.
getTaxonId() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
getTaxonId() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getTaxonId() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getTaxonId() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Deprecated.
use ExpressionExperimentValueObject.getTaxonObject() instead
getTaxonId() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getTaxonId() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getTaxonId() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
getTaxonId() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getTaxonId() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getTaxonId() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Taxon (species) of a gene hit — the gene's Taxon.id.
getTaxonId() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject
getTaxonID() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Deprecated.
use ArrayDesignValueObject.getTaxonObject() instead
getTaxonIdForGemmaRest() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getTaxonName() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getTaxonName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getTaxonName() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getTaxonName() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
getTaxonNcbiId() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getTaxonObject() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getTaxonObject() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: FIXME: this should be named simply "taxon", but that field is already taken for Gemma Web, see ExpressionExperimentValueObject.getTaxon().
getTaxonScientificName() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getTaxonScientificName() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: Scientific name of a gene hit's taxon (e.g.
getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes
getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
getTechnology() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getTechnologyType() - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
getTechnologyType() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getTechnologyType() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: What kind of platform it is — ONECOLOR, TWOCOLOR, SEQUENCING, GENELIST, OTHER.
getTechnologyType() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getTechnologyType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getTechnologyTypeUsageFrequency() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the dataset usage frequency by technology type.
getTechnologyTypeUsageFrequency() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getTechnologyTypeUsageFrequency(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the dataset usage frequency by technology type for the given dataset IDs.
getTechnologyTypeUsageFrequency(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getTechnologyTypeUsageFrequency(Filters, Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
getTechnologyTypeUsageFrequency(Filters, Set) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
getTechnologyTypeUsageFrequency(Filters, Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getTechnologyTypeUsageFrequency(Filters, Set) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getTerm() - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Deprecated.
use OntologyResource.getLabel() instead.
getTerm() - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
getTerm() - Method in class ubic.gemma.model.common.description.BibRefAnnotation
getTerm() - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
getTerm() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm: An associated ontology term if available.
getTerm(String) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getTerm(String) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getTerm(String) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getTerm(String) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Retrieve a GO term by ID or URI.
getTerm(String) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getTerm(String) - Method in class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService: Always null: MONDO owns these URIs, and this service must not answer for them.
getTerm(String) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Looks for a OntologyTerm that has the match in URI given
getTerm(String, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain a term for the given URI.
getTerm(String, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getTermAspect(String) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getTermAspect(String) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getTermAspect(Characteristic) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getTermAspect(Characteristic) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getTermCount() - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Annotation-diversity metric: distinct URIs that landed in this bucket.
getTermDefinition(String) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Return a definition for a GO ID.
getTermDefinition(String) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getTermId(OntologyTerm) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Obtain the ontology term ID, also known as the OBO ID, for a given term.
getTermIndividuals(String) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getTermIndividuals(String) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getTermIndividuals(String) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getTermIndividuals(String) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Retrieve a GO individuals by ID or URI.
getTermIndividuals(String) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getTermIndividuals(String) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain all the individuals for a given term URI.
getTermLabel() - Method in class ubic.gemma.core.ontology.model.OntologyXref: The declaring term's label, as the read that produced this cross-reference had it; null when that read had no label to give.
getTermReplacedBy() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: The successor this term names, IAO:0100001 term replaced by — where a curator holding the deprecated URI should re-bind to.
getTermReplacedByLabel() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: Preferred label of AnnotationsWebService.OntologyTermValueObject.termReplacedBy, so a client can render the re-bind without a second round trip.
getTerms() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
getTerms() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
getTerms(Collection, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Return all the terms matching the given URIs.
getTerms(Collection, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getTermsScanned() - Method in class ubic.gemma.rest.GoTermsWebService.GoTermGeneCountValueObject
getTermUri() - Method in class ubic.gemma.core.ontology.model.OntologyXref: The URI of the term that declares this cross-reference (e.g.
getTermUri() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getTermUri() - Method in class ubic.gemma.rest.GoTermsWebService.GoTermGeneCountValueObject
getTermUri(String) - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils: Convert a CELLxGENE ontology term ID into a URI.
getTermUri(OntologyTerm) - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils: Convert a CELLxGENE ontology term into a URI.
getTextFname() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getTextValue(Node) - Static method in class ubic.gemma.core.util.XMLUtils: Make the horrible DOM API slightly more bearable: get the text value we know this element contains.
getThirdQuartile() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
getThreePrimeDistance() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getThreePrimeDistanceMeasurementMethod() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getThreePrimeDistances(String, ThreePrimeDistanceMethod) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis: Uses default mapping settings
getThreePrimeDistances(BlatResult, ThreePrimeDistanceMethod) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis: Given a physical location, find how close it is to the 3' end of a gene it is in, using default mapping settings.
getThreshold() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Threshold applied to the hitlist.
getThreshold() - Method in class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
getThresholdQvalue() - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
getThrowable() - Method in class ubic.gemma.cli.batch.BatchTaskProcessingResult
getTicket() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
getTicket() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
getTicket() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService.TargetAddition
getTicket() - Method in class ubic.gemma.rest.TicketsWebService.AddTargetsResult
getTicket() - Method in class ubic.gemma.rest.TicketsWebService.RemovedTargetResult
getTicket(Long) - Method in class ubic.gemma.rest.TicketsWebService: Retrieve a single ticket, including its full event log.
getTicketCountOpen() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
getTicketEvents(Long, CursorArg, LimitArg) - Method in class ubic.gemma.rest.TicketsWebService: Retrieve only the event log for a ticket.
getTicketId() - Method in class ubic.gemma.rest.WorkflowWebService.AdvanceWorkflowRequest
getTickets(boolean, Long, TicketPriority, TicketType, TicketState, TicketTargetType, Date, OffsetArg, LimitArg, CursorArg) - Method in class ubic.gemma.rest.TicketsWebService: List tickets with optional filters and offset/limit or cursor pagination.
getTimeoutSeconds() - Method in class ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskCommand
getTimestamp() - Method in class ubic.gemma.core.util.BuildInfo
getTimestamp() - Method in class ubic.gemma.rest.monitoring.InfoWebService.BuildBlock
getTimestamp() - Method in class ubic.gemma.rest.util.BuildInfoValueObject
getTissue() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
getTitle() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition: Short column label, e.g.
getTitle() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
getTitle() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
getTitle() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
getTitle() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket: The ticket title.
getTitle() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
getTitle() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getTitle() - Method in class ubic.gemma.model.common.description.BibliographicReference
getTitle() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getTitle() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject: Short column label MultiQC uses, e.g.
getTitle() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
getTitle() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getTitle() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
getTitleInDataset() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: This is used to store the title for the sample as found in the GDS file, if it differs from the one in the GSE file
getTmpDir() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
getToken() - Method in class ubic.gemma.rest.AuthWebService.LoginResponse
getTokenNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer: Deprecated.
getTokenNames() - Method in class ubic.gemma.rest.util.args.FilterArgParser: Deprecated.
getToLabel() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getToLabel() - Method in class ubic.gemma.rest.AnnotationsWebService.CanonicalUriValueObject: The label that goes with AnnotationsWebService.CanonicalUriValueObject.getToUri(); it moves with the URI.
getTolerance() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition
getTopHits(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
getTopHits(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
getTopicality() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary: Whether this relation says something about the subject TERM, or records a parameter of one experiment.
getTopicality() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: TERM_LEVEL when the relation says what the subject term is or where it came from; EXPERIMENT_LEVEL when it records how one experiment was run (a dose, a duration, a sample's sex).
getTopLoadedProbes(ExpressionExperiment, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDao
getTopLoadedProbes(ExpressionExperiment, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImpl
getTopLoadedProbes(ExpressionExperiment, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadService
getTopLoadedProbes(ExpressionExperiment, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadServiceImpl
getTopLoadedProbes(ExpressionExperiment, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
getTopLoadedProbes(ExpressionExperiment, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl
getTopLoadedVectors(ExpressionExperiment, int, int) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService
getTopLoadedVectors(ExpressionExperiment, int, int) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
getTopMarkers() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
getTopPerturbedGenes() - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-gene ranking of how many public EEs carry that gene as a perturbation-target annotation — a gene URI whose own category is genotype.
getTopTerms() - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Top representative terms in this bucket, sorted desc by EE-mention count.
getToRedo() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
getToRemove() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand
getTotalBases() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getTotalCells() - Method in class ubic.gemma.core.analysis.report.HomeStats: Total individual cells measured across all single-cell experiments — sum of BioAssay.numberOfCells for assays attached to EEs with a SingleCellDimension.
getTotalElements() - Method in class ubic.gemma.persistence.util.CursorPage
getTotalElements() - Method in class ubic.gemma.persistence.util.Slice
getTotalElements() - Method in class ubic.gemma.rest.AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
getTotalElements() - Method in class ubic.gemma.rest.util.CursorPaginatedResponseDataObject
getTotalElements() - Method in class ubic.gemma.rest.util.PaginatedResponseDataObject
getTotalRecords() - Method in class ubic.gemma.core.loader.entrez.EntrezQuery
getTotalSpots() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
getTotalTime(String, TimeUnit) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor: Obtain the total time spent instantiating and initializing a bean.
getTotalTime(TimeUnit) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor: Obtain the total time spent instantiating and initializing beans.
getToUri() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
getToUri() - Method in class ubic.gemma.rest.AnnotationsWebService.CanonicalUriValueObject: The URI Gemma reports for it.
getTransformation(Class) - Method in interface ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactory
getTransformation(Class) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactoryImpl: Obtain a single-cell data transformation.
getTransformExecutor() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Executor service to use to transform single-cell data.
getTranspose() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
getTreatmentProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getTreatments() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getTreatmentSubcategories() - Method in class ubic.gemma.core.analysis.report.HomeStats: Treatment-category terms broken down by bucket (see treatment-buckets.json): approved_drug, hormone, vitamin, toxin, vehicle, biologic (PR / NCBI Gene), pathogen (NCBITaxon), control, plus the other_chemical catchall (unbucketed CHEBI) and other catchall (non-CHEBI).
getTriage(Long) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Every ruling on an annotation set, most recent first.
getTriageJudgeKind() - Method in class ubic.gemma.rest.PipelineStatusValueObject: Whether PipelineStatusValueObject.triageVerdict came from an agent or a curator; null when nothing has been triaged.
getTriageVerdict() - Method in class ubic.gemma.rest.PipelineStatusValueObject: The effective triage ruling across this dataset's annotation sets — fine, wont_fix, might_fix or must_fix — or null when nothing has been triaged.
getTripleKey() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
getTripleKey() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: Identifies the subject/predicate/object triple irrespective of basis, so a client can group the side-by-side rows that one relation legitimately produces.
getTroubled() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getTroubled() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails: If you are trying to check for trouble of an expression experiment, you might consider using the method ExpressionExperimentService.isTroubled(ubic.gemma.model.expression.experiment.ExpressionExperiment) which also checks the parenting array designs
getTroubled() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getTroubled() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
getTroubled() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsUpdateRequest
getTroubleDetails() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getTroubleDetails() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getTroubleDetails() - Method in class ubic.gemma.rest.PipelineStatusValueObject
getTroubleDetails(boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getTroubleDetails(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Checks trouble of this EE and all its Array Designs and returns compilation of trouble info.
getTrueRowIndex(int) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getTstat() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getTStat() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
getTsvFormatBuilder(String, BuildInfo, Date, String...) - Static method in class ubic.gemma.core.util.TsvUtils: Preconfigure a CSVFormat.Builder with desirable defaults.o
getType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
getType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: The sample type (ie.
getType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
getType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
getType() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
getType() - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
getType() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
getType() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
getType() - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
getType() - Method in class ubic.gemma.core.loader.util.anndata.Layer: Get the encoding type of this layer.
getType() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
getType() - Method in interface ubic.gemma.core.ontology.model.DatatypeProperty
getType() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
getType() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterService.LintResult
getType() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getType() - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
getType() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getType() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
getType() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
getType() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
getType() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getType() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getType() - Method in class ubic.gemma.model.common.measurement.Measurement
getType() - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
getType() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getType() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
getType() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
getType() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
getType() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getType() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
getType() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getType() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getType() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSynonymValueObject: Synonym scope, mirroring the OBO/IAO predicates and the AnnotationsWebService.MatchedVia tokens: exact_synonym, narrow_synonym, broad_synonym, related_synonym, alt_label.
getType() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetMetadataFileValueObject: Enum name of the metadata file type — use this value as the {type} path parameter on GET /datasets/{id}/metadata/{type} to fetch the file.
getType() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: "categorical" | "continuous".
getType() - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
getType() - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
getType() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
getType() - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
getTypes() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getU() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getU() - Method in class ubic.gemma.core.util.math.linalg.SingularValueDecomposition
getUnchanged() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport
getUnchanged() - Method in class ubic.gemma.rest.DatasetsWebService.CurationSectionChange
getUniqueItem(NodeList) - Static method in class ubic.gemma.core.util.XMLUtils: Obtain a single item from a NodeList.
getUniqueResult() - Method in interface ubic.gemma.core.loader.util.parser.Parser: Obtain a unique result from the parser.
getUnit() - Method in class ubic.gemma.model.common.measurement.Measurement
getUnit() - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
getUnit() - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
getUnit(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils
getUnitId() - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
getUnitNameCV() - Method in class ubic.gemma.model.common.measurement.Unit
getUnknownCellTypeIndicator() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
getUnknownCellTypeIndicator(Dataframe.Column) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer: Extract the unknown cell type indicator from a set of values.
getUnknownParameters() - Method in exception class ubic.gemma.rest.util.UnknownQueryParameterException: The rejected parameter names, in the order they appeared in the query string.
getUnmatchedKeys() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics: Report row keys that could not be matched to any bioAssay of the experiment.
getUnmatchedKeys() - Method in class ubic.gemma.rest.DatasetsWebService.SequencingQcMetricsValueObject: Report row keys that matched no bioAssay — mostly SRA run accessions, which the FASTQ-level modules key by and which Gemma does not record.
getUnprefixedName(ExpressionExperimentSubSet) - Static method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSetUtils: Obtain the unprefixed name of a subset, i.e., the name without the source experiment name and delimiter.
getUnresolvedUris() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport: URIs in the desired set that didn't resolve against an ontology.
getUns() - Method in class ubic.gemma.core.loader.util.anndata.AnnData: Obtain additional free-form data stored under uns.
getUntil() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
getUntil() - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
getUpdated() - Method in class ubic.gemma.rest.DatasetsWebService.CurationSectionChange
getUpdatedArrayDesigns() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getUpdatedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
getUpdatedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
getUpdatedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
getUpdatedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
getUpdatedAt() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
getUpdateDate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getUpdatedEEIdsPerTaxon() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getUpdatedExpressionExperiments() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getUpdatedObjects() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getUpdatedSinceDate(Class, Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Get auditables that have been updated since the given date.
getUpdatedSinceDate(Class, Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getUpdatedSinceDate(Class, Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getUpdatedSinceDate(Class, Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getUpperTail() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getUpperTail() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getUpregulatedCount() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Deprecated.
use DiffExResultSetSummaryValueObject.getNumberOfUpregulatedProbes() instead.
getUpregulatedCount() - Method in class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
getUptime() - Method in class ubic.gemma.rest.monitoring.InfoWebService.InfoValueObject
getUptimeMillis() - Method in class ubic.gemma.rest.monitoring.InfoWebService.UptimeBlock
getUri() - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat: Ontology URI (CHEBI, OBI, EFO, …).
getUri() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.Annotation
getUri() - Method in interface ubic.gemma.core.ontology.model.OntologyResource: A URI if known, otherwise null.
getUri() - Method in class ubic.gemma.core.ontology.model.OntologyTerm.TaxonConstraint
getUri() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
getUri() - Method in class ubic.gemma.core.ontology.search.OntologySearchService.Result
getUri() - Method in class ubic.gemma.core.ontology.simple.AbstractOntologyResourceSimple
getUri() - Method in class ubic.gemma.model.common.description.DatabaseEntry
getUri() - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
getUri() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
getUri() - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
getUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationCategoryValueObject
getUri() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSimpleValueObject
getUri() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject
getUri() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonConstraintValueObject: Full NCBITaxon URI, e.g.
getUri() - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermRef
getUri() - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
getUri(Long) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Obtain a suitable ontology ID for a given factor value ID.
getUri(String) - Static method in class ubic.gemma.core.loader.entrez.pubmed.PubMedUtils
getUri(String) - Static method in class ubic.gemma.core.loader.expression.arrayExpress.ArrayExpressUtils
getUri(String) - Static method in class ubic.gemma.core.loader.expression.sra.SraUtils
getUri(String) - Static method in class ubic.gemma.core.loader.expression.synapse.SynapseUtils
getUri(String) - Static method in class ubic.gemma.core.loader.expression.zenodo.ZenodoUtils
getUri(String) - Static method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneUtils
getUri(String) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyUtils
getUri(String, GeoSource, GeoFormat, GeoScope, GeoAmount) - Static method in class ubic.gemma.core.loader.expression.geo.service.GeoUtils: Obtain a URI for GEO entry.
getUri(DatabaseEntry) - Static method in class ubic.gemma.core.loader.util.ExternalDatabaseUtils: Obtain a URI for a given database entry.
getUri(DatabaseEntryValueObject) - Static method in class ubic.gemma.core.loader.util.ExternalDatabaseUtils: Obtain a URI for a given database entry.
getUri(ExternalDatabase) - Static method in class ubic.gemma.core.loader.util.ExternalDatabaseUtils: Obtain a URI for a given external database.
getUri(FactorValue) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Obtain a suitable ontology ID for a given factor value.
getUriExactMatches() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Full-URI equality matchers.
getUriMigrations() - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: The whole canonicalization table, from-URI → [to-URI, to-label, rule, lane].
getUriPrefixes() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: valueUri.startsWith(prefix) matchers.
getUris() - Method in class ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskCommand
getUrl() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
getUrl() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getUrl() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getUrl() - Method in class ubic.gemma.core.util.SimpleDownloader.URLAndDestination
getUrl(String, GeoSource, GeoFormat, GeoScope, GeoAmount) - Static method in class ubic.gemma.core.loader.expression.geo.service.GeoUtils: Obtain a URL for GEO entry.
getUrlForSupplementaryMaterial(GeoRecordType, String, String, GeoSource) - Static method in class ubic.gemma.core.loader.expression.geo.service.GeoUtils
getUrlId() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: id used by url on the client side
getUsage() - Method in class ubic.gemma.apps.CompleteCli
getUsage() - Method in class ubic.gemma.apps.SingleCellDataTransformCli: Adjust usage to reflect the transformation-specific options.
getUsage() - Method in class ubic.gemma.cli.util.AbstractCLI: Describe the intended usage for the command.
getUsageCount() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject
getUsageCount() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject
getUse10xChemistry() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig: Chemistry used for single-cell sequencing.
getUsefulQuantitationTypes(Collection) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getUsefulQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
getUser() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getUser() - Method in class ubic.gemma.rest.AuthWebService.LoginResponse
getUser(String) - Method in class ubic.gemma.rest.RootWebService: Retrieve user information.
getUseRawX() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
getUserCanWrite() - Method in interface ubic.gemma.core.security.model.SecureValueObject: Indicate if the current user can modify this object.
getUserCanWrite() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getUserCanWrite() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getUserCanWrite() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getUserCanWrite() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getUserCanWrite() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getUserGroupGrantedAuthority(Securable) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice
getUserGroupGrantedAuthority(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
getUserId() - Method in class ubic.gemma.rest.GroupsWebService.MemberAddRequest
getUsername() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
getUsername() - Method in class ubic.gemma.rest.AuthWebService.LoginRequest
getUsername() - Method in class ubic.gemma.rest.GroupsWebService.MemberAddRequest
getUserName() - Method in class ubic.gemma.core.security.authentication.LoginDetailsValueObject
getUserName() - Method in interface ubic.gemma.core.security.model.User
getUserName() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getUserName() - Method in class ubic.gemma.rest.GroupsWebService.GroupMemberValueObject
getUserName() - Method in class ubic.gemma.rest.RootWebService.UserValueObject
getUserName(Securable) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice
getUserName(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
getUserOwned() - Method in interface ubic.gemma.core.security.model.SecureValueObject: Indicate if the current user owns the object.
getUserOwned() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getUserOwned() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getUserOwned() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
getUserOwned() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
getUserOwned() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getUsers(boolean) - Method in class ubic.gemma.rest.AdminWebService: Admin user listing.
getUsersGeneGroups(boolean, Long, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
getUsersGeneGroups(boolean, Long, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
getUsersGeneGroupsValueObjects(boolean, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Returns just the current users gene sets
getUsersGeneGroupsValueObjects(boolean, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
getV() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getV() - Method in class ubic.gemma.core.util.math.linalg.SingularValueDecomposition
getV() - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
getV() - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
getValidated() - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta: Diffex "validated" highlight flag.
getValue() - Method in enum class ubic.gemma.core.loader.entrez.EntrezRetmode
getValue() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic
getValue() - Method in class ubic.gemma.core.loader.expression.sra.model.SraBase
getValue() - Method in enum class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaFieldType
getValue() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
getValue() - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Label of the annotated term — the value as curated.
getValue() - Method in class ubic.gemma.model.common.description.Characteristic
getValue() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
getValue() - Method in class ubic.gemma.model.common.description.Value
getValue() - Method in class ubic.gemma.model.common.measurement.Measurement
getValue() - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
getValue() - Method in class ubic.gemma.model.expression.experiment.FactorValue: Deprecated.
use FactorValue.getMeasurement() or FactorValue.getCharacteristics() to retrieve the value.
getValue() - Method in class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject: Deprecated.
use either AbstractFactorValueValueObject.getCharacteristics() or AbstractFactorValueValueObject.getMeasurementObject()
getValue() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getValue() - Method in class ubic.gemma.model.expression.experiment.Statement: Deprecated.
use Statement.getSubject() instead
getValue() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject
getValue() - Method in class ubic.gemma.persistence.service.FilteringDao.ConjunctSpec
getValue() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getValue() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject
getValue() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSynonymValueObject: The synonym text.
getValue() - Method in class ubic.gemma.rest.AnnotationsWebService.PriorCurationValueObject: The label stored alongside the term in the corpus.
getValue() - Method in class ubic.gemma.rest.AnnotationsWebService.RuledOutTermValueObject
getValue() - Method in class ubic.gemma.rest.CompletionsWebService.CompletionValueObject: The candidate completion value (id, short name, URI, etc.
getValue() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getValue() - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
getValue() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit
getValue() - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
getValue() - Method in class ubic.gemma.rest.util.args.AbstractArg: Obtain the value represented by this argument.
getValue() - Method in interface ubic.gemma.rest.util.args.Arg: Obtain the value represented by this argument.
getValue() - Method in class ubic.gemma.rest.util.args.LimitArg: Obtain the value of the limit ensuring that it is smaller than LimitArg.MAXIMUM
getValue() - Method in class ubic.gemma.rest.util.args.QueryArg
getValue(int, int) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
getValue(int, int) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
getValue(Integer) - Method in class ubic.gemma.rest.util.args.LimitArg: Obtain the value of the limit and ensure it is smaller than a given maximum.
getValue(Set) - Method in class ubic.gemma.rest.util.args.ExcludeArg
getValue(FactorValue, String) - Static method in class ubic.gemma.model.expression.experiment.FactorValueUtils: Produce a value for representing a factor value.
getValueAsDouble() - Method in class ubic.gemma.model.common.measurement.Measurement: Retrieve the value of this measurement as a double.
getValueAsFloat() - Method in class ubic.gemma.model.common.measurement.Measurement
getValueAsInt() - Method in class ubic.gemma.model.common.measurement.Measurement
getValueAsLong() - Method in class ubic.gemma.model.common.measurement.Measurement
getValueDefinition() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: The definition of the value, if it is an ontology term, as supplied by the ontology.
getValueId() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: A unique ontology identifier (i.e.
getValueNoMaximum() - Method in class ubic.gemma.rest.util.args.LimitArg: Obtain the value of the limit, explicitly disregarding the maximum defined by LimitArg.MAXIMUM.
getValueObject() - Method in class ubic.gemma.model.common.BaseValueObject
getValueObject(OntologyTerm) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Converts the given Ontology Term to a Gene Ontology Value Object.
getValueObject(OntologyTerm) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getValueObjects(Collection) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Converts the given collection of Ontology Terms to Gene Ontology Value Objects.
getValueObjects(Collection) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getValueObjects(Gene) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Returns GO Terms VOs for the given Gene.
getValueObjects(Gene) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getValueObjectTransformer() - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
getValueObjectTransformer() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getValueObjectTransformer() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getValues() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.RunMetrics
getValues() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics: Sample-level metrics: the values from report rows whose key IS this assay's accession.
getValues() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getValues() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
getValues() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
getValues() - Method in class ubic.gemma.persistence.service.FilteringDao.ConjunctSpec
getValues() - Method in class ubic.gemma.rest.DatasetsWebService.RunQcMetricsValueObject
getValues() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject: Symmetric, row-major, N×N Pearson correlation matrix.
getValues() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject: Sample-level metrics, from report rows keyed by this assay's accession.
getValues() - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection: Either double[][] (encoding=json) or a String holding base64-encoded little-endian Float32 cells (encoding=base64f32).
getValues(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries: Get a subset of the values.
getValues(GeoPlatform, Integer, String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
getValues(GeoPlatform, Integer, String, Integer[]) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
getValues(FactorValue) - Static method in class ubic.gemma.model.expression.experiment.FactorValueUtils
getValuesForFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.util.FactorValueVector
getValuesForFactors() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
getValueType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getValueUri() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic
getValueUri() - Method in interface ubic.gemma.core.ontology.model.AnnotationProperty: The URI of this annotation's value when the value is a URI resource, else null (literal values, blank nodes).
getValueUri() - Method in class ubic.gemma.model.common.description.AnnotationValueObject: URI of the annotated term.
getValueUri() - Method in class ubic.gemma.model.common.description.Characteristic
getValueUri() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
getValueUri() - Method in class ubic.gemma.model.common.description.Value
getValueUri() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
getValueUri() - Method in class ubic.gemma.model.expression.experiment.Statement: Deprecated.
use Statement.getSubjectUri() instead
getValueUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
getValueUri() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject
getValueUri() - Method in class ubic.gemma.rest.AnnotationsWebService.PriorCurationValueObject: The term prior curators chose.
getValueUri() - Method in class ubic.gemma.rest.AnnotationsWebService.RuledOutTermValueObject
getValueUri() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
getVar() - Method in class ubic.gemma.core.loader.util.anndata.AnnData
getVar(Class) - Method in class ubic.gemma.core.loader.util.anndata.AnnData
getVariables() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getVariables() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getVarianceFraction() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
getVarianceFractions() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getVarianceFractions() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getVariances() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: An array of values representing the fraction of the variance each component accounts for
getVariances() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
getVariances() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject: Variances (squared SD or robust variance), parallel to DatasetsWebService.MeanVarianceValueObject.means: a point is (means[i], variances[i]).
getVariances() - Method in class ubic.gemma.rest.DatasetsWebService.SimpleSVDValueObject: An array of values representing the fraction of the variance each component accounts for
getVarPost() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
getVarPrior() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
getVector() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
getVectors() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getVectors() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
getVectorType() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject: Vector type this QT is associated to.
getVectorTypes() - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Obtain all the data vector types that are associated with quantitation types.
getVectorTypes() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
getVectorTypes() - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
getVectorTypes() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
getVectorTypes() - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
getVectorTypes() - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
getVendor() - Method in class ubic.gemma.rest.monitoring.InfoWebService.JavaBlock
getVerdict() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
getVersion() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
getVersion() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
getVersion() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
getVersion() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
getVersion() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Obtain the version of this ontology if available — the value of owl:versionInfo (typically a release date or version string), falling back to owl:versionIRI.
getVersion() - Method in class ubic.gemma.core.util.BuildInfo
getVersion() - Method in class ubic.gemma.persistence.util.Cursor
getVersion() - Method in class ubic.gemma.rest.monitoring.InfoWebService.BuildBlock
getVersion() - Method in class ubic.gemma.rest.monitoring.InfoWebService.JavaBlock
getVersion() - Method in class ubic.gemma.rest.monitoring.InfoWebService.OsBlock
getVersion() - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject
getVersion() - Method in class ubic.gemma.rest.util.BuildInfoValueObject
getVersion(String, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain the version (release) of the ontology that owns the given term URI.
getVersion(String, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getViaSubClassOf() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject: How this term was reached from the one that was asked about, on /annotations/parents and /annotations/children only.
getViolation() - Method in class ubic.gemma.rest.util.OntologyTermValidationException.Located
getViolations() - Method in exception class ubic.gemma.rest.util.OntologyTermValidationException
getVisualizationValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getVisualizationValues() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getVm() - Method in class ubic.gemma.rest.monitoring.InfoWebService.JavaBlock
getVMatrix() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult: Row names: biomaterials; column names: eigengene number (from 0)
getVMatrix() - Method in class ubic.gemma.rest.DatasetsWebService.SimpleSVDValueObject
getVocabulary() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getVocabulary() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getVolume() - Method in class ubic.gemma.model.common.description.BibliographicReference
getVolume() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getWarnings() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getWarnings() - Method in class ubic.gemma.rest.util.ResponseDataObject: A list of warnings applicable to the request.
getWebLink() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getWebLink() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getWebLinks() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getWebLinks() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getWebUri() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getWeeklyReport() - Method in interface ubic.gemma.core.analysis.report.WhatsNewService: Generate the report from last week.
getWeeklyReport() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
getWeights() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
getWeights() - Method in class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator
getWelcome() - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject
getWellComposedErrorBody(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper: Obtain a WellComposedErrorBody for the exception.
getWellComposedErrorBody(NotFoundException) - Method in class ubic.gemma.rest.providers.NotFoundExceptionMapper
getWellComposedErrorBody(CurationCommitConflictException) - Method in class ubic.gemma.rest.providers.CurationCommitConflictExceptionMapper
getWellComposedErrorBody(MalformedArgException) - Method in class ubic.gemma.rest.providers.MalformedArgExceptionMapper
getWellComposedErrorBody(OntologyTermValidationException) - Method in class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapper
getWellComposedErrorBody(UnknownQueryParameterException) - Method in class ubic.gemma.rest.providers.UnknownQueryParameterExceptionMapper
getWireName() - Method in enum class ubic.gemma.model.common.search.SearchMatchType: Stable snake-case token for JSON wire contracts (matches the curation-UI / agent vocabulary).
getWorkflowQueue(String, String, String, String, Date, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.WorkflowWebService: Curator worklist: datasets currently in a given workflow state.
getWorkflowState() - Method in class ubic.gemma.model.analysis.Investigation
getWorkflowStateEnteredAt() - Method in class ubic.gemma.model.analysis.Investigation
getWriteHoldCount() - Method in class ubic.gemma.core.util.locking.FileLockInfo
getWriter() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli
getX() - Method in class ubic.gemma.core.loader.util.anndata.AnnData: Obtain the main layer named X.
getXLabels() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getXLabels() - Method in interface ubic.gemma.core.visualization.Heatmap
getXLabels() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getXSampleCount() - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
getXValue(int) - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
getYLabels() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
getYLabels() - Method in interface ubic.gemma.core.visualization.Heatmap
getYLabels() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
getYSampleCount() - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
getYValue(int) - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
getZ() - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
getZ() - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
getZ(int, int) - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
getZValue(int, int) - Method in class ubic.gemma.core.visualization.TransposedHeatMapDataset
gitHash(String) - Method in class ubic.gemma.rest.util.BuildInfoValueObject.BuildInfoValueObjectBuilder
GO - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
GOEvidenceCode - Enum Class in ubic.gemma.model.association: This enumeration was originally based on GO, but is used for all entities that have evidenciary aspects; Thus it has been expanded to include: Terms from RGD (rat genome database) IED = Inferred from experimental data IAGP = Inferred from association of genotype and phenotype IPM = Inferred from phenotype manipulation QTM = Quantitative Trait Measurement And our own custom code IIA which means Inferred from Imported Annotation to distinguish IEAs that we ourselves have computed See https://geneontology.org/docs/guide-go-evidence-codes/ for documentation of GO evidence codes.
GOGroupValueObject - Class in ubic.gemma.model.genome.gene
GOGroupValueObject() - Constructor for class ubic.gemma.model.genome.gene.GOGroupValueObject
GOGroupValueObject(String, String, Long, String, Collection, String, String) - Constructor for class ubic.gemma.model.genome.gene.GOGroupValueObject: Method to create a display object from scratch
GoldenPath - Class in ubic.gemma.core.goldenpath: Perform useful queries against GoldenPath (UCSC) databases.
GoldenPath(Taxon) - Constructor for class ubic.gemma.core.goldenpath.GoldenPath: Create a GoldenPath database for a given taxon.
GoldenPathQuery - Class in ubic.gemma.core.goldenpath
GoldenPathQuery(Taxon) - Constructor for class ubic.gemma.core.goldenpath.GoldenPathQuery
GoldenPathQueryFactory - Interface in ubic.gemma.core.goldenpath: Factory for GoldenPathQuery instances.
GoldenPathQueryFactoryImpl - Class in ubic.gemma.core.goldenpath: Default GoldenPathQueryFactory that constructs a real GoldenPathQuery bound to the configured GoldenPath database for the supplied taxon.
GoldenPathQueryFactoryImpl() - Constructor for class ubic.gemma.core.goldenpath.GoldenPathQueryFactoryImpl
GoldenPathSequenceAnalysis - Class in ubic.gemma.core.goldenpath: Using the Goldenpath databases for comparing sequence alignments to gene locations.
GoldenPathSequenceAnalysis(Taxon) - Constructor for class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis
GoldenPathSequenceAnalysisFactory - Interface in ubic.gemma.core.goldenpath: Factory for GoldenPathSequenceAnalysis instances.
GoldenPathSequenceAnalysisFactoryImpl - Class in ubic.gemma.core.goldenpath: Default GoldenPathSequenceAnalysisFactory that constructs a real GoldenPathSequenceAnalysis bound to the configured GoldenPath database for the supplied taxon.
GoldenPathSequenceAnalysisFactoryImpl() - Constructor for class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysisFactoryImpl
GoMetric - Interface in ubic.gemma.core.ontology
GoMetric.Metric - Enum Class in ubic.gemma.core.ontology
GoMetricImpl - Class in ubic.gemma.core.ontology
GoMetricImpl() - Constructor for class ubic.gemma.core.ontology.GoMetricImpl
googleAnalytics4Provider(AuthenticationTrustResolver) - Method in class ubic.gemma.rest.analytics.ga4.AnalyticsConfig
GoogleAnalytics4Provider - Class in ubic.gemma.rest.analytics.ga4: Implementation of the AnalyticsProvider interface for Google Analytics 4 collect API.
GoogleAnalytics4Provider(String, String) - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
GoogleAnalytics4Provider(RestClient, String, String) - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Create a new Google Analytics 4 provider.
GoTermGeneCountValueObject(String, long, int, boolean, int) - Constructor for class ubic.gemma.rest.GoTermsWebService.GoTermGeneCountValueObject
GoTermsWebService - Class in ubic.gemma.rest: RESTful interface for reverse GO-term lookup: GO term URI → genes annotated with it.
GoTermsWebService() - Constructor for class ubic.gemma.rest.GoTermsWebService
GoTermsWebService.GoTermGeneCountValueObject - Class in ubic.gemma.rest: Wire payload for GET /goTerms/{termUri}/genes/count.
grabGeoRecords(AdminWebService.GeoGrabRequest) - Method in class ubic.gemma.rest.AdminWebService: Scrape GEO record metadata by accession without importing into Gemma.
granted - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockBulkResult
grantedAuthority(Sid) - Static method in class ubic.gemma.core.security.acl.domain.Sids: Granted-authority name carried by the sid, or null if sid is not a granted-authority sid.
greaterOrEq - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
greaterThan - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
GREENRED_COLORMAP - Static variable in class ubic.gemma.core.util.graphics.ColorMap
groupAgentSecurityContext(ManualAuthenticationService, String, String) - Method in class ubic.gemma.core.config.DataSourceConfig: Lazy factory for the GROUP_AGENT SecurityContext.
GroupAuthority - Class in ubic.gemma.model.common.auditAndSecurity: Authority for groups (kind of like a "user role", but for group-based authorization)
GroupAuthority - Interface in ubic.gemma.core.security.model: Represents an GrantedAuthority conferred by a group membership.
GroupAuthority() - Constructor for class ubic.gemma.model.common.auditAndSecurity.GroupAuthority
GroupAuthority.Factory - Class in ubic.gemma.model.common.auditAndSecurity
groupByIfNecessary(Sort, String...) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: If the sort refers to one of the one-to-many relations, multiple rows will be returned per entity, so the query has to use a group by clause to keep pagination correct.
GroupCreateRequest() - Constructor for class ubic.gemma.rest.GroupsWebService.GroupCreateRequest
groupExists(String) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
groupExists(String) - Method in interface ubic.gemma.core.security.authentication.GroupManager: Check if a group with a given name exists.
groupExists(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
groupExists(String) - Method in interface ubic.gemma.core.security.authentication.UserReadService
groupExists(String) - Method in class ubic.gemma.core.security.authentication.UserReadServiceImpl
groupExists(String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
GroupManager - Interface in ubic.gemma.core.security.authentication: Extension of GroupManager.
GroupMemberValueObject(Long, String, String, boolean) - Constructor for class ubic.gemma.rest.GroupsWebService.GroupMemberValueObject
groups - Variable in class ubic.gemma.rest.AdminWebService.UserValueObject
GroupSummaryValueObject(Long, String, String, int) - Constructor for class ubic.gemma.rest.GroupsWebService.GroupSummaryValueObject
GroupsWebService - Class in ubic.gemma.rest: RESTful CRUD + member management for user groups (gap §3c of GEMMA_UI_ENDPOINT_GAP.md).
GroupsWebService(UserManager, UserReadService) - Constructor for class ubic.gemma.rest.GroupsWebService
GroupsWebService.GroupCreateRequest - Class in ubic.gemma.rest: Body for POST /groups.
GroupsWebService.GroupMemberValueObject - Class in ubic.gemma.rest: Lightweight per-member projection — just the fields needed to render a member-list row.
GroupsWebService.GroupSummaryValueObject - Class in ubic.gemma.rest: Lightweight projection for list pages — only the fields the curation UI needs to render a row.
GroupsWebService.GroupUpdateRequest - Class in ubic.gemma.rest: Body for PATCH /groups/{id}.
GroupsWebService.GroupValueObject - Class in ubic.gemma.rest: Single-group response (no members list — use GroupsWebService.GroupWithMembersValueObject for that).
GroupsWebService.GroupWithMembersValueObject - Class in ubic.gemma.rest: Full response including member summaries; used for GET /groups/{id}?includeSummaries=true and the membership-mutating endpoints so the caller doesn't need a follow-up GET.
GroupsWebService.MemberAddRequest - Class in ubic.gemma.rest: Body for POST /groups/{id}/members.
GroupUpdateRequest() - Constructor for class ubic.gemma.rest.GroupsWebService.GroupUpdateRequest
GroupValueObject(Long, String, String, int, List) - Constructor for class ubic.gemma.rest.GroupsWebService.GroupValueObject
GroupWithMembersValueObject(Long, String, String, int, List, List) - Constructor for class ubic.gemma.rest.GroupsWebService.GroupWithMembersValueObject
growthProtocol - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
guessAliases(String, String) - Static method in class ubic.gemma.persistence.util.SubqueryUtils: Given a prefix and an object alias, guess a reasonable sequence of aliases to use in a query.
guessIsBackground(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
guessPrimitiveType(String, String, Object) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
guessQuantitationTypeParameters(QuantitationType, String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
guessQuantitationTypeParameters(QuantitationType, String, String, Object) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser: Attempt to fill in the details of the quantitation type.
guessScaleType(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
guessType(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
GZIP - Annotation Interface in ubic.gemma.rest.annotations: Used to annotate endpoints that will have their payload compressed with gzip unconditionally.
GzipHeaderDecorator - Class in ubic.gemma.rest.providers: Automagically add the Content-Encoding: gzip header to endpoints annotated with GZIP.
GzipHeaderDecorator() - Constructor for class ubic.gemma.rest.providers.GzipHeaderDecorator
GzipHeaderDecoratorAfterGZipEncoder - Class in ubic.gemma.rest.providers: Adds a Content-Encoding: gzip after the context has been intercepted by GZipEncoder.
GzipHeaderDecoratorAfterGZipEncoder() - Constructor for class ubic.gemma.rest.providers.GzipHeaderDecoratorAfterGZipEncoder
GZIPs - Annotation Interface in ubic.gemma.rest.annotations: Container for repeated GZIP declarations.

H

H2Dialect - Class in ubic.gemma.persistence.hibernate: H2 dialect override for Gemma tests.
H2Dialect() - Constructor for class ubic.gemma.persistence.hibernate.H2Dialect
H5AD - Enum constant in enum class ubic.gemma.core.loader.expression.cellxgene.FileType
H5Attribute - Class in ubic.gemma.core.loader.util.hdf5: Represents an HDF5 attribute.
H5Dataset - Class in ubic.gemma.core.loader.util.hdf5: Represents an HDF5 dataset.
H5Dataset.H5Dataspace - Class in ubic.gemma.core.loader.util.hdf5: Represents a dataspace selection of a H5Dataset.
H5Exception - Exception Class in ubic.gemma.core.loader.util.hdf5
H5Exception(HDF5Exception) - Constructor for exception class ubic.gemma.core.loader.util.hdf5.H5Exception
H5File - Class in ubic.gemma.core.loader.util.hdf5
H5FundamentalType - Enum Class in ubic.gemma.core.loader.util.hdf5: Represents all the fundamental H5 types from which all other types are derived.
H5Group - Class in ubic.gemma.core.loader.util.hdf5
H5Location - Class in ubic.gemma.core.loader.util.hdf5: Represents a location which is either a H5File or a H5Group.
H5Location(long) - Constructor for class ubic.gemma.core.loader.util.hdf5.H5Location
H5Type - Class in ubic.gemma.core.loader.util.hdf5
H5Utils - Class in ubic.gemma.core.loader.util.hdf5
H5Utils() - Constructor for class ubic.gemma.core.loader.util.hdf5.H5Utils
handleGeneProductChangedGIs(Gene, Map) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneWriteService: Handle NCBI-GI rotations for the products of an existing gene.
handleGeneProductChangedGIs(Gene, Map) - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl
hasAnalysis(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService
hasAnalysis(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
hasAnnotation - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Relates a FactorValue to one of its annotation which can be either a subject or an object of one if its Statement or its measurement.
hasAnyOption(CommandLine, String...) - Static method in class ubic.gemma.cli.util.OptionsUtils: Check if any of the given options is present in the command line.
hasAnyValue(Characteristic, Value...) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Check if the given characteristic has any of the specified values.
hasAttribute(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
hasAttribute(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location: Check if an attribute exists.
hasAttribute(String, String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location: Check if an attribute for a given path exists.
hasBatchInformation() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails: Indicate if the batch information is present.
hasBrowser(ExpressionExperiment) - Method in interface ubic.gemma.core.visualization.cellbrowser.CellBrowserService: Check if a particular ExpressionExperiment has a Cell Browser dataset configured.
hasBrowser(ExpressionExperiment) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserServiceImpl
hasCategory(Characteristic, Category) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Check if a given characteristics has a specific category.
hasColNames() - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
hasColNames() - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Check if this matrix has a valid set of column names.
hasData() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
hasErrorObjects() - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter: Indicate if error objects have been reported.
hasEvent(Auditable, Class) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
hasEvent(Auditable, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
hasEvidence() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssertion
hasFullRank() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition: Returns whether the matrix A has full rank.
hash(String, String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Hash an ontology term.
hash(Identifiable...) - Static method in class ubic.gemma.persistence.util.IdentifiableUtils: Hash identifiables in a proxy-safe way using their IDs.
hashBlatResult(BlatResult) - Static method in class ubic.gemma.core.analysis.sequence.ProbeMapUtils: Compute a hash for the result based only on the characteristics of the alignment (that is, not the Id)
hashBlatResult(BlatResultValueObject) - Static method in class ubic.gemma.core.analysis.sequence.ProbeMapUtils: Compute a hash for the result based only on the characteristics of the alignment (that is, not the Id)
hashCode() - Method in class ubic.gemma.cli.batch.BatchTaskProcessingResult
hashCode() - Method in class ubic.gemma.cli.completion.CompletionSource.Completion
hashCode() - Method in class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator.CommandMeta
hashCode() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
hashCode() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.RunMetrics
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat
hashCode() - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat
hashCode() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket
hashCode() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig
hashCode() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
hashCode() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
hashCode() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
hashCode() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
hashCode() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
hashCode() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
hashCode() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
hashCode() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
hashCode() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig
hashCode() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic
hashCode() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleContactMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
hashCode() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraBase
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackageSet
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExternalId
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFiles
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPlatform
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPool
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
hashCode() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
hashCode() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
hashCode() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
hashCode() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
hashCode() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
hashCode() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
hashCode() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
hashCode() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
hashCode() - Method in class ubic.gemma.core.loader.util.mapper.EntityMapper.MappingStatistics
hashCode() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound
hashCode() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.Annotation
hashCode() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
hashCode() - Method in record class ubic.gemma.core.ontology.lexical.LexicalOntologyIndex.Hit: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTerm: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata.Taxon: Returns a hash code value for this object.
hashCode() - Method in class ubic.gemma.core.ontology.model.OntologyXref
hashCode() - Method in class ubic.gemma.core.ontology.ols.OlsTerm
hashCode() - Method in class ubic.gemma.core.ontology.search.OntologySearchResult
hashCode() - Method in class ubic.gemma.core.ontology.simple.AbstractOntologyResourceSimple
hashCode() - Method in class ubic.gemma.core.ontology.simple.OntologyStatementSimple
hashCode() - Method in class ubic.gemma.core.pipeline.JobSnapshot
hashCode() - Method in class ubic.gemma.core.pipeline.SchedulerHandle
hashCode() - Method in class ubic.gemma.core.pipeline.SubmitRequest
hashCode() - Method in class ubic.gemma.core.search.SearchContext
hashCode() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
hashCode() - Method in class ubic.gemma.core.security.acl.domain.AclEntry: Note that this does not use the ID, to avoid getting duplicate entries.
hashCode() - Method in class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
hashCode() - Method in class ubic.gemma.core.security.acl.domain.AclImpl
hashCode() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity: Important so caching operates properly.
hashCode() - Method in class ubic.gemma.core.security.acl.domain.AclPrincipalSid
hashCode() - Method in record class ubic.gemma.core.security.audit.AuditEventPayload.None: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.DifferentialExpressionAnalysisPayload: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.ReleaseDetailsUpdatePayload: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.SampleRemovalPayload: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload: Returns a hash code value for this object.
hashCode() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellSubSetsCreatedPayload: Returns a hash code value for this object.
hashCode() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterService.LintResult
hashCode() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
hashCode() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
hashCode() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
hashCode() - Method in class ubic.gemma.core.util.locking.FileLockInfo
hashCode() - Method in record class ubic.gemma.core.util.runtime.CpuInfo: Returns a hash code value for this object.
hashCode() - Method in class ubic.gemma.core.util.runtime.FileLockInfo
hashCode() - Method in record class ubic.gemma.core.util.runtime.MemInfo: Returns a hash code value for this object.
hashCode() - Method in class ubic.gemma.core.util.SimpleDownloader.URLAndDestination
hashCode() - Method in class ubic.gemma.core.util.SimpleRetryContext
hashCode() - Method in class ubic.gemma.core.util.SimpleRetryPolicy
hashCode() - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject
hashCode() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix: Returns a hash code based on this entity's identifiers.
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.Baseline
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.Contrast
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize: Returns a hash code based on this entity's identifiers.
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
hashCode() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
hashCode() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector: Returns a hash code based on this entity's identifiers.
hashCode() - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
hashCode() - Method in class ubic.gemma.model.analysis.ProtocolValueObject
hashCode() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
hashCode() - Method in class ubic.gemma.model.association.Gene2GOAssociation
hashCode() - Method in class ubic.gemma.model.association.ReferenceAssociation
hashCode() - Method in class ubic.gemma.model.common.AbstractDescribable: The default hash code for a describable is based on its name, ignoring case.
hashCode() - Method in class ubic.gemma.model.common.AbstractIdentifiable: Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
hashCode() - Method in record class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject.LastEventTriple: Returns a hash code value for this object.
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition: Constant, deliberately — the same choice, for the same reasons, as AnnotationSetTriage.hashCode().
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage: Constant, deliberately.
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision: Constant, deliberately — the same choice, for the same reasons, as AnnotationSetTriage.hashCode(): hashing the business key would mean hashing a LAZY proxy, and an id-based hash moves the object between buckets when it is persisted.
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.User
hashCode() - Method in class ubic.gemma.model.common.BaseValueObject
hashCode() - Method in class ubic.gemma.model.common.description.AnnotationRelation: Constant, deliberately.
hashCode() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
hashCode() - Method in class ubic.gemma.model.common.description.BibRefAnnotation
hashCode() - Method in class ubic.gemma.model.common.description.Category
hashCode() - Method in class ubic.gemma.model.common.description.Characteristic: Constant, deliberately.
hashCode() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
hashCode() - Method in class ubic.gemma.model.common.description.CitationValueObject
hashCode() - Method in class ubic.gemma.model.common.description.DatabaseEntry
hashCode() - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
hashCode() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
hashCode() - Method in class ubic.gemma.model.common.description.PublicationAssociation
hashCode() - Method in class ubic.gemma.model.common.description.Value
hashCode() - Method in class ubic.gemma.model.common.IdentifiableValueObject
hashCode() - Method in class ubic.gemma.model.common.measurement.Measurement
hashCode() - Method in class ubic.gemma.model.common.measurement.Unit
hashCode() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
hashCode() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
hashCode() - Method in class ubic.gemma.model.common.search.SearchResult
hashCode() - Method in class ubic.gemma.model.common.search.SearchResultValueObject
hashCode() - Method in class ubic.gemma.model.common.search.SearchSettings
hashCode() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
hashCode() - Method in class ubic.gemma.model.expression.arrayDesign.AlternateName
hashCode() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
hashCode() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject
hashCode() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
hashCode() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
hashCode() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector: Returns a hash code based on this entity's identifiers.
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject
hashCode() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
hashCode() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
hashCode() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject
hashCode() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef
hashCode() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
hashCode() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef
hashCode() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef
hashCode() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
hashCode() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
hashCode() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
hashCode() - Method in record class ubic.gemma.model.expression.experiment.ExpressionExperimentIdAndShortName: Returns a hash code value for this object.
hashCode() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject
hashCode() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
hashCode() - Method in class ubic.gemma.model.expression.experiment.FactorValue
hashCode() - Method in class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
hashCode() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
hashCode() - Method in class ubic.gemma.model.expression.experiment.Geeq
hashCode() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
hashCode() - Method in class ubic.gemma.model.expression.experiment.PreboardedExperiment
hashCode() - Method in class ubic.gemma.model.expression.experiment.Statement: Constant, and the SAME constant Characteristic.hashCode() returns.
hashCode() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
hashCode() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
hashCode() - Method in class ubic.gemma.model.genome.Chromosome
hashCode() - Method in class ubic.gemma.model.genome.gene.GeneAlias
hashCode() - Method in class ubic.gemma.model.genome.gene.GeneProduct
hashCode() - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject
hashCode() - Method in class ubic.gemma.model.genome.gene.GeneSetMember
hashCode() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
hashCode() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
hashCode() - Method in class ubic.gemma.model.genome.gene.GOGroupValueObject
hashCode() - Method in class ubic.gemma.model.genome.gene.Multifunctionality
hashCode() - Method in class ubic.gemma.model.genome.PhysicalLocation
hashCode() - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
hashCode() - Method in class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
hashCode() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
hashCode() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
hashCode() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
hashCode() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
hashCode() - Method in class ubic.gemma.model.genome.Taxon
hashCode() - Method in class ubic.gemma.model.pipeline.PipelineJob
hashCode() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
hashCode() - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
hashCode() - Method in class ubic.gemma.model.util.UninitializedCollection
hashCode() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLock
hashCode() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
hashCode() - Method in record class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao.BioSequenceLite: Returns a hash code value for this object.
hashCode() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
hashCode() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm
hashCode() - Method in class ubic.gemma.persistence.util.Cursor
hashCode() - Method in class ubic.gemma.persistence.util.FactorValueVector
hashCode() - Method in class ubic.gemma.persistence.util.Filter
hashCode() - Method in class ubic.gemma.persistence.util.Filters
hashCode() - Method in class ubic.gemma.persistence.util.Sort
hashCode() - Method in class ubic.gemma.persistence.util.Subquery.Alias
hashCode() - Method in class ubic.gemma.persistence.util.Subquery
hashCode() - Method in class ubic.gemma.rest.AdminWebService.ReindexAcceptedResponse
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationCategoryValueObject
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.LexicalTermMetadataValueObject
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSimpleValueObject
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSynonymValueObject
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonConstraintValueObject
hashCode() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonValueObject
hashCode() - Method in class ubic.gemma.rest.AuthWebService.LoginResponse
hashCode() - Method in class ubic.gemma.rest.CompletionsWebService.CompletionValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.BatchEffectStatisticsValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetMetadataFileValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.EntityRef
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject.Fit
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermRef
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject.Row
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.RunQcMetricsValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.Section
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.SequencingQcMetricsValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.SimpleSVDValueObject
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
hashCode() - Method in class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject
hashCode() - Method in class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject
hashCode() - Method in class ubic.gemma.rest.GeneWebService.GeneDifferentialExpressionGroupValueObject
hashCode() - Method in class ubic.gemma.rest.GoTermsWebService.GoTermGeneCountValueObject
hashCode() - Method in class ubic.gemma.rest.monitoring.HealthWebService.ComponentValueObject
hashCode() - Method in class ubic.gemma.rest.monitoring.HealthWebService.HealthValueObject
hashCode() - Method in class ubic.gemma.rest.monitoring.InfoWebService.BuildBlock
hashCode() - Method in class ubic.gemma.rest.monitoring.InfoWebService.InfoValueObject
hashCode() - Method in class ubic.gemma.rest.monitoring.InfoWebService.JavaBlock
hashCode() - Method in class ubic.gemma.rest.monitoring.InfoWebService.OsBlock
hashCode() - Method in class ubic.gemma.rest.monitoring.InfoWebService.UptimeBlock
hashCode() - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject
hashCode() - Method in class ubic.gemma.rest.RootWebService.UserValueObject
hashCode() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
hashCode() - Method in class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
hashCode() - Method in class ubic.gemma.rest.util.args.SortArg.Sort
hashCode() - Method in class ubic.gemma.rest.util.BuildInfoValueObject
hashCode() - Method in class ubic.gemma.rest.util.ResponseErrorObject
hashCode() - Method in class ubic.gemma.rest.util.Sendfile
hashCode() - Method in class ubic.gemma.rest.util.SortValueObject
hashCode() - Method in class ubic.gemma.rest.util.WellComposedError
hashCode() - Method in class ubic.gemma.rest.util.WellComposedErrorBody
hashCode() - Method in class ubic.gemma.rest.util.WellComposedWarning
hashCode(Object) - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
hashCode(List) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
hashSeeds(Collection) - Static method in class ubic.gemma.core.ontology.providers.OntologySlimMeta: SHA-256 over the sorted seed list.
hasInteraction() - Method in interface ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult: Indicate if this two-way ANOVA result has an interaction effect.
hasInteractions() - Method in interface ubic.gemma.core.util.math.linearmodels.GenericAnovaResult
hasIntercept() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
hasMeasurement - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Relates a FactorValue to its measurement.
hasMissingValues() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
hasMissingValues() - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
hasMissingValues() - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix
hasMissingValues() - Method in class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
hasMissingValues() - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
hasMissingValues() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
hasMissingValues() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
hasMissingValues() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
hasMissingValues() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
hasMissingValues() - Method in class ubic.gemma.core.util.matrix.AbstractMatrix: Test for the presence of missing values (null, or in the case of numbers, NaN)
hasOption(CommandLine, String, Predicate) - Static method in class ubic.gemma.cli.util.OptionsUtils: Check if an option is present, and if so make sure that the predicate is satisfied.
hasPermission(Acl, List) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
hasPermission(Acl, List) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProvider
hasPermission(Acl, List) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProvider
hasPermission(Acl, List) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCollectionFilteringProvider
hasPermission(Acl, List) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationOwnedCollectionFilteringProvider
hasPermission(Acl, List) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationPrivateCollectionFilteringProvider
hasPermission(Authentication, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProvider
hasPermission(Authentication, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider: Deprecated.
use AclEntryAfterInvocationCollectionFilteringProvider.hasPermission(Authentication, List) instead to benefit from bulk-loading of ACLs
hasPermission(Authentication, Object) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProvider
hasPermission(Authentication, Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationByAssociationFilteringProvider
hasPermission(Authentication, Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCollectionFilteringProvider: Deprecated.
use AclEntryAfterInvocationCollectionFilteringProvider.hasPermission(Authentication, List) instead to benefit from bulk-loading of ACLs
hasPermission(Authentication, Object) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectReadProvider
hasPermission(Authentication, List) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProvider: Save time by getting the associated (parent) domain objects.
hasPermission(Authentication, List) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider: Bulk-processing version of AclEntryAfterInvocationCollectionFilteringProvider.hasPermission(Authentication, Object).
hasPermission(Authentication, List) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProvider
hasPermission(Authentication, List) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationByAssociationCollectionFilteringProvider: Save time by getting the associated (parent) domain objects.
hasPermission(Authentication, List) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCollectionFilteringProvider: Bulk-processing version of AclEntryAfterInvocationCollectionFilteringProvider.hasPermission(Authentication, Object).
hasPermission(Authentication, List) - Method in class ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectCollectionReadProvider
hasProblematicBatchInformation() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails: Indicate if the batch information is present, but problematic.
hasProcessedExpressionData(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Test if the dataset has preferred expression data vectors.
hasProcessedExpressionData(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
hasProcessedExpressionData(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Test if the given experiment has processed data vectors.
hasProcessedExpressionData(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
hasRecordedEvidence(JsonNode) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Whether a supporting-evidence payload actually records something — i.e.
hasRepresentation - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Relates a Measurement to its representation.
hasResiduals() - Method in interface ubic.gemma.core.util.math.linearmodels.AnovaResult
hasResultType(Class) - Method in class ubic.gemma.model.common.search.SearchSettings: Check if this is configured to search a given result type.
hasRole - Static variable in class ubic.gemma.core.ontology.jena.RO: RO:0000087 "has role" — links a chemical (or other material entity) to a role it bears.
hasRow(R) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
hasRow(R) - Method in interface ubic.gemma.core.util.matrix.Matrix2D
hasRowNames() - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
hasRowNames() - Method in interface ubic.gemma.core.util.matrix.Matrix2D
hasScreeningResult() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTargetStatusRequest: True once the JSON carried a screeningResult key, even if its value was null.
hasScreeningResultReason() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTargetStatusRequest: True once the JSON carried a screeningResultReason key, even if its value was null.
hasSignificantBatchConfound(BioAssaySet) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService: Check if a given BioAssaySet has a significant batch confound.
hasSignificantBatchConfound(BioAssaySet) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
hasSignificantBatchConfound(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService: Check if a given experiment has a significant batch confound.
hasSignificantBatchConfound(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl
hasSingleCellData(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector: Detection is not supported at the sample level.
hasSingleCellData(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
hasSingleCellData(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.LoomSingleCellDetector
hasSingleCellData(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
hasSingleCellData(GeoSample) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Indicate if the given GEO sample has single-cell data.
hasSingleCellData(GeoSample, boolean) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector: Check if a GEO sample contains single-cell data.
hasSingleCellData(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector
hasSingleCellData(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Detects if a GEO series has single-cell data either at the series-level or in individual samples.
hasSingleCellData(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector: Indicate if the given GEO series has single-cell data.
hasSingleCellData(GeoSeries) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Indicate if the given GEO series has single-cell data.
hasSingleCellData(GeoSeries, GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
hasSingleCellData(GeoSeries, GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector: Check if a sample contains single-cell data in the context of its series.
hasSingleCellData(GeoSeries, GeoSample) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SeriesAwareSingleCellDetector
hasSingleCellDataInCellXGene(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO series has single-cell data in CELLxGENE.
hasSingleCellDataInCellXGene(GeoSeries, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO series has single-cell data in CELLxGENE.
hasSingleCellDataInSeries(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO series has single-cell data at the series-level.
hasSingleCellDataInSeries(GeoSeries, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO series has single-cell data at the series-level.
hasSingleCellDataInSra(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO sample has single-cell data in SRA.
hasSingleCellDataInSra(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO series has single-cell data in SRA.
hasSingleCellDataInSra(GeoSeries, Collection, Collection) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
hasSingleCellQuantitationTypes(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Indicate if the given experiment has single-cell quantitation types.
hasSingleCellQuantitationTypes(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
hasSingletonBatches() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails: Indicate if the dataset has one or more singleton batches (i.e.
hasSize() - Element in annotation interface ubic.gemma.model.annotations.MayBeUninitialized: Indicate that the collection may be uninitialized but always has a size.
hasSourceMetadata(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Whether a source metadata document is stored for this experiment.
hasSourceMetadata(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
hasSourceMetadata(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
hasSourceMetadata(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
hasSubject(Statement, Characteristic) - Static method in class ubic.gemma.model.expression.experiment.StatementUtils: Test if the given statement has the given subject.
hasSvd(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService: Check if a dataset has a SVD analysis.
hasSvd(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
hasUninformativeBatchInformation() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails: Indicate if the batch information is present, but uninformative.
hasUnit - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Relates a Measurement to its unit, if any.
hasUsableData() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
hasValue - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Relates a Measurement to its value.
hasValue(Characteristic, Value) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Check if the given characteristic has a particular value.
HDA - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Direct Assay (HDA)
HEADER - Static variable in class ubic.gemma.cli.util.HelpUtils
HEADER - Static variable in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
HEADERS - Enum constant in enum class ubic.gemma.rest.util.LocationType
HealthIndicator - Interface in ubic.gemma.rest.monitoring.health: Single-method contract for a component health probe used by the /rest/v2/health endpoint.
HealthResult - Class in ubic.gemma.rest.monitoring.health: Outcome of a HealthIndicator.check() call: a UP/DOWN status plus an ordered map of detail key-value pairs (e.g.
HealthResult.Status - Enum Class in ubic.gemma.rest.monitoring.health
HealthValueObject(String, Map) - Constructor for class ubic.gemma.rest.monitoring.HealthWebService.HealthValueObject
HealthWebService - Class in ubic.gemma.rest.monitoring: Aggregated process-health endpoint at /rest/v2/health.
HealthWebService(List) - Constructor for class ubic.gemma.rest.monitoring.HealthWebService
HealthWebService.ComponentValueObject - Class in ubic.gemma.rest.monitoring
HealthWebService.HealthValueObject - Class in ubic.gemma.rest.monitoring
heap - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse
Heatmap - Interface in ubic.gemma.core.visualization: Minimal interface for a labelled heatmap.
HeatmapDataService - Class in ubic.gemma.rest: Assembles HeatmapDataValueObject payloads for the GET /datasets/{id}/heatmap-data endpoint.
HeatmapDataService() - Constructor for class ubic.gemma.rest.HeatmapDataService
HeatmapDataValueObject - Class in ubic.gemma.rest: Wire payload for GET /datasets/{id}/heatmap-data.
HeatmapDataValueObject() - Constructor for class ubic.gemma.rest.HeatmapDataValueObject
HeatmapDataValueObject.ColumnMeta - Class in ubic.gemma.rest
HeatmapDataValueObject.FactorEntry - Class in ubic.gemma.rest: One ExperimentalFactorValueObject plus, for continuous factors, the per-sample measurement map (keyed by bioAssayId).
HeatmapDataValueObject.GeneRef - Class in ubic.gemma.rest: Compact gene reference: official symbol + full name + Gemma ID + NCBI gene ID.
HeatmapDataValueObject.MatrixSection - Class in ubic.gemma.rest
HeatmapDataValueObject.RowMeta - Class in ubic.gemma.rest
HelpUtils - Class in ubic.gemma.cli.util
HelpUtils() - Constructor for class ubic.gemma.cli.util.HelpUtils
HEP - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Expression Pattern (HEP)
HGI - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Genetic Interaction (HGI)
HI_C - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
Hibernate4Metrics - Class in ubic.gemma.core.metrics.binder.jpa: Metrics for Hibernate 4.
Hibernate4Metrics(SessionFactory, String, Iterable) - Constructor for class ubic.gemma.core.metrics.binder.jpa.Hibernate4Metrics: Create a HibernateMetrics.
Hibernate4QueryMetrics - Class in ubic.gemma.core.metrics.binder.jpa: Query metrics for Hibernate 4.
Hibernate4QueryMetrics(SessionFactory, String, Iterable) - Constructor for class ubic.gemma.core.metrics.binder.jpa.Hibernate4QueryMetrics: Create a HibernateQueryMetrics.
HibernateConfig - Class in ubic.gemma.persistence.hibernate: Renovations Phase 3: Java-config replacement for applicationContext-hibernate.xml.
HibernateConfig() - Constructor for class ubic.gemma.persistence.hibernate.HibernateConfig
HibernateSearchException - Exception Class in ubic.gemma.core.search.source: Wraps a Hibernate Search runtime exception in a checked SearchException.
HibernateSearchException(String, SearchException) - Constructor for exception class ubic.gemma.core.search.source.HibernateSearchException
HibernateSearchSource - Class in ubic.gemma.core.search.source: Search source backed by Hibernate Search 7's local-Lucene backend.
HibernateSearchSource() - Constructor for class ubic.gemma.core.search.source.HibernateSearchSource
HibernateSessionFactoryBean - Class in ubic.gemma.persistence.hibernate: Spring FactoryBean that builds a Hibernate SessionFactory using Hibernate's native Configuration bootstrap (not JPA).
HibernateSessionFactoryBean() - Constructor for class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
HibernateStatsResponse() - Constructor for class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
HibernateUtils - Class in ubic.gemma.persistence.hibernate: Pre-phase-2 this class did deep Hibernate-internal introspection (ClassMetadata, AbstractEntityPersister, reflective field access for batchSize and eager).
HibernateUtils() - Constructor for class ubic.gemma.persistence.hibernate.HibernateUtils
HIGH - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketPriority
highExpressionCut() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the highExpressionCut record component.
highlight(String, String) - Method in class ubic.gemma.core.search.DefaultHighlighter
highlight(String, String) - Method in interface ubic.gemma.core.search.Highlighter: Produce a highlight for a given field.
Highlighter - Interface in ubic.gemma.core.search: Custom highlighter for search results.
highlightTerm(String, String, String) - Method in class ubic.gemma.core.search.DefaultHighlighter
highlightTerm(String, String, String) - Method in interface ubic.gemma.core.search.OntologyHighlighter: Produce a highlight for a given ontology term.
highlightTerm(Highlighter, String, String, String) - Method in class ubic.gemma.core.search.source.OntologySearchSource
HikariCPMetrics - Class in ubic.gemma.core.metrics.binder.database
HikariCPMetrics(HikariDataSource) - Constructor for class ubic.gemma.core.metrics.binder.database.HikariCPMetrics
HintingEntityMapper<T> - Interface in ubic.gemma.core.loader.util.mapper: Interface for mappers that can provide hints of identifier candidates.
Histogram - Class in ubic.gemma.core.util.math.distribution: A simple histogram.
Histogram(String, int, double, double) - Constructor for class ubic.gemma.core.util.math.distribution.Histogram
Histogram(String, int, DoubleMatrix1D) - Constructor for class ubic.gemma.core.util.math.distribution.Histogram
history - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowStateResponse
historyFor(AnnotationSet, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionService: Every ruling on one finding, most recent first.
historyFor(AnnotationSet, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionServiceImpl
historyForKey(Investigation, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionService: Every decision on one key, most recent first.
historyForKey(Investigation, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionServiceImpl
hit(String) - Static method in class ubic.gemma.core.geoscrape.GeoRecordMatcher.MatchResult
Hit(String, double) - Constructor for record class ubic.gemma.core.ontology.lexical.LexicalOntologyIndex.Hit: Creates an instance of a Hit record class.
HitListSize - Class in ubic.gemma.model.analysis.expression.diff: The number of probes meeting a given q-value threshold in the result set.
HitListSize() - Constructor for class ubic.gemma.model.analysis.expression.diff.HitListSize
HitListSize.Factory - Class in ubic.gemma.model.analysis.expression.diff
hitPercentage - Variable in class ubic.gemma.rest.AdminWebService.CacheStatRow: Percentage in [0, 100]; null if stats unavailable or never queried.
hits - Variable in class ubic.gemma.rest.AdminWebService.CacheStatRow
HMP - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Mutant Phenotype (HMP)
HomeStats - Class in ubic.gemma.core.analysis.report: Cached snapshot of public-home-page statistics.
HomeStats() - Constructor for class ubic.gemma.core.analysis.report.HomeStats
HomeStats.AccessionSourceStat - Class in ubic.gemma.core.analysis.report
HomeStats.AddedInWindow - Class in ubic.gemma.core.analysis.report: Count of public experiments created within one trailing window.
HomeStats.CategoryStat - Class in ubic.gemma.core.analysis.report
HomeStats.FactorValueCategoryStat - Class in ubic.gemma.core.analysis.report
HomeStats.PerturbedGeneStat - Class in ubic.gemma.core.analysis.report
HomeStats.RecentExperiment - Class in ubic.gemma.core.analysis.report
HomeStats.TaxonStat - Class in ubic.gemma.core.analysis.report
HomeStats.TermStat - Class in ubic.gemma.core.analysis.report: A single annotation term with its EE-mention count — used inside HomeStats.TreatmentBucketStat.topTerms for the catchall-iteration loop.
HomeStats.TreatmentBucketStat - Class in ubic.gemma.core.analysis.report
HomeStatsRefresher - Class in ubic.gemma.core.analysis.report: Refreshes HomeStats on a daily cron AND on every Spring context refresh (startup).
HomeStatsRefresher() - Constructor for class ubic.gemma.core.analysis.report.HomeStatsRefresher
HomeStatsService - Interface in ubic.gemma.core.analysis.report: Read + refresh the cached public home-page statistics snapshot.
HomeStatsServiceImpl - Class in ubic.gemma.core.analysis.report: Computes + caches the public home-page statistics snapshot.
HomeStatsServiceImpl() - Constructor for class ubic.gemma.core.analysis.report.HomeStatsServiceImpl
HomologeneConfig - Class in ubic.gemma.core.loader.genome.gene.ncbi.homology
HomologeneConfig() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneConfig
HomologeneFetcher - Class in ubic.gemma.core.loader.genome.gene.ncbi.homology: Grabs urls like ftp:///ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data
HomologeneFetcher() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher
homologeneService(GeneService, TaxonReadService) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneConfig
HomologeneService - Interface in ubic.gemma.core.loader.genome.gene.ncbi.homology
HomologeneServiceImpl - Class in ubic.gemma.core.loader.genome.gene.ncbi.homology: Reads in the homologene list as specified in the Gemmea.properties file.
HomologeneServiceImpl(GeneService, TaxonReadService, Resource) - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl
How many factors and tags an annotation-set payload proposes. - Section in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCounts
How the username is supplied - Section in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder
HTML - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoFormat
HTP - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Experiment (HTP)
httpAccessDecisionManager(RoleHierarchyVoter) - Method in class ubic.gemma.rest.security.RestSecurityConfig: Legacy AccessDecisionManager bean carried over from the gemma-web XML.
HttpFetcher - Class in ubic.gemma.core.loader.util.fetcher: A generic class for fetching files via HTTP and writing them to a local file system.
HttpFetcher() - Constructor for class ubic.gemma.core.loader.util.fetcher.HttpFetcher
httpStatus - Variable in class ubic.gemma.rest.AdminWebService.CurationAgentHealthResponse: HTTP status code from the upstream service; 0 when the request didn't complete.
HUMAN - Enum constant in enum class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat.BlattableGenome
HumanDevelopmentOntologyService - Class in ubic.gemma.core.ontology.providers: Deprecated.
this ontology was last updated in unmaintained since 2013
HumanDevelopmentOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.HumanDevelopmentOntologyService: Deprecated.
HumanPhenotypeOntologyService - Class in ubic.gemma.core.ontology.providers: Human Phenotype Ontology
HumanPhenotypeOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.HumanPhenotypeOntologyService
humanPhenotypeOntologyServiceOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig

I

IAGP - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from association of genotype and phenotype (RGD code)
IAO - Class in ubic.gemma.core.ontology.jena
IAO() - Constructor for class ubic.gemma.core.ontology.jena.IAO
IBA - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: A type of phylogenetic evidence whereby an aspect of a descendant is inferred through the characterization of an aspect of a ancestral gene.
IBD - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
IC - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
id - Variable in class ubic.gemma.model.common.IdentifiableValueObject
id - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
id - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
id - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
id - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse
id - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageResponse
id - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
id() - Method in record class ubic.gemma.model.expression.experiment.ExpressionExperimentIdAndShortName: Returns the value of the id record component.
ID - Enum constant in enum class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao.SummarySort
IDA - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
Identifiable - Interface in ubic.gemma.model.common: Interface for objects that have a numerical id.
IdentifiableUtils - Class in ubic.gemma.persistence.util: Utilities for Identifiable.
IdentifiableUtils() - Constructor for class ubic.gemma.persistence.util.IdentifiableUtils
IdentifiableValueObject<O> - Class in ubic.gemma.model.common: Base implementations for value objects representing persistent objects
IdentifiableValueObject() - Constructor for class ubic.gemma.model.common.IdentifiableValueObject: Default empty constructor for bean-style initialization.
IdentifiableValueObject(Long) - Constructor for class ubic.gemma.model.common.IdentifiableValueObject: Constructor that sets the common property of all identifiable objects, the ID.
IdentifiableValueObject(O) - Constructor for class ubic.gemma.model.common.IdentifiableValueObject: Constructor for a given entity.
IdentifiableValueObject(IdentifiableValueObject) - Constructor for class ubic.gemma.model.common.IdentifiableValueObject: Copy constructor.
identifier - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject: Stable, space-free handle for this ontology — its well-known abbreviation when it has one (CLO, HPO, TGEMO, …), otherwise its cache name.
Identifiers() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
identify(String) - Method in interface ubic.gemma.core.ontology.chembl.ChemblCodeResolver: Identify a code against ChEMBL.
identify(String) - Method in class ubic.gemma.core.ontology.chembl.ChemblCodeResolverImpl
identifyingMetadata - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
identifyingMetadata - Variable in class ubic.gemma.rest.PreboardedWebService.CreatePreboardedRequest
identifyingMetadata - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
identifyOutliersByMedianCorrelation(DoubleMatrix) - Method in interface ubic.gemma.core.analysis.preprocess.OutlierDetectionService: Identify outliers by sorting by median, then looking for non-overlap of first quartile-second quartile range This is exposed for efficiency in geeq score calculation, use this#identifyOutliers(ExpressionExperiment, boolean, boolean) to have the correlation matrix computed correctly for you.
identifyOutliersByMedianCorrelation(DoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceImpl
identifyOutliersByMedianCorrelation(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.OutlierDetectionService: Identify outliers by median correlation for the given dataset.
identifyOutliersByMedianCorrelation(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceImpl
identity(BlatResult) - Static method in class ubic.gemma.core.analysis.sequence.BlatAssociationScorer: Fraction identity computation, as in psl.c.
idleConnections - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
idleTimeoutMillis - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
ids - Variable in class ubic.gemma.persistence.util.EntityUrlBuilder.SomeEntitiesUrl
IEA - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
IED - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from experimental data (RGD code)
IEEE_F32BE - Static variable in class ubic.gemma.core.loader.util.hdf5.H5Type
IEEE_F64BE - Static variable in class ubic.gemma.core.loader.util.hdf5.H5Type
IEP - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
IGC - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from Genomic Context; This evidence code can be used whenever information about the genomic context of a gene product forms part of the evidence for a particular annotation.
IGI - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
IGNORE_TRANSIENT_SUFFIX - Static variable in class ubic.gemma.core.security.acl.voter.AclEntryVoter: Suffix used by config attributes to ignore transient entities.
IgnoreAcl - Annotation Interface in ubic.gemma.core.security.acl.annotation: Mark a method as ignored for ACL.
ignoreCellTypeFactor(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
ignoreCompatibleCellTypeFactor(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: When re-creating, ignore a compatible cell type factor that may already exist.
ignoreDataVectors(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Skip single-cell data vectors if possible, or at least skip transformation that would normally be applied to them to make them usable.
ignoreErrors(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig.GeoRetrieveConfigBuilder: Ignore errors when retrieving additional information.
ignoreExistingCellTypeAssignment(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: If true, ignore existing cell type assignment with the same name.
ignoreExistingOtherCellLevelCharacteristics(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: If true, ignore existing other CLCs with the same names.
ignoreMinimumDesignElementsThreshold() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the ignoreMinimumDesignElementsThreshold record component.
ignoreMinimumSamplesThreshold() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the ignoreMinimumSamplesThreshold record component.
ignoreSamplesLackingData(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Ignore individual samples that lack or have incomplete data.
ignoreUnmatchedCellIds(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: When parsing SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder.cellTypeAssignmentFile and SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder.otherCellLevelCharacteristicsFile, ignore cell IDs that cannot be matched to a sample.
ignoreUnmatchedCharacteristics(boolean) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExperimentSubSetsCreationConfig.SingleCellExperimentSubSetsCreationConfigBuilder: Whether to allow unmapped characteristics.
ignoreUnmatchedFactorValues(boolean) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExperimentSubSetsCreationConfig.SingleCellExperimentSubSetsCreationConfigBuilder: Whether to allow unmapped factor values.
IIA - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Added by Gemma: Inferred from Imported Annotation.
IKR - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: A type of phylogenetic evidence characterized by the loss of key sequence residues.
IlluminaProbeReader - Class in ubic.gemma.core.loader.expression.arrayDesign: Parse an Illumina "manifest.txt" file (tab-delimited).
IlluminaProbeReader() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
IMP - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
impliesAnInducer(String) - Static method in enum class ubic.gemma.model.common.description.RelationInferenceDirection: Whether this predicate names an INDUCER rather than something that can bear the disease itself.
importDataset(DatasetsWebService.DatasetImportRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI workflow-step endpoint: kick off an async GEO (or ArrayExpress) accession load.
importDesign(ExpressionExperiment, InputStream) - Method in interface ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporter: This is the main builder director method of the application: It processes the input file containing information about the experimental design for a given expression experiment.
importDesign(ExpressionExperiment, InputStream) - Method in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl
importGeoBatch(AdminWebService.ImportGeoBatchRequest) - Method in class ubic.gemma.rest.AdminWebService: Batch GEO accession import.
ImportGeoBatchRequest() - Constructor for class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest
ImportGeoBatchResponse() - Constructor for class ubic.gemma.rest.AdminWebService.ImportGeoBatchResponse
IMR - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from Missing Residues.
in - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
IN - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
IN - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
IN() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
IN_PROGRESS - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketState
IN_PROGRESS - Enum constant in enum class ubic.gemma.model.expression.experiment.GeoScrapeWatermark.Status
INCLUDE - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.ScreeningResult: Admit / accept / act on this target.
includeBioAssays(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder
includeBiologicalCharacteristics(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig.SingleCellVectorInitializationConfigBuilder: Initialize CompositeSequence.getBiologicalCharacteristic().
includeCellIds(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig.SingleCellVectorInitializationConfigBuilder
includeCharacteristics(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder
includeClcs(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder
includeCtas(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder
includeData(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig.SingleCellVectorInitializationConfigBuilder
includeDataIndices(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig.SingleCellVectorInitializationConfigBuilder
IncludedResultSetInfoValueObject - Class in ubic.gemma.model.analysis.expression.diff
IncludedResultSetInfoValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
includeIndices(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder
includeMaskedCellsInLibrarySize(boolean) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder: Include masked cells in the library size calculation.
includeProtocol(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder
includeRefuted(boolean) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery: Also return relations a source states do NOT hold.
incompleteRecords - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeDryRunResponse: Accessions examined on degraded information — GEO served unusable MINiML, so the record was kept on its summary rather than failing the batch.
incrementOccurrenceCount() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
incrementWarnings() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
indeterminateProgress() - Static method in class ubic.gemma.cli.util.AnsiEscapeCodes: Indicate an indeterminate progress.
index(boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
index(boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
index(boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
index(boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Index the ontology for performing full-text searches.
index(Class) - Method in interface ubic.gemma.core.search.indexer.IndexerService: Reindex the given entity class with the default number of loader threads.
index(Class) - Method in class ubic.gemma.core.search.indexer.IndexerServiceImpl
index(Class, int) - Method in interface ubic.gemma.core.search.indexer.IndexerService: Reindex the given entity class with an explicit number of loader threads.
index(Class, int) - Method in class ubic.gemma.core.search.indexer.IndexerServiceImpl
indexBase - Variable in class ubic.gemma.rest.AdminWebService.SearchIndicesResponse: Filesystem root (gemma.search.dir) under which per-entity index dirs live.
IndexerService - Interface in ubic.gemma.core.search.indexer: Drives Hibernate Search 7's mass-indexer (built-in MassIndexer) across the @Indexed entity roots Gemma actually searches.
IndexerServiceImpl - Class in ubic.gemma.core.search.indexer: Drives Hibernate Search 7's MassIndexer for one entity class at a time.
IndexerServiceImpl() - Constructor for class ubic.gemma.core.search.indexer.IndexerServiceImpl
IndexerTask - Interface in ubic.gemma.core.tasks.maintenance: Marker interface for the async mass-indexer task.
IndexerTaskCommand - Class in ubic.gemma.core.tasks.maintenance: Command for the asynchronous mass-indexer task; one boolean per indexable entity root.
IndexerTaskCommand() - Constructor for class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
IndexerTaskImpl - Class in ubic.gemma.core.tasks.maintenance: Asynchronous mass-indexer task.
IndexerTaskImpl() - Constructor for class ubic.gemma.core.tasks.maintenance.IndexerTaskImpl
indexExperimentsTrigger(Object, SecurityContext) - Method in class ubic.gemma.core.config.SchedulerConfig: Every working day at 23:00.
IndexGemmaCLI - Class in ubic.gemma.apps: Build or rebuild the Hibernate Search 7 mass index for one or more entity classes.
IndexGemmaCLI() - Constructor for class ubic.gemma.apps.IndexGemmaCLI
indexName - Variable in class ubic.gemma.rest.AdminWebService.IndexStatusValueObject: Hibernate Search index name (the sub-directory name under indexBase).
indexOf(Object) - Method in class ubic.gemma.core.datastructure.sparse.SparseArrayList
indexOf(Object) - Method in class ubic.gemma.core.datastructure.sparse.SparseRangeArrayList
indexOf(Object) - Method in class ubic.gemma.model.util.UninitializedList
indexOf(T) - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
indexOfAllElements(List) - Static method in class ubic.gemma.core.util.ListUtils
indexOfCaseInsensitiveStringElements(List) - Static method in class ubic.gemma.core.util.ListUtils: Get a case-insensitive mapping of string elements to their first occurrence in a List.
indexOfElements(List) - Static method in class ubic.gemma.core.util.ListUtils: Get a mapping of element to their first occurrence in a List.
indexPath - Variable in class ubic.gemma.rest.AdminWebService.IndexStatusValueObject: Absolute path to the on-disk index directory, or null if gemma.search.dir is unset.
IndexStatusValueObject() - Constructor for class ubic.gemma.rest.AdminWebService.IndexStatusValueObject
indices - Variable in class ubic.gemma.rest.AdminWebService.SearchIndicesResponse
individual - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
infection - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
inferenceMode - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject
inferQuantitationType(ExpressionDataMatrix) - Static method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtils: Infer a QuantitationType from expression data.
InferredQuantitationMismatchException - Exception Class in ubic.gemma.core.analysis.preprocess.detect: Exception raised when the quantitation of an ExpressionDataMatrix does not agree with the one inferred.
InferredQuantitationMismatchException(QuantitationType, QuantitationType, String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.detect.InferredQuantitationMismatchException
inferSamplesFromCellIdsOverlap(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: When parsing SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder.cellTypeAssignmentFile and SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder.otherCellLevelCharacteristicsFile, use the overlap between the cell IDs from the file and those from the SingleCellDimension to infer sample associations.
INFO_UPDATE_INTERVAL - Static variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
InfoValueObject(InfoWebService.BuildBlock, InfoWebService.JavaBlock, InfoWebService.OsBlock, InfoWebService.UptimeBlock) - Constructor for class ubic.gemma.rest.monitoring.InfoWebService.InfoValueObject
InfoWebService - Class in ubic.gemma.rest.monitoring: Discrete process-info endpoint at /rest/v2/info.
InfoWebService(BuildInfo) - Constructor for class ubic.gemma.rest.monitoring.InfoWebService
InfoWebService.BuildBlock - Class in ubic.gemma.rest.monitoring
InfoWebService.InfoValueObject - Class in ubic.gemma.rest.monitoring
InfoWebService.JavaBlock - Class in ubic.gemma.rest.monitoring
InfoWebService.OsBlock - Class in ubic.gemma.rest.monitoring
InfoWebService.UptimeBlock - Class in ubic.gemma.rest.monitoring
inGemma() - Method in class ubic.gemma.persistence.util.Pointcuts: Matches stuff within Gemma package.
init() - Method in class ubic.gemma.core.loader.expression.arrayExpress.util.ArrayExpressUtil
init() - Method in class ubic.gemma.core.loader.expression.geo.util.GeoUtil
init() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIUtil
init() - Method in class ubic.gemma.core.util.NetDatasourceUtil
init() - Method in class ubic.gemma.rest.providers.MetricsApplicationEventListener
init(ColorMatrix) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
initArchiveHandler(String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
initAutomaticallyGeneratedExperimentSet(Collection, Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
initAutomaticallyGeneratedExperimentSet(Collection, Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl: Instantiate non-persistent experiment set with description = "Automatically generated for ## EEs.".
initConfig() - Method in class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.DatasetFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.PlatformFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.SeriesFetcher
initConfig() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher
initConfig() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
initConfig() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonFetcher
initConfig() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
initConfig() - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
initFilterBean() - Method in class ubic.gemma.rest.servlet.CorsFilter
InitialDataPopulator - Class in ubic.gemma.persistence.initialization: Populate some initial data for tests.
InitialDataPopulator(boolean) - Constructor for class ubic.gemma.persistence.initialization.InitialDataPopulator
initializationCancelled - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject
initialize(boolean, boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
initialize(boolean, boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
initialize(boolean, boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
initialize(boolean, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Initialize this ontology service.
initialize(InputStream, boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
initialize(InputStream, boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
initialize(InputStream, boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
initialize(InputStream, boolean) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
initialize(InputStream, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Initialize this ontology service from a stream.
initialize(ConfigurableWebApplicationContext) - Method in class ubic.gemma.rest.context.RestInitializeContext
initializeCachedFilteringResult(O) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao: Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from cache.
initializeCachedFilteringResult(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
initializeCachedFilteringResult(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
initializeCachedFilteringResult(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
initializeCachedFilteringResult(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
initializeCachedFilteringResult(Taxon) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
InitializeDatabaseCli - Class in ubic.gemma.apps: Initialize the database.
InitializeDatabaseCli() - Constructor for class ubic.gemma.apps.InitializeDatabaseCli
initializing - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject: True while the background load thread is alive.
initializingCount - Variable in class ubic.gemma.rest.AdminWebService.OntologiesResponse
initSize() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay: Sets the display size
insertAce(int, Permission, Sid, boolean) - Method in class ubic.gemma.core.security.acl.domain.AclImpl
inSituOligonucleotide - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
inSubquery - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
InsufficientDataException - Exception Class in ubic.gemma.core.analysis.preprocess.filter: Exception raised when there is insufficient data to perform a filtering operation.
InsufficientDataException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException
InsufficientDesignElementsException - Exception Class in ubic.gemma.core.analysis.preprocess.filter: Exception indicating that there is insufficient design elements (rows) to perform a particular filter.
InsufficientDesignElementsException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.filter.InsufficientDesignElementsException
InsufficientSamplesException - Exception Class in ubic.gemma.core.analysis.preprocess.filter: Exception indicating that there are insufficient samples (columns) in the dataset to perform a particular filter.
InsufficientSamplesException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.filter.InsufficientSamplesException
INT - Enum constant in enum class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaFieldType
INT - Enum constant in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType
intArrayToBytes(int[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
intArrayToBytes(int[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
INTEGER - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
IntegerMatrix<R,C> - Class in ubic.gemma.core.util.matrix
IntegerMatrix(int, int) - Constructor for class ubic.gemma.core.util.matrix.IntegerMatrix
interaction(FactorValue, FactorValue) - Static method in class ubic.gemma.model.analysis.expression.diff.Baseline: Create a baseline for an interaction of factors.
interaction(FactorValue, FactorValue) - Static method in class ubic.gemma.model.analysis.expression.diff.Contrast: Create an interaction of two categorical factors.
INTERCEPT_COEFFICIENT_NAME - Static variable in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
INTERIM - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus
INTERNAL_ONLY - Enum constant in enum class ubic.gemma.model.annotations.WithheldFromApi.Reason: The member cannot mean anything to a client, so publishing it would mislead rather than inform.
InternalPipelineWebService - Class in ubic.gemma.rest: Service-to-service push callback for scheduler-side pipelines reporting progress / terminal state.
InternalPipelineWebService() - Constructor for class ubic.gemma.rest.InternalPipelineWebService
InternalPipelineWebService.PostEventRequest - Class in ubic.gemma.rest
interpolate(double[], double[], double[]) - Static method in class ubic.gemma.core.util.math.Smooth: Linearlly interpolate values from a given data set Similar implementation of R's stats.approxfun(..., rule = 2) where values outside the interval ['min(x)', 'max(x)'] get the value at the closest data extreme.
InvalidEncodingAttributeException - Exception Class in ubic.gemma.core.loader.util.anndata: Exception raised when an encoding-type attribute has an unexpected value.
InvalidEncodingAttributeException(String) - Constructor for exception class ubic.gemma.core.loader.util.anndata.InvalidEncodingAttributeException
InvalidQuantitationTypeConversionException - Exception Class in ubic.gemma.core.analysis.expression.diff: Exception raised when a log2 conversion fails.
InvalidQuantitationTypeConversionException(QuantitationTypeConversionException, DifferentialExpressionAnalysisConfig) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.InvalidQuantitationTypeConversionException
inverted() - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
Investigation - Class in ubic.gemma.model.analysis: An abstract concept of a scientific study
Investigation() - Constructor for class ubic.gemma.model.analysis.Investigation
invoke() - Method in class ubic.gemma.core.scheduler.SecureMethodInvokingJobDetailFactoryBean
invokeAll(Collection) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
invokeAll(Collection, long, TimeUnit) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
invokeAny(Collection) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
invokeAny(Collection, long, TimeUnit) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
IPI - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
IPM - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from phenotype manipulation (RGD code)
IRD - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Inferred from Rapid Divergence.
IS_OUTLIER - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssayCategories
ISA - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
isAbortOnError() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Indicate if this CLI should abort on error or move on to the next experiment.
isAccepted() - Method in class ubic.gemma.model.common.description.PublicationAssociation
isAcceptsTargets() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
isAcceptsTargets() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: Whether experiments may be added to this ticket after it was opened.
isAccessDenied() - Method in class ubic.gemma.model.common.BaseValueObject
isAccountNonExpired() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
isAccountNonLocked() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
isActive() - Method in class ubic.gemma.cli.pipeline.PipelineJobReporter
isAdded() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService.TargetAddition: False when the target was already on the ticket.
isAdjustLibrarySizes() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig: Perform adjustment of library sizes to better reflect the number of reads in the source sample.
isAdmin - Variable in class ubic.gemma.rest.AdminWebService.CreateUserRequest: Optional; defaults to false.
isAdmin - Variable in class ubic.gemma.rest.AdminWebService.UpdateUserRequest
isAdmin - Variable in class ubic.gemma.rest.AdminWebService.UserValueObject
isAdvanceLinkedTickets() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
isAffected(String) - Static method in class ubic.gemma.core.util.SymbolFontPua: Whether the text holds any codepoint this class would change.
isAffyControlsFilterApplied() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
isAffymetrixExonArray(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
isAffyPlatform(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
isAggregated(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateService: Check if a particular quantitation type is aggregated.
isAggregated(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl
isAggressiveQtRemoval() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isAllowArrayExpressDesign() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isAllowMappingDesignElementsToGeneSymbols() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig
isAllowPredictedGenes() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isAllowSubSeriesLoad() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isAllowSuperSeriesLoad() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isAlreadyPresentInDatabase() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
isAlreadyPresentOnGene() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
isamax_j(int, double[], int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method finds the index of the element of a vector that has the maximum absolute value.
isAnalyzed(BioMaterial) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Check whether a sample takes part in a differential expression analysis.
isAnnData(DatasetAsset) - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils: Check if the given dataset asset is in AnnData format.
isAnnotationUri(String) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Check if a URI refers to an annotation of a factor value.
isAnyMissing() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
isApplicable(WriterInterceptorContext, GZIP) - Method in class ubic.gemma.rest.providers.AbstractGzipHeaderDecorator: Check if the given GZIP annotation applies to the given context.
isApplicable(WriterInterceptorContext, GZIP) - Method in class ubic.gemma.rest.providers.GzipHeaderDecorator
isApplicable(WriterInterceptorContext, GZIP) - Method in class ubic.gemma.rest.providers.GzipHeaderDecoratorAfterGZipEncoder
isApplied() - Method in class ubic.gemma.model.expression.experiment.DesignApplyOutcome
isApplied() - Method in class ubic.gemma.rest.DatasetsWebService.CurationCommitReport
isApplyFixes() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig: If true, attempt to fix any issues are found.
isArrayExpress - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest
isArrayExpress() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isAssigneeIdSet() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
isAtLeast(SearchSettings.SearchMode) - Method in enum class ubic.gemma.model.common.search.SearchSettings.SearchMode: Check if a search mode is at least as thorough as the given one.
isAtMost(SearchSettings.SearchMode) - Method in enum class ubic.gemma.model.common.search.SearchSettings.SearchMode: Check if a search mode is at most as thorough as the given one.
isAutoCorrectable() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
isAutomaticallyGenerated(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
isAutomaticallyGenerated(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl: Determines if set was automatically generated by matching the description to that used in ubic.gemma.core.analysis.expression .coexpression.ExpressionExperimentSetService.AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION
isAutoSeek() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Indicate if auto-seek is enabled.
isBackgroundChannelA(String) - Static method in class ubic.gemma.persistence.util.ChannelUtils: For two-color arrays: Given the quantitation type name, determine if it represents the channel A background.
isBackgroundChannelB(String) - Static method in class ubic.gemma.persistence.util.ChannelUtils: For two-color arrays: Given the quantitation type name, determine if it represents the channel B background.
isBackgroundSubtracted(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
isBareBcrypt(String) - Static method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder
isBaseline(String) - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary
isBaselineCondition(Characteristic) - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection: Check if a given characteristic indicate a baseline condition.
isBaselineCondition(FactorValue) - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection: Check if a given factor value indicates a baseline condition.
isBaselineCondition(Statement) - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection: Check if a given statement indicates a baseline condition.
isBasicFVs() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Indicate if this is using the BioMaterialValueObject.fVBasicVOs or BioMaterialValueObject.factorValueObjects for representing factor values.
isBasicsChanged() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
isBasicsPresent() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
isBatchCorrected() - Method in class ubic.gemma.model.expression.experiment.Geeq
isBatchCorrected() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
isBatchFactor(ExperimentalFactor) - Static method in class ubic.gemma.model.expression.experiment.ExperimentFactorUtils: Check if a factor is a batch factor.
isBatchFactor(ExperimentalFactorValueObject) - Static method in class ubic.gemma.model.expression.experiment.ExperimentFactorUtils: Check if a given factor VO is a batch factor.
isBiologicalProcess(OntologyTerm) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
isBiologicalProcess(OntologyTerm) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
isBlacklisted(String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
isBlacklisted(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
isBlacklisted(String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
isBlacklisted(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
isBlacklisted(ArrayDesign) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
isBlacklisted(ArrayDesign) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
isBlacklisted(ArrayDesign) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
isBlacklisted(ArrayDesign) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
isBlacklisted(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
isBlacklisted(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
isBlacklisted(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
isBlacklisted(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
isBlackListed(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
isBlackListed(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
isBodySet() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
isCanonical(Chromosome) - Static method in class ubic.gemma.persistence.service.genome.ChromosomeUtils: This method is only familiar with chromosomes as named in the UCSC GoldenPath database and would have to be modified if the 'rules' are broken by some other source used.
isCellIdColumn(Dataframe.Column) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer: Check if the given dataframe column contains cell identifiers.
isCellTypeColumn(Dataframe.Column) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer: Check if a given column contains cell types.
isChecked() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
isChild() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: child term from a root
isCollection() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
isConsumerDone() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
isContiguous(int[]) - Static method in class ubic.gemma.core.util.ArrayUtils
isContinuous() - Method in class ubic.gemma.model.analysis.expression.diff.Contrast: Indicate if this contrast is continuous.
isCorroborated() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject: Whether this row stands on its own.
isCount(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils: Check if a given quantitation type contains counting data.
isCpuSupported() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation: Check if the current CPU supports AVX instruction set required by Cell Ranger.
isCreated() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.AttachedAnnotationSet
isCredentialsNonExpired() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
isCsc() - Method in class ubic.gemma.core.loader.util.anndata.SparseMatrix: Indicate if this matrix is stored in CSC.
isCsNative() - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
isCsr() - Method in class ubic.gemma.core.loader.util.anndata.SparseMatrix: Indicate if this matrix is stored in CSR.
isCurationDetailsPresent() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
isCurationNoteChanged() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
isDataWasBatchCorrected() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
isDeclared() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonConstraintValueObject: Whether the ontology declares an in_taxon constraint for this term.
isDeExcluded(FactorValue) - Static method in class ubic.gemma.model.expression.experiment.FactorValueUtils: Check if a factor value marks its samples for exclusion from differential expression analysis.
isDeIncludeExcludeFactor(ExperimentalFactor) - Static method in class ubic.gemma.model.expression.experiment.ExperimentFactorUtils: Check if a factor exists only to carry the DE_Include/DE_Exclude markers.
isDeIncludeExcludeMarker(FactorValue) - Static method in class ubic.gemma.model.expression.experiment.FactorValueUtils: Check if a factor value is one of the two DE_Include/DE_Exclude markers.
isDense() - Method in class ubic.gemma.core.loader.util.anndata.Layer: Check if the matrix encoded in this layer is dense.
isDeprecated() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta: Indicate if the property is deprecated.
isDesignPresent() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
isDetailsIncomplete() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord: True when the detailed MINiML fetch for this record failed and was tolerated (GeoRetrieveConfig.isIgnoreErrors()), so the record is returned with whatever the eutils summary gave and without sample details.
isDirectory() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
isDirectory() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetMetadataFileValueObject: True when the underlying metadata is organised as a directory; in that case the file cannot be downloaded directly via /metadata/{type} — request a specific sub-type (e.g.
isDoDownload() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
isDone() - Method in class ubic.gemma.core.job.progress.ProgressData
isDone() - Method in interface ubic.gemma.core.job.SubmittedTask
isDryRun() - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
isDryRun() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
isDryRun() - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
isDryRun() - Method in class ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskCommand
isDueDateSet() - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
isDummy() - Method in class ubic.gemma.model.genome.gene.GeneProduct
isEditable() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
isEditableByCurrentUser(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Determine if the current user can edit the securable.
isEditableByCurrentUser(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isEditableByGroup(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService: Determine if the given group is allowed to edit an object.
isEditableByGroup(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isEditableByUser(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService: Determine if the given user is allowed to edit an object.
isEditableByUser(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isEmailAlert() - Method in interface ubic.gemma.core.job.SubmittedTask
isEmailAlert() - Method in class ubic.gemma.core.job.TaskCommand: Should an email be sent to the user when the job is done?
isEmpty() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata
isEmpty() - Method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex
isEmpty() - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap
isEmpty() - Method in class ubic.gemma.model.util.UninitializedCollection
isEmpty() - Method in class ubic.gemma.persistence.util.Filters: Check if this contains an empty conjunction, or if all its clauses are empty.
isEmptyInternal() - Method in class ubic.gemma.core.config.PropertySourcesConfiguration: Deprecated.
isEnableAuthorities() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
isEnabled() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
isEnabled() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
isEnabled() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
isEnabled() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Check if this ontology is enabled.
isEnabled() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
isEnabled() - Method in interface ubic.gemma.core.security.model.User
isEnabled() - Method in class ubic.gemma.model.common.auditAndSecurity.User
isEnabled() - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
isEnabled() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
isEnabled() - Method in class ubic.gemma.rest.GroupsWebService.GroupMemberValueObject
isEnabled() - Method in class ubic.gemma.rest.RootWebService.UserValueObject
isEnableGroups() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
isEndSequenceOf - Static variable in class ubic.gemma.core.ontology.jena.RO
isEntriesInheriting() - Method in class ubic.gemma.core.security.acl.domain.AclImpl
isErrorFound() - Method in class ubic.gemma.model.common.BaseValueObject
isExactIdentifierMatch() - Method in class ubic.gemma.model.common.search.SearchResult: Whether this result was produced by an exact-identifier lookup (numeric id, short name, accession, NCBI id).
isExcludeSampleIdentifiers() - Method in class ubic.gemma.cli.options.ExpressionDataFileOptionValue
isExclusive() - Method in class ubic.gemma.core.util.runtime.FileLockInfo: Indicate if this lock is exclusive.
isExperimentTags() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig
isExpired(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
isExpressed(double, ScaleType) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics: Check if a value is expressed on a given scale.
isExternal() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl: Indicate that the entity will have an external URL generated by EntityUrlBuilder.EntityUrl.external().
isFactorValueUri(String) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils
isFailed() - Method in class ubic.gemma.core.job.progress.ProgressData
isFileOption(Option) - Static method in class ubic.gemma.cli.util.OptionsUtils
isFillResults() - Method in class ubic.gemma.model.common.search.SearchSettings: Indicate if result objects (i.e.
isFilterablePropertyDeprecated(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
isFilterablePropertyDeprecated(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
isFilterablePropertyDeprecated(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
isFilterablePropertyDeprecated(String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Indicate if the given property is deprecated.
isFilterablePropertyDeprecated(String) - Method in interface ubic.gemma.persistence.service.FilteringService
isFilterablePropertyDeprecated(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
isFilterablePropertyDeprecated(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
isFilterablePropertyUsingSubquery(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
isFilterablePropertyUsingSubquery(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
isFilterablePropertyUsingSubquery(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
isFilterablePropertyUsingSubquery(String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Indicate if the given property is using a subquery for filtering.
isFilterablePropertyUsingSubquery(String) - Method in interface ubic.gemma.persistence.service.FilteringService
isFilterablePropertyUsingSubquery(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
isFilterablePropertyUsingSubquery(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
isFixed() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterService.LintResult: Indicate if the issue was fixed or not.
isForce() - Method in class ubic.gemma.cli.options.DataFileOptionValue: Indicate if existing files should be overwritten.
isForce() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Check if forcing is enabled.
isForce() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
isForceAnalysis() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
isForceAnalysis() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
isForcedBaseline(FactorValue) - Static method in class ubic.gemma.core.analysis.expression.diff.BaselineSelection: Check if this factor value is the baseline, overriding other possible baselines.
isForceLoadInProgress() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService: True when the in-flight load came from an explicit forceLoad request — the admin refresh endpoint — as opposed to startup.
isFound() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound: Whether ChEMBL identified the code at all.
isFound() - Method in class ubic.gemma.core.ontology.ols.OlsTerm: Whether OLS resolved a term for the IRI.
isFreeText(Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Check if the given characteristic is a free-text value.
isFreeTextCategory(Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Check if the given characteristic has or is a free-text category.
isFunctional() - Method in interface ubic.gemma.core.ontology.model.OntologyProperty
isFunctional() - Method in class ubic.gemma.core.ontology.simple.OntologyPropertySimple
isGeneColumn(Dataframe.Column) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer: Check if a given column contains gene identifiers.
isGeneExpressionAssay(OntologyTerm) - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils: Determine if the given assay corresponds to a single cell assay producing gene expression data.
isGenePix() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
isGEOAffyDataUsable(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform: Refers to a list of platforms for which the data from GEO is usually not usable and/or which we always reanalyze from CEL files - exon arrays.
isGoId(String) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyUtils: Check if a given string is a GO ID.
isGranted(List, List, boolean) - Method in class ubic.gemma.core.security.acl.domain.AclImpl: Determines authorization.
isGrantedAuthority(Sid) - Static method in class ubic.gemma.core.security.acl.domain.Sids: True if the sid identifies a granted authority (group/role).
isGranting() - Method in class ubic.gemma.core.security.acl.domain.AclEntry
isGroup(String) - Method in class ubic.gemma.core.loader.util.hdf5.H5Location: Check if the given path refers to a H5 group.
isGZipped(String) - Static method in class ubic.gemma.core.util.FileTools
isHasBatchInformation() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
isHasBatchInformation() - Method in class ubic.gemma.rest.PipelineStatusValueObject
isHasBeenShrunken() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
isHasCellBrowser() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Indicate if this experiment has a Cell Browser associated with it.
isHasCoexpressionAnalysis() - Method in class ubic.gemma.rest.PipelineStatusValueObject
isHasDifferentialExpressionAnalysis() - Method in class ubic.gemma.rest.PipelineStatusValueObject
isHasIntercept() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
isHasMissing() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
isHasProblematicBatchInformation() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
isHasSingletonBatch() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
isHasUninformativeBatchInformation() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
isHeldBy(String, Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
isHeldBy(Investigation, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService: Whether username holds an unexpired lock.
isHeldBy(Investigation, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl
isHidden() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition: True when MultiQC hides this column by default in its own report.
isHidden() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject: True when MultiQC hides this column by default in its own report.
isHuman(Taxon) - Static method in class ubic.gemma.persistence.service.genome.taxon.TaxonUtils
isIdempotent() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowTransition
isIgnoreCellTypeFactor() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
isIgnoreCompatibleCellTypeFactor() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: When re-creating, ignore a compatible cell type factor that may already exist.
isIgnoreDataVectors() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Skip single-cell data vectors if possible, or at least skip transformation that would normally be applied to them to make them usable.
isIgnoreErrors() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig: Ignore errors when retrieving additional information.
isIgnoreExistingCellTypeAssignment() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: If true, ignore existing cell type assignment with the same name.
isIgnoreExistingOtherCellLevelCharacteristics() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: If true, ignore existing other CLCs with the same names.
isIgnoreFailingSubsets() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Keep processing other subsets when encountering an AnalysisException on a subset.
isIgnoreMinimumDesignElementsThreshold() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: If true, the ExpressionExperimentFilter.MINIMUM_DESIGN_ELEMENTS is ignored.
isIgnoreMinimumSamplesThreshold() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: If true, ExpressionExperimentFilter.MINIMUM_SAMPLES is ignored.
isIgnoreSamplesLackingData() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Ignore individual samples that lack or have incomplete data.
isIgnoreUnmatchedCellIds() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: When parsing SingleCellDataLoaderConfig.cellTypeAssignmentFile and SingleCellDataLoaderConfig.otherCellLevelCharacteristicsFile, ignore cell IDs that cannot be matched to a sample.
isIgnoreUnmatchedCharacteristics() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExperimentSubSetsCreationConfig: Whether to allow unmapped characteristics.
isIgnoreUnmatchedFactorValues() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExperimentSubSetsCreationConfig: Whether to allow unmapped factor values.
isIncludeBioAssays() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig
isIncludeBiologicalCharacteristics() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig: Initialize CompositeSequence.getBiologicalCharacteristic().
isIncludeCellIds() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig
isIncludeCharacteristics() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig
isIncludeClcs() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig
isIncludeCtas() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig
isIncludeData() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig
isIncludeDataIndices() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig
isIncludeIndices() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig
isIncludeInteractions() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: Whether interactions among the factors should be included.
isIncludeMaskedCellsInLibrarySize() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig: Include masked cells in the library size calculation.
isIncludeProtocol() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig
isIncludeRefuted() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
isIncludeTaxon() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
isIndexBioSequences() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexDatasetGroups() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexDatasets() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexDesignElements() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexGeneGroups() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexGenes() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexPlatforms() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexPublications() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isInferSamplesFromCellIdsOverlap() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: When parsing SingleCellDataLoaderConfig.cellTypeAssignmentFile and SingleCellDataLoaderConfig.otherCellLevelCharacteristicsFile, use the overlap between the cell IDs from the file and those from the SingleCellDimension to infer sample associations.
isInitializationThreadAlive() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
isInitializationThreadAlive() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
isInitializationThreadAlive() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
isInitializationThreadAlive() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Check if the initialization thread is alive.
isInitializationThreadCancelled() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
isInitializationThreadCancelled() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
isInitializationThreadCancelled() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
isInitializationThreadCancelled() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Check if the initialization thread is cancelled.
isInitialized() - Method in class ubic.gemma.core.context.AbstractAsyncFactoryBean
isInitialized() - Method in interface ubic.gemma.core.context.AsyncFactoryBean: Indicate if this bean has been initialized or if its initialization is pending.
isInitialized(Object) - Static method in class ubic.gemma.model.util.ModelUtils: Check if an object is initialized.
isInteraction() - Method in class ubic.gemma.core.util.math.linearmodels.AnovaEffect
isInteraction() - Method in class ubic.gemma.model.analysis.expression.diff.Baseline
isInteraction() - Method in class ubic.gemma.model.analysis.expression.diff.Contrast: Indicate if this contrast is an interaction of two or more factors.
isKeepPooledSample() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig: Keep the pooled sample (if any) in the dataset.
isKeepUnknownSample() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig: Keep the unknown sample (if any) in the dataset.
isKnownIdSpace(String) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Check if a given prefix is a known OBO ID space.
isLastAttempt() - Method in class ubic.gemma.core.util.SimpleRetryContext: Indicate if this is the last attempt, any raised exception will bubble up to SimpleRetry.execute(SimpleRetryCallable, Object)
isLegacySha1Hex(String) - Static method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder
isLibraryStrategy() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig: FIll library strategy.
isLintChildWithIncorrectParent() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig: Check for SecuredChild that have an incorrect parent ACL entry.
isLintChildWithoutParent() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig: Check for SecuredChild that lack a parent ACL entry.
isLintDanglingIdentities() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig: Check for ACL entries that point to non-existing securables.
isLintNotChildWithParent() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig: Check for SecuredNotChild that have a parent ACL entry.
isLintPermissions() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig: Check for missing or incorrect permissions on ACL entries.
isLintSecurablesLackingIdentities() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig: Check for securables that lack ACL entries.
isLoadDone() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
isLoaderDone() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
isLoadPlatformOnly() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isLog2cpm(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils: Check if a given quantitation type holds log2 CPM.
isLoggedIn() - Method in class ubic.gemma.core.security.authentication.LoginDetailsValueObject
isLogTransformed(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils: Check if a given QT holds log-transformed data.
isLowExpressionFilterApplied() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
isLowVarianceFilterApplied() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Indicate if the low variance filter was applied.
isLowVarianceFilterApplied() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
ISM - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
isMakeArchiveFile() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Whether to create archive files.
isMakePreferred() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig: Make the resulting QT preferred.
isMandatory() - Method in class ubic.gemma.core.util.runtime.FileLockInfo: Indicate if this lock is mandatory (i.e.
isManualBatchConfoundActive() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualBatchConfoundActive() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
isManualBatchEffectActive() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualBatchEffectActive() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
isManualHasBatchConfound() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualHasBatchConfound() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
isManualHasNoBatchEffect() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualHasNoBatchEffect() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
isManualHasStrongBatchEffect() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualHasStrongBatchEffect() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
isManualQualityOverride() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualQualityOverride() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
isMarkQuantitationTypeAsPreferred() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig: Mark the QT as preferred.
isMarkQuantitationTypeAsRecomputedFromRawData() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig: Mark the quantitation type as recomputed from raw data.
isMarkSingleCellTypeAssignmentAsPreferred() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: If only one CTA is present, mark it as preferred.
isMasked() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: Indicate if this vector is "masked", i.e.
isMaskOutliers() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Mask outliers in the data by replacing the affected columns with Double.NaN.
isMatched() - Method in class ubic.gemma.core.geoscrape.GeoRecordMatcher.MatchResult
isMatrixWasFiltered() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
isMeasurement() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: Indicate if this FactorValue is a measurement.
isMerged(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
isMerged(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
isMerged(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
isMerged(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
isMerged(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
isMerged(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
isMergee(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
isMergee(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
isMergee(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
isMergee(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
isMergee(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
isMergee(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
isMeshHeadings() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig: Fill MeSH headings.
isMightNotHaveDataInFile() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: Indicate if the data might be separate, as for some RNA-seq studies.
isMigratedToStatement() - Method in class ubic.gemma.model.common.description.Characteristic: Deprecated.
isMinimumCellsFilterApplied() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Indicate if the minimum cells filter was applied.
isMinPresentFilterApplied() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
isMissing(int, int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
isMissing(int, int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
isMissing(int, int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
isMissing(int, int) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
isMissing(int, int) - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Check if the value at a given index is missing.
isMissing(int, int) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
isMissing(int, int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
isMissing(int, int) - Method in class ubic.gemma.core.util.matrix.StringMatrix: Strings are considered missing if they are whitespace, null or empty.
isModerateStatistics() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Whether moderated test statistics should be used.
isModerateStatistics() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: Whether to moderate test statistics via empirical Bayes
isModifiable() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject: If modifying the set is constrained by existing analyses.
isModified() - Method in interface ubic.gemma.model.common.GemmaSessionBackedValueObject
isModified() - Method in class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject
isModified() - Method in class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject
isMouse(Taxon) - Static method in class ubic.gemma.persistence.service.genome.taxon.TaxonUtils
isMultiQC() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
isMutable() - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
isMutable() - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
isNameIsFromAuthority() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
isNamePrefixed() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
isNeedsAttention() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
isNeedsAttention() - Method in class ubic.gemma.rest.PipelineStatusValueObject: The curator flag that predates the agent workflow: a human marked this dataset as wanting a look.
isNegative(Filter) - Method in class ubic.gemma.persistence.util.Filter: Check if a filter is negative.
isNormalized(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
isNoSequencesFilterApplied() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
isNoVectors() - Method in class ubic.gemma.model.expression.experiment.Geeq
isNoVectors() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
ISO - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
isObjectAlreadyRemoved() - Method in class ubic.gemma.model.common.BaseValueObject
isObjectTransient(Object) - Method in interface ubic.gemma.core.security.acl.ObjectTransientnessRetrievalStrategy: Determine if the given object is transient.
isObjectTransient(Object) - Method in class ubic.gemma.core.security.acl.ObjectTransientnessRetrievalStrategyImpl
isObsolete() - Method in class ubic.gemma.core.ontology.lexical.LexicalAnnotationProperty
isObsolete() - Method in interface ubic.gemma.core.ontology.model.OntologyResource: Whether the resource is marked as obsolete.
isObsolete() - Method in class ubic.gemma.core.ontology.simple.OntologyIndividualSimple
isObsolete() - Method in class ubic.gemma.core.ontology.simple.OntologyPropertySimple
isObsolete() - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
isObsolete() - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
isObsolete() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject
isolate - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
isOntologyEnabled() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
isOntologyLoaded() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
isOntologyLoaded() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
isOntologyLoaded() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
isOntologyLoaded() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Used for determining if the Ontology has finished loading into memory.
isOrdered() - Method in class ubic.gemma.core.loader.util.anndata.CategoricalArray
isOutlier() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics: True when the assay is flagged as an outlier, so the caller need not join a second call.
isOutlier() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
isOutlier() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject: Whether the assay is flagged as an outlier (BioAssay.getIsOutlier()), so a caller plotting these against the correlation matrix does not need a second request.
isOutliersFilterApplied() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
isOutliersFilterApplied() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
isOwnedByCurrentUser() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
isOwnedByCurrentUser(Securable) - Method in interface ubic.gemma.core.security.SecurityService
isOwnedByCurrentUser(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isOwner(Acl, String) - Static method in class ubic.gemma.core.security.util.SecurityUtil
isPackageInstalled(String) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedTransformation: Check if a Python package is installed.
isPaired() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
isPaired(Boolean) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata.SequencingMetadataBuilder: Whether the reads are paired.
isPersist() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Indicate if this analysis should be persisted.
isPersist() - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
isPivoting() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition
isPostProcessOnly() - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
isPreferred() - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: Indicate if this assignment is the preferred one.
isPreferred() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Indicate if this assignment is the preferred one.
isPreferred(Class) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType: Check if a given quantitation type is preferred for a particular vector type.
isPreferred(QuantitationType) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser: Determine if a quantitation type is 'preferred'.
isPreferSinglePrecision() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Prefer single-precision for storage, even if the data is available with double-precision.
isPrincipal(Sid) - Static method in class ubic.gemma.core.security.acl.domain.Sids: True if the sid identifies a principal (user).
isPrivate() - Element in annotation interface ubic.gemma.rest.annotations.CacheControl
isPrivate(Acl) - Static method in class ubic.gemma.core.security.util.SecurityUtil: Test whether the given ACL is constraining access to users who are at privileges above "anonymous".
isPrivate(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Determine if a securable is private (i.e.
isPrivate(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isProbeIdsAreImageClones() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: If true, biological characteristics imaging the probes will be created.
isProducerDone() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
isProducerDone() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
isProducerDone() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
isPropagate() - Method in class ubic.gemma.rest.GoTermsWebService.GoTermGeneCountValueObject
isPublic - Variable in class ubic.gemma.rest.ExperimentSetsWebService.ExperimentSetRequest
isPublic() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
isPublic() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
isPublic(Acl) - Static method in class ubic.gemma.core.security.util.SecurityUtil
isPublic(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Determine if a securable is public (i.e.
isPublic(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isPublications() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig
isPublicationsPresent() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
isQuantityValued(String, String) - Static method in enum class ubic.gemma.model.common.description.RelationTopicality: Whether a relation with this predicate relates two concepts at all.
isRat(Taxon) - Static method in class ubic.gemma.persistence.service.genome.taxon.TaxonUtils
isRatio(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
isReadable(Class, Type, Annotation[], MediaType) - Method in class ubic.gemma.rest.providers.PathProvider
isReadableByCurrentUser(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Determine if the current user can read an object.
isReadableByCurrentUser(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isReadableByGroup(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService: Determine if members of a group is allowed to read an object.
isReadableByGroup(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isReadableByUser(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService
isReadableByUser(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isReadOnly() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock: Indicate if this lock is read-only.
isReadOnly() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition: Indicate if this lock acquisition is read-only.
isReadOnly() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLock
isReady() - Method in class ubic.gemma.core.ontology.search.JenaTextOntologySearchService
isReady() - Method in interface ubic.gemma.core.ontology.search.OntologySearchService: Whether the underlying jena-text index is available and non-empty.
isRecreateCellTypeFactorIfNecessary() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Re-create the cell type factor if necessary.
isRemappedUri(String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils
isRemove() - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand: If set to true, the annotations passed in will be deleted.
isRemovePrimaryPublication() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
isReordered() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject: Only mutated via BioAssayDimensionValueObject.reorder(List).
isReorganized() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: True if the data has been rearranged relative to the bioassay dimension (as a matter of practice the bioassay dimension should be set to null if it is not valid; this boolean is an additional check)
isRepetitiveValuesFilterApplied() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Indicate if the repetitive values filter was applied.
isReplaceExistingCellTypeAssignment() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: If there is already a cell type assignment with the same name, replace it with the new one.
isReplaceExistingOtherCellLevelCharacteristics() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: If there are already other CLCs with the same names, replace them with the new ones.
isReplaceExistingQuantitationType() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig: Replace the vectors of an existing QT.
isReportPresent() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics: True when a MultiQC report was found and parsed.
isReportPresent() - Method in class ubic.gemma.rest.DatasetsWebService.SequencingQcMetricsValueObject: True when a MultiQC report was found and read.
isRequireSequences() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Set to true if design elements lacking associated BioSequences for the element should be removed.
isResiduals() - Method in class ubic.gemma.core.util.math.linearmodels.AnovaEffect
isResultObjectUrlExternal() - Method in class ubic.gemma.model.common.search.SearchResultValueObject: Indicate if the result URL is external (i.e., outside of Gemma).
isResultObjectUrlExternal() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject: Indicate that the result object URL is external and not under Gemma's control.
isRetracted() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
isRetracted() - Method in class ubic.gemma.model.common.description.CitationValueObject
isRevert() - Method in class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
isRNASeq(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
isRNASeq(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
isRoot() - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
isRoot() - Method in interface ubic.gemma.core.ontology.model.OntologyTerm
isRoot() - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
isRoot() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: root of a query
isRuledOutTruncated() - Method in class ubic.gemma.rest.AnnotationsWebService.NegativeEvidenceValueObject: Whether AnnotationsWebService.NegativeEvidenceValueObject.getRuledOut() was capped.
isRunningAsAdmin() - Static method in class ubic.gemma.core.security.util.SecurityUtil
isRunningRemotely() - Method in interface ubic.gemma.core.job.SubmittedTask
ISS - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
isSampleCharacteristics() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig
isSampleCharsPresent() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
isSampleDetails() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig: Fill sample details.
isSampleNameColumn(Dataframe.Column) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer: Check if a given dataframe column contains sample names.
isSampleNameColumn(Dataframe.Column) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfigurer
isSearchBibrefs() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isSearchBioSequences() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isSearchEnabled() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
isSearchEnabled() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
isSearchEnabled() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
isSearchEnabled() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Check if this ontology has full-text search enabled.
isSearchExperiments() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isSearchExperimentSets() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isSearchGenes() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isSearchGeneSets() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isSearchPlatforms() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isSearchProbes() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isSeeded() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
isSelf() - Method in class ubic.gemma.core.util.runtime.FileLockInfo: Indicate if this process info belongs to the current process.
isSelfSufficient() - Method in enum class ubic.gemma.model.common.description.AnnotationRelationBasis: Whether a relation resting on this basis alone is strong enough to report without corroboration from another.
isSeparateSampleFromAssaysIdentifiers() - Method in class ubic.gemma.cli.options.CellMetadataFileOptionValue
isSeparateSampleFromAssaysIdentifiers() - Method in class ubic.gemma.cli.options.DesignFileOptionValue
isServerReachable(ShellDelegatingBlat.BlattableGenome, boolean) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat: Check if the gfServer for a given genome is reachable.
isServerRunning() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat: Check if the gfServer is running.
isShared() - Method in interface ubic.gemma.core.util.locking.LockedPath: Indicate if the lock is shared.
isShared() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
isShared(Acl) - Static method in class ubic.gemma.core.security.util.SecurityUtil
isShared(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Determine if a securable is shared (i.e.
isShared(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
isShortNameChangeAllowed() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
isShouldBePublic() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig: If true, securables should be public.
isShrunken() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary: Whether this is the result of emprical bayes shrinkage of variance estimates
isShutdown() - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
isSidLoaded(List) - Method in class ubic.gemma.core.security.acl.domain.AclImpl
isSignalChannelA(String) - Static method in class ubic.gemma.persistence.util.ChannelUtils: For two-color arrays: Given the quantitation type name, determine if it represents the channel A signal.
isSignalChannelB(String) - Static method in class ubic.gemma.persistence.util.ChannelUtils: For two-color arrays: Given the quantitation type name, determine if it represents the channel B signal.
isSingle() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
isSingleBatch() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails: Indicate if the experiment was determined to have just one batch, or false for any other state (including we don't know).
isSingleBatch() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
isSingleCell(GeoSample, boolean) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO sample is single-cell by looking up its metadata.
isSingleCell(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO series is single-cell by looking up its metadata.
isSingleCell(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Indicate if the given experiment is a single-cell experiment.
isSingleCell(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
isSingleNuclei(GeoSample, boolean) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO sample is single-nuclei by looking up its metadata.
isSingleNuclei(GeoSeries) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Check if a GEO series is single-nuclei by looking up its metadata.
isSingleton() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory
isSingleton() - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
isSingleton() - Method in class ubic.gemma.persistence.initialization.BootstrappedDataSourceFactory
isSingleton() - Method in class ubic.gemma.rest.util.OpenApiFactory
isSlimRebuildInFlight() - Method in class ubic.gemma.core.ontology.providers.ChebiOntologyService
isSlimRebuildInFlight() - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService
isSlimRebuildInFlight() - Method in interface ubic.gemma.core.ontology.providers.SlimmableOntologyService
isSolidMatch() - Method in class ubic.gemma.rest.AnnotationsWebService.NegativeEvidenceValueObject: Whether any term matched the query outright (preferred label or declared synonym).
isSourceMetadata() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig: Rebuild Investigation.sourceMetadata from the series this refetch parsed.
isSparse() - Method in class ubic.gemma.core.loader.util.anndata.Layer: Check if the matrix encoded in this layer is sparse.
isSplitByPlatform() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isStandardLocation() - Method in class ubic.gemma.cli.options.DataFileOptionValue: Write the file to the standard location in the ${gemma.appdata.home}/dataFiles directory.
isStandardOutput() - Method in class ubic.gemma.cli.options.DataFileOptionValue: Write the file to standard output.
isStartSequenceOf - Static variable in class ubic.gemma.core.ontology.jena.RO
isStateless(Class, SessionFactory) - Static method in class ubic.gemma.persistence.hibernate.HibernateUtils: Stateless-ness inference used to be derived from the entity's mapping (eager associations / non-lazy collections forced extra queries).
isStateless(Query, SessionFactory) - Static method in class ubic.gemma.persistence.hibernate.HibernateUtils
isSubsequenceOf - Static variable in class ubic.gemma.core.ontology.jena.RO
isSubSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
isSubSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
isSubSeriesStatus() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig: Fill sub-series status.
isSubset() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
isSubstitutable() - Method in enum class ubic.gemma.core.ontology.model.OntologyXref.Strength: Whether the foreign identifier may be swapped for the declaring term without changing what is being asserted.
isSubsumed(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
isSubsumed(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
isSubsumed(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
isSubsumed(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
isSubsumed(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
isSubsumed(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
isSubsumedOrMerged(ArrayDesign) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
isSubsumer(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
isSubsumer(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
isSubsumer(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
isSubsumer(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
isSubsumer(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
isSubsumer(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
issue(Authentication) - Method in class ubic.gemma.rest.security.TokenStore: Mint a new opaque token for the given authenticated principal.
isSuitableForDEA(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
isSuitableForDEA(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
isSuperSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
isSuperSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
isSupplementary() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService: Flat lexical catalogues are supplementary: they back-fill names the conventional ontologies lack, and their LexicalOntologyIndex exact-name boost is not on the same scale as a Jena index's raw scores, so their hits rank below every conventional-ontology hit rather than merging with them.
isSupplementary() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Check if this source supplements the conventional ontologies rather than standing beside them as a peer.
isSupplementary() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: True when this candidate came from a flat lexical catalogue (MGI names, Cellosaurus) rather than a conventional ontology.
isSupported(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics: Check if sparsity metrics can be computed for a given collection of vectors.
isSuppressMatching() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isSuppressPostProcessing() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isSymbolIsFromAuthority() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
isTagsPresent() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
isTermId(String) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Check if a string is in the format of an OBO term ID.
isTermId(String, boolean) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Check if a string is in the format of an OBO term ID.
isTerminal() - Method in enum class ubic.gemma.model.pipeline.JobState
isTerminated() - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
isTermLevelOnly() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
isTermObsolete() - Method in interface ubic.gemma.core.ontology.model.OntologyTerm: Deprecated.
use OntologyResource.isObsolete() instead
isTermObsolete() - Method in class ubic.gemma.core.ontology.simple.OntologyTermSimple
isTermUri(String) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Check if a string is in the format of an ontology URI.
isTranspose() - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
isTranspose() - Method in interface ubic.gemma.core.visualization.Heatmap: Indicate if this heatmap is transposed.
isTranspose() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
isTrimNonCanonicalChromosomehits() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isTroubled() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
isTroubled() - Method in class ubic.gemma.rest.PipelineStatusValueObject
isTroubled(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Check if the dataset is either troubled or uses a troubled platform.
isTroubled(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
isTruncated(Path) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleH5FileInSeriesSingleCellDetector
isTruncated(Path) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AnnDataDetector
isTwoChannel(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Test if this experiment was run on a two-color microarray platform.
isTwoChannel(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
isUncategorized(Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Check if the given characteristic is uncategorized.
isUsable() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord: Curator judgement about whether this is loadable.
isUseBioAssayIds() - Method in class ubic.gemma.cli.options.CellMetadataFileOptionValue
isUseBioAssayIds() - Method in class ubic.gemma.cli.options.DesignFileOptionValue
isUseBioAssayIds() - Method in class ubic.gemma.cli.options.ExpressionDataFileOptionValue
isUseCellIdsIfSampleNameIsMissing() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: When parsing SingleCellDataLoaderConfig.cellTypeAssignmentFile and SingleCellDataLoaderConfig.otherCellLevelCharacteristicsFile, allow for a missing sample_id column, in which case barcodes are used to infer the sample a cell belongs to.
isUseCharacteristics() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isUseCursorFetchIfSupported() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig
isUsedAsCategory() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage: Whether the term is used as a CATEGORY.
isUsedAsTerm() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
isUseDatabase() - Method in class ubic.gemma.model.common.search.SearchSettings: Use the database for finding results.
isUseDatabase() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isUseDataFromGEO() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
isUseDoublePrecision() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig: Use double precision for loading MEX data.
isUseEnsembl() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isUseEnsemblIds() - Method in class ubic.gemma.cli.options.SingleCellExpressionDataFileOptionValue
isUseEsts() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isUseFullTextIndex() - Method in class ubic.gemma.model.common.search.SearchSettings: Use the full-text index for finding results.
isUseGeneOntology() - Method in class ubic.gemma.model.common.search.SearchSettings: Include results from the Gene Ontology (GO).
isUseGo() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isUseIndices() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
isUseInferredRelations() - Method in class ubic.gemma.model.common.search.SearchSettings: Widen the search into terms Gemma knows are related to the ones matched -- so that ticking "Leigh syndrome" still returns a dataset annotated only as a SURF1 mutant.
isUseKnownGene() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isUseMiRNA() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isUseMrnas() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isUseMultipleRowsForAssays() - Method in class ubic.gemma.cli.options.DesignFileOptionValue
isUseOntology() - Method in class ubic.gemma.model.common.search.SearchSettings: Use the ontology and ontology inference for finding results.
isUserAdmin() - Static method in class ubic.gemma.core.security.util.SecurityUtil: Returns true if the current user has admin authority.
isUserAgent() - Static method in class ubic.gemma.core.security.util.SecurityUtil: Returns true if the current caller holds the agent authority.
isUserAnonymous() - Static method in class ubic.gemma.core.security.util.SecurityUtil: Returns true if the user is anonymous.
isUseRawColumnNames() - Method in class ubic.gemma.cli.options.CellMetadataFileOptionValue
isUseRawColumnNames() - Method in class ubic.gemma.cli.options.DesignFileOptionValue
isUseRawColumnNames() - Method in class ubic.gemma.cli.options.ExpressionDataFileOptionValue
isUserCurator() - Static method in class ubic.gemma.core.security.util.SecurityUtil: Returns true if the current caller holds the curator authority.
isUserCuratorOrAdmin() - Static method in class ubic.gemma.core.security.util.SecurityUtil: Returns true if the current caller curates: a curator, or an administrator.
isUseRefGene() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isUserFlaggedOutlier() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
isUserLoggedIn() - Static method in class ubic.gemma.core.security.util.SecurityUtil: Returns true if the user is non-anonymous.
isUserNotLoggedIn() - Method in class ubic.gemma.model.common.BaseValueObject
isUserOwned() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
isUsesSubquery() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta: Indicate if the property uses a subquery for filtering.
isUseWeights() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Set true for RNA-seq data sets
isUseWeights() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: Whether to use weighted regression based on mean-variance relationships (voom)
isValid() - Method in interface ubic.gemma.core.util.locking.LockedPath: Indicate if the lock is valid.
isValidFraction(double) - Static method in class ubic.gemma.core.util.math.Stats: Test whether a value is a valid fractional or probability value.
isValidPearsonCorrelation(double) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Test if a value is a reasonable Pearson correlation (in the range -1 to 1; values outside of this range are acceptable within a small roundoff.
isWantedQuantitationType(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: Some quantitation types are 'skippable' - they are easily recomputed from other values, or are not necessary in the system.
isWarnedAboutGenePix() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
isWildcard(SearchSettings) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Check if the query is a wildcard query.
isWriteable(Class, Type, Annotation[], MediaType) - Method in class ubic.gemma.rest.providers.MexBundlerProvider
isWriteable(Class, Type, Annotation[], MediaType) - Method in class ubic.gemma.rest.providers.PathProvider
isWriteable(Class, Type, Annotation[], MediaType) - Method in class ubic.gemma.rest.providers.SendfileProvider
isWriteLocked() - Method in class ubic.gemma.core.util.locking.FileLockInfo
isZeroVarianceFilterApplied() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
isZipped(String) - Static method in class ubic.gemma.core.util.FileTools
Item() - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest.Item
ITEM - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionScope: One thing: this tag, this value, this deletion.
iterator() - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
iterator() - Method in class ubic.gemma.core.loader.util.anndata.Dataframe
iterator() - Method in class ubic.gemma.model.common.search.SearchResultSet
iterator() - Method in class ubic.gemma.model.util.UninitializedCollection
iterator() - Method in class ubic.gemma.persistence.util.Filters: Obtain an iterator over the clauses contained in this conjunction.
🛑 It is not the whole story, and is not a substitute for library selection - Section in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule
🛑 It must be cleared - Section in class ubic.gemma.core.security.util.ActingIdentity

J

JacksonConfig - Class in ubic.gemma.rest.util: Configuration for JSON serialization with Jackson.
JacksonConfig() - Constructor for class ubic.gemma.rest.util.JacksonConfig
JavaBlock(String, String, String) - Constructor for class ubic.gemma.rest.monitoring.InfoWebService.JavaBlock
jCacheCacheManager() - Method in class ubic.gemma.persistence.cache.EhcacheConfig: The single JCache CacheManager shared by Spring's application-cache abstraction.
JdbcDriverDeregistrationListener - Class in ubic.gemma.rest.servlet: Deregister JDBC drivers loaded by the webapp ClassLoader on context shutdown.
JdbcDriverDeregistrationListener() - Constructor for class ubic.gemma.rest.servlet.JdbcDriverDeregistrationListener
JenaTextOntologySearchService - Class in ubic.gemma.core.ontology.search: Jena-text 4.10 / Lucene 9 implementation of OntologySearchService.
JenaTextOntologySearchService(Path, boolean) - Constructor for class ubic.gemma.core.ontology.search.JenaTextOntologySearchService: Construct a search service backed by the TDB at tdbDir.
JerseyClientAbortLogFilter - Class in ubic.gemma.rest.servlet: Suppresses noisy SEVERE log records that Jersey emits when a client disconnects mid-response.
JerseyClientAbortLogFilter() - Constructor for class ubic.gemma.rest.servlet.JerseyClientAbortLogFilter
jiang - Enum constant in enum class ubic.gemma.core.ontology.GoMetric.Metric
jobEvents(Long, Long, Long, Integer) - Method in class ubic.gemma.rest.AdminPipelineWebService
JobInfo - Class in ubic.gemma.model.common.auditAndSecurity
JobInfo() - Constructor for class ubic.gemma.model.common.auditAndSecurity.JobInfo
JobInfo.Factory - Class in ubic.gemma.model.common.auditAndSecurity
JobReconciler - Class in ubic.gemma.core.pipeline: Closes the "scheduler ran but never phoned home" gap.
JobReconciler() - Constructor for class ubic.gemma.core.pipeline.JobReconciler
JobsListResponse() - Constructor for class ubic.gemma.rest.AdminWebService.JobsListResponse
JobSnapshot - Class in ubic.gemma.core.pipeline: Scheduler-side state read via PipelineScheduler.poll(SchedulerHandle).
JobSnapshot(JobState, String, String) - Constructor for class ubic.gemma.core.pipeline.JobSnapshot
JobState - Enum Class in ubic.gemma.model.pipeline: Lifecycle of one PipelineJob.
join(String...) - Static method in class ubic.gemma.core.util.ShellUtils
JSON - Enum constant in enum class ubic.gemma.core.analysis.service.ExpressionExperimentDataFileType
JSON - Enum constant in enum class ubic.gemma.core.loader.entrez.EntrezRetmode
JSON_BULK_DATA_FILE_SUFFIX - Static variable in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
JSON_SIGNIFICANT_DIGITS - Static variable in class ubic.gemma.core.util.RoundingUtils: Significant digits kept in JSON responses.
JsonMatrixWriter - Class in ubic.gemma.core.datastructure.matrix.io: Writes a BulkExpressionDataMatrix to a JSON format.
JsonMatrixWriter() - Constructor for class ubic.gemma.core.datastructure.matrix.io.JsonMatrixWriter
judge(AnnotationSet, TriageVerdict, String, TriageJudgeKind, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService: Record or replace judgedBy's ruling on annotationSet.
judge(AnnotationSet, TriageVerdict, String, TriageJudgeKind, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
judgedAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageResponse
judgedBy - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageResponse
judgeKind - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionRequest: agent or curator — who decided.
judgeKind - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse
judgeKind - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageRequest: agent or curator — who decided.
judgeKind - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageResponse
judgeKind - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionRequest
judgeKind - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse

K

kappa - Enum constant in enum class ubic.gemma.core.ontology.GoMetric.Metric
keepPooledSample(boolean) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder: Keep the pooled sample (if any) in the dataset.
keepSamples(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries: Only keep the given samples.
keepUnknownSample(boolean) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder: Keep the unknown sample (if any) in the dataset.
KEY - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionScope: Everything under one key, INCLUDING siblings that have not been proposed yet.
KEY_PREFIX - Static variable in interface ubic.gemma.core.logging.log4j.ThreadContextPopulator: Recommended prefix to use to organize ThreadContext keys,
Keyword - Class in ubic.gemma.model.common.description: Hibernate Search 7 mapping: indexed root for keyword phrases attached to a BibliographicReference.
Keyword() - Constructor for class ubic.gemma.model.common.description.Keyword
Keyword.Factory - Class in ubic.gemma.model.common.description
killed(String) - Method in class ubic.gemma.cli.pipeline.PipelineJobReporter: Terminal cancelled.
kind - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
kind - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
kind - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
kind - Variable in class ubic.gemma.rest.InternalPipelineWebService.PostEventRequest
kind - Variable in class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
kind - Variable in class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest: Sub-discriminator on PROPOSAL rows.
kind() - Method in class ubic.gemma.core.pipeline.LuigiPipelineScheduler
kind() - Method in class ubic.gemma.core.pipeline.MockPipelineScheduler
kind() - Method in class ubic.gemma.core.pipeline.NextflowPipelineScheduler
kind() - Method in interface ubic.gemma.core.pipeline.PipelineScheduler: Which scheduler is this.
KruskalWallis - Class in ubic.gemma.core.util.math: Perform a Kruskal-Wallis test.
KruskalWallis() - Constructor for class ubic.gemma.core.util.math.KruskalWallis
kurtosis(DoubleArrayList, double, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the kurtosis (aka excess) of a data sequence, which is -3 + moment(data,4,mean) / standardDeviation4.
kwStatistic(DoubleArrayList, IntArrayList) - Static method in class ubic.gemma.core.util.math.KruskalWallis

L

label() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTerm: Returns the value of the label record component.
label() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata.Taxon: Returns the value of the label record component.
LABEL_MISMATCH - Enum constant in enum class ubic.gemma.core.ontology.TermViolation.Reason: The URI resolves (locally or via OLS) but the submitted label is not the term's label — the signature of a hallucinated or mis-copied term.
LABEL_PREFIX - Enum constant in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia: Query is a prefix of the preferred label (or the label is a prefix of the query, when the query is the longer of the two).
LABEL_TOKENS - Enum constant in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia: Every content token in the query (after lowercase + length-≥-2 + stop-word strip) appears as a substring of the preferred label.
labelOf(String) - Method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex: What a term resolved through this index is called, according to the same artifact that resolved it; null when that artifact carried no usable label for it.
languageLevel - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject
LAST - Enum constant in enum class ubic.gemma.persistence.util.Sort.NullMode
LAST - Enum constant in enum class ubic.gemma.rest.util.args.SortArg.Sort.NullMode
lastAttempt - Variable in class ubic.gemma.core.util.SimpleRetryContext: Indicate if this is the last attempt, any raised exception will bubble up to SimpleRetry.execute(SimpleRetryCallable, Object)
LastEventTriple(AuditEvent, AuditEvent, AuditEvent) - Constructor for record class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject.LastEventTriple: Creates an instance of a LastEventTriple record class.
lastIndexOf(Object) - Method in class ubic.gemma.core.datastructure.sparse.SparseArrayList
lastIndexOf(Object) - Method in class ubic.gemma.core.datastructure.sparse.SparseRangeArrayList
lastIndexOf(Object) - Method in class ubic.gemma.model.util.UninitializedList
lastModified - Variable in class ubic.gemma.rest.AdminWebService.IndexStatusValueObject: mtime of the on-disk index directory; null if missing / unconfigured / unreadable.
lastRanAt - Variable in class ubic.gemma.rest.AdminWebService.AgentRunsBlock: Most recent createdAt across PROPOSAL-role AnnotationSet rows; null if none.
lastRequest - Variable in class ubic.gemma.rest.AdminWebService.SessionPrincipalValueObject: Most recent SessionInformation#getLastRequest() across this principal's sessions.
lastScannedAccession - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeDryRunResponse: The last record the scan LOOKED at, matched or not — cursor on this rather than on the oldest candidate.
lastScannedDate - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeDryRunResponse: Release date of `lastScannedAccession`, so `until` can be stepped without a lookup.
lastUpdated() - Method in record class ubic.gemma.core.security.audit.payload.ReleaseDetailsUpdatePayload: Returns the value of the lastUpdated record component.
lastUpdated(Curatable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService: Deprecated.

Convenience overload — resolves target type from the entity.
lastUpdated(Curatable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImpl
lastUpdated(TicketTargetType, Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService: Deprecated.

The most recent occurredAt across all open tickets for the target.
lastUpdated(TicketTargetType, Long) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImpl
latencyMillis - Variable in class ubic.gemma.rest.AdminWebService.CurationAgentHealthResponse
latestAnnotationSet - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
latestProposal - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
Layer - Class in ubic.gemma.core.loader.util.anndata: Represents a layer.
Layer(H5File, String) - Constructor for class ubic.gemma.core.loader.util.anndata.Layer
lazyInitByDefaultPostProcessor() - Static method in class ubic.gemma.cli.config.CliComponentScanConfig: Re-creates the bare <bean class="ubic.gemma.core.context.LazyInitByDefaultPostProcessor"/> from the legacy XML.
LazyInitByDefaultPostProcessor - Class in ubic.gemma.core.context: Mark beans as lazy-init by default.
LazyInitByDefaultPostProcessor() - Constructor for class ubic.gemma.core.context.LazyInitByDefaultPostProcessor
LE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
LE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
LE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
LeastSquaresFit - Class in ubic.gemma.core.util.math.linearmodels: For performing "bulk" linear model fits, but also offers simple methods for simple univariate and multivariate regression for a single vector of dependent variables (data).
LeastSquaresFit(DoubleMatrix1D, DoubleMatrix1D) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: Least squares fit between two vectors.
LeastSquaresFit(DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: Stripped-down interface for simple use.
LeastSquaresFit(DoubleMatrix2D, DoubleMatrix2D) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: ANOVA not possible (use the other constructors)
LeastSquaresFit(DoubleMatrix2D, DoubleMatrix2D, DoubleMatrix2D) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: Weighted least squares fit between two matrices
LeastSquaresFit(DesignMatrix, DoubleMatrix2D, DoubleMatrix2D) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: Preferred interface for weighted least squares fit between two matrices
LeastSquaresFit(DesignMatrix, DoubleMatrix) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: Preferred interface if you want control over how the design is set up.
LeastSquaresFit(DesignMatrix, DoubleMatrix, DoubleMatrix2D) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: Weighted least squares fit between two matrices
LeastSquaresFit(ObjectMatrix, DenseDoubleMatrix2D) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
LeastSquaresFit(ObjectMatrix, DenseDoubleMatrix2D, boolean) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
LeastSquaresFit(ObjectMatrix, DoubleMatrix) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: NamedMatrix allows easier handling of the results.
LeastSquaresFit(ObjectMatrix, DoubleMatrix, boolean) - Constructor for class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit: NamedMatrix allows easier handling of the results.
LEFT - Enum constant in enum class ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod
LEGACY - Enum constant in enum class ubic.gemma.model.common.description.PublicationAssociationSource: Provenance unknown — the row predates this table and was backfilled from the bare INVESTIGATION.PRIMARY_PUBLICATION_FK / RELEVANT_PUBLICATIONS link, which records no authority at all.
LegacyAwareDaoAuthenticationProvider - Class in ubic.gemma.core.security.authentication: DaoAuthenticationProvider that understands Gemma's two pre-Phase-2 legacy password formats, both bare 40-char hex SHA-1 with no prefix: Username-salt (post-2009-11-23): SHA-1(rawPassword + "{" + username + "}") — configured via <s:salt-source user-property="username"/>.
LegacyAwareDaoAuthenticationProvider() - Constructor for class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider
length() - Method in record class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao.BioSequenceLite: Returns the value of the length record component.
LEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
LEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
LEQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
lessOrEq - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
lessThan - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
level - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
LexicalAnnotationProperty - Class in ubic.gemma.core.ontology.lexical: A plain AnnotationProperty for flat lexical vocabularies.
LexicalAnnotationProperty(String, String) - Constructor for class ubic.gemma.core.ontology.lexical.LexicalAnnotationProperty
LexicalOntologyIndex - Class in ubic.gemma.core.ontology.lexical: A Jena-agnostic, in-memory Lucene 9 full-text index over a flat lexical vocabulary.
LexicalOntologyIndex.Hit - Record Class in ubic.gemma.core.ontology.lexical
LexicalOntologyTerm - Class in ubic.gemma.core.ontology.lexical: A term from a flat lexical vocabulary (Cellosaurus, MGI strains, ...).
LexicalOntologyTerm(String, String) - Constructor for class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
LexicalOntologyTerm(String, String, LexicalTermMetadata) - Constructor for class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
LexicalTerm - Record Class in ubic.gemma.core.ontology.lexical: A single term from a flat lexical vocabulary: a URI, a primary label, zero or more synonyms, and whatever descriptive metadata the source carries.
LexicalTerm(String, String) - Constructor for record class ubic.gemma.core.ontology.lexical.LexicalTerm
LexicalTerm(String, String, List) - Constructor for record class ubic.gemma.core.ontology.lexical.LexicalTerm
LexicalTerm(String, String, List, LexicalTermMetadata) - Constructor for record class ubic.gemma.core.ontology.lexical.LexicalTerm: Creates an instance of a LexicalTerm record class.
LexicalTermMetadata - Record Class in ubic.gemma.core.ontology.lexical: Descriptive metadata carried alongside a LexicalTerm — the flat-vocabulary equivalent of the annotation properties (definition, species, category) that a real ontology term carries.
LexicalTermMetadata(List, String, String, String, String, String) - Constructor for record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Creates an instance of a LexicalTermMetadata record class.
LexicalTermMetadata.Taxon - Record Class in ubic.gemma.core.ontology.lexical: An organism an entry derives from.
LexicalTermMetadataValueObject(List, String, String, String, String) - Constructor for class ubic.gemma.rest.AnnotationsWebService.LexicalTermMetadataValueObject: Creates a new LexicalTermMetadataValueObject instance.
librarySize() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns the value of the librarySize record component.
librarySource - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
libraryStrategy - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
libraryStrategy(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig.GeoRetrieveConfigBuilder: FIll library strategy.
licenses(boolean) - Method in enum class ubic.gemma.model.common.description.RelationInferenceDirection: Whether a term sitting on the given end may be used to infer the other end.
liftStatementTimeout(Session) - Static method in class ubic.gemma.persistence.hibernate.HibernateUtils
like - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
LIKE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
LIKE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
LIKE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
likelyExternalReference(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
likelyId(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
likelyProbeDescription(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
likelyProbeOrganism(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
likelySequence(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
limit - Variable in class ubic.gemma.rest.AdminWebService.BlacklistListResponse: Effective limit applied (capped at 1000).
LimitArg - Class in ubic.gemma.rest.util.args: Argument used to represent a limit.
lin - Enum constant in enum class ubic.gemma.core.ontology.GoMetric.Metric
LINEAR - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: This is effectively the opposite of "log-transformed" (or any other transformation)
LinearModelAnalyzer - Class in ubic.gemma.core.analysis.expression.diff: Handles fitting linear models with continuous or fixed-level covariates.
LinearModelAnalyzer() - Constructor for class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
LinearModelSummary - Interface in ubic.gemma.core.util.math.linearmodels
LinearModelSummaryUtils - Class in ubic.gemma.core.util.math.linearmodels
LinearModelSummaryUtils() - Constructor for class ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtils
LineMapParser<K,T> - Class in ubic.gemma.core.loader.util.parser: The difference between this class and BasicLineMapParser is more flexibility in how keys are provided.
LineMapParser() - Constructor for class ubic.gemma.core.loader.util.parser.LineMapParser
LineParser<T> - Interface in ubic.gemma.core.loader.util.parser: A Parser that processes its input line-by-line.
link(String, String, EntrezQuery, String, EntrezRetmode, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Retrieve related records from an Entrez database from a previous EntrezUtils.search(String, String, EntrezRetmode, String) query.
Link - Class in ubic.gemma.core.loader.expression.cellxgene.model
Link() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.Link
LinkAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Computing coexpression links for an expression experiment
LinkAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.LinkAnalysisEvent
linkById(String, String, String, String, EntrezRetmode, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Retrieve related records from an Entrez database by ID.
linkParentsInNewTransaction(Class, List) - Method in interface ubic.gemma.core.security.authorization.acl.AclLinterHelperService: Link each of identifiers to the parent ACL identity its entity resolves to, in a new transaction that commits independently of the caller's.
linkParentsInNewTransaction(Class, List) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterHelperServiceImpl
lintAcls(Class, Long, AclLinterConfig) - Method in interface ubic.gemma.core.security.authorization.acl.AclLinterService
lintAcls(Class, Long, AclLinterConfig) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceImpl
lintAcls(Class, AclLinterConfig) - Method in interface ubic.gemma.core.security.authorization.acl.AclLinterService
lintAcls(Class, AclLinterConfig) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceImpl
lintAcls(AclLinterConfig) - Method in interface ubic.gemma.core.security.authorization.acl.AclLinterService
lintAcls(AclLinterConfig) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceImpl
lintChildWithIncorrectParent(boolean) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder: Check for SecuredChild that have an incorrect parent ACL entry.
lintChildWithoutParent(boolean) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder: Check for SecuredChild that lack a parent ACL entry.
lintDanglingIdentities(boolean) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder: Check for ACL entries that point to non-existing securables.
lintNotChildWithParent(boolean) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder: Check for SecuredNotChild that have a parent ACL entry.
lintPermissions(boolean) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder: Check for missing or incorrect permissions on ACL entries.
lintQuantitationType(QuantitationType, ExpressionDataMatrix) - Static method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtils
lintQuantitationType(QuantitationType, ExpressionDataMatrix, boolean) - Static method in class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtils: Check if a given quantitation type adequately describes a given expression data matrix.
LintResult(Class, Long, String, boolean) - Constructor for class ubic.gemma.core.security.authorization.acl.AclLinterService.LintResult: Creates a new LintResult instance.
lintSecurablesLackingIdentities(boolean) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder: Check for securables that lack ACL entries.
list(Query) - Method in interface ubic.gemma.persistence.hibernate.TypedResultTransformer: Execute the query with this transformer wired in, returning the typed list.
list(Query) - Static method in class ubic.gemma.persistence.util.QueryUtils
listAll() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
listAll() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
listAll() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
listAll() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
listAll() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
listAll() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
listAnnotationSets(DatasetArg, String, String, String, String) - Method in class ubic.gemma.rest.AnnotationSetsWebService: List annotation sets attached to a dataset, newest first.
listAnnotationSetsAcross(String, String, String, String, String, String, OffsetArg, LimitArg, String) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Cross-experiment list of annotation sets, paginated.
listAvailableGroups() - Method in interface ubic.gemma.core.security.authentication.BaseUserService: A list of groups available to the current user (will be security-filtered)...might need to allow anonymous.
listAvailableGroups() - Method in interface ubic.gemma.core.security.authentication.UserReadService: A list of all groups available — facade-level ACL filtering is bypassed here.
listAvailableGroups() - Method in class ubic.gemma.core.security.authentication.UserReadServiceImpl
listAvailableGroups() - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
listBlacklistEntries(int, int) - Method in class ubic.gemma.rest.AdminWebService: Lists current blacklist entries.
listByBatch(Query, String, Collection, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
listByBatch(Query, String, Collection, int, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
listByIdentifiableBatch(Query, String, Collection, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
listByIdentifiableBatch(Query, String, Collection, int, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
listDatasetAnnotationSets(DatasetArg, String, String, String, String) - Method in class ubic.gemma.rest.DatasetsWebService
listDirectoryFiles(File) - Static method in class ubic.gemma.core.util.FileTools: Given a File representing a directory, return the (non-directory) files it contains.
ListExpressionDataFIleLocksCli - Class in ubic.gemma.apps: List all locks within Gemma's data directories.
ListExpressionDataFIleLocksCli() - Constructor for class ubic.gemma.apps.ListExpressionDataFIleLocksCli
listFiles(String, File, Collection) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
listFiles(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
listIterator() - Method in class ubic.gemma.model.util.UninitializedList
listIterator(int) - Method in class ubic.gemma.model.util.UninitializedList
listMyBatches(PipelineJobBatch.BatchState, Integer) - Method in class ubic.gemma.rest.AdminPipelineWebService
listOrResolvePreboarded(String, String) - Method in class ubic.gemma.rest.PreboardedWebService: Listing endpoint: by accession (returns the single matching preboarded, 404 if none) or by state (queue view, returns the most-recent preboarded in that state — full pagination deferred).
ListQuantitationTypesCli - Class in ubic.gemma.apps
ListQuantitationTypesCli() - Constructor for class ubic.gemma.apps.ListQuantitationTypesCli
listSubDirectories(File) - Static method in class ubic.gemma.core.util.FileTools: Given a File representing a directory, return the subdirectories it contains.
listSummaries(AnnotationSetRole, AnnotationSetSource, String, AgentCurationKind, String, List, int, int, AnnotationSetDao.SummarySort, boolean) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: Cross-experiment thin metadata projection: every AnnotationSet matching the supplied filter, sliced by offset / limit.
listSummaries(AnnotationSetRole, AnnotationSetSource, String, AgentCurationKind, String, List, int, int, AnnotationSetDao.SummarySort, boolean) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
listSummaries(AnnotationSetRole, AnnotationSetSource, String, AgentCurationKind, String, List, int, int, AnnotationSetDao.SummarySort, boolean) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
listSummaries(AnnotationSetRole, AnnotationSetSource, String, AgentCurationKind, String, List, int, int, AnnotationSetDao.SummarySort, boolean) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
ListUtils - Class in ubic.gemma.core.util: Utilities and algorithms for List.
ListUtils() - Constructor for class ubic.gemma.core.util.ListUtils
LITE - Enum constant in enum class ubic.gemma.core.ontology.providers.OntologyService.LanguageLevel: OWL/Lite
LITERATURE - Enum constant in enum class ubic.gemma.model.common.description.DatabaseType
LITERATURE_SEARCH - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: Agent-driven literature search — find publications relevant to a dataset (or a candidate set of publications for triage).
liveCount - Variable in class ubic.gemma.rest.AdminWebService.ThreadBlock
LN - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Data is log-transformed with a natural log.
load(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader: download the gene_info and gene2accession files, then call load
load(File) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
load(File) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoader
load(InputStream) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
load(InputStream) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoader
load(InputStream, String) - Method in interface ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService
load(InputStream, String) - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl
load(Long) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
load(Long) - Method in interface ubic.gemma.core.security.authentication.UserReadService
load(Long) - Method in class ubic.gemma.core.security.authentication.UserReadServiceImpl
load(Long) - Method in interface ubic.gemma.core.security.authentication.UserService
load(Long) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
load(Long) - Method in class ubic.gemma.persistence.service.AbstractDao
load(Long) - Method in class ubic.gemma.persistence.service.AbstractService
load(Long) - Method in interface ubic.gemma.persistence.service.BaseDao: Loads the entity with given id from the persistent storage.
load(Long) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
load(Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
load(Long) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
load(Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
load(Long) - Method in interface ubic.gemma.persistence.service.common.description.DatabaseEntryReadService
load(Long) - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryReadServiceImpl
load(Long) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
load(Long) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService
load(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl
load(Long, CacheMode) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Load an experiment by ID with a specific cache mode.
load(Long, CacheMode) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
load(String) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoader
load(String, String) - Method in interface ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService: Work flow is: The file is first checked to see if readable, and the taxon checked to see it is in Gemma.
load(String, String) - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl
load(String, String, String, String, boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
load(String, String, String, String, Taxon) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
load(Collection) - Method in class ubic.gemma.persistence.service.AbstractDao
load(Collection) - Method in class ubic.gemma.persistence.service.AbstractService
load(Collection) - Method in interface ubic.gemma.persistence.service.BaseDao: Loads entities with given ids form the persistent storage.
load(Collection) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
load(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
load(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
load(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
load(ExpressionExperiment, ArrayDesign, SingleCellDataLoaderConfig) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderService: Load single-cell data, the data type is automatically detected.
load(ExpressionExperiment, ArrayDesign, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl
load(ExpressionExperiment, ArrayDesign, SingleCellDataType, SingleCellDataLoaderConfig) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderService: Load a specific single-cell data type.
load(ExpressionExperiment, ArrayDesign, SingleCellDataType, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl
load(Taxon) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
load(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
load(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
load(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
load(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
load(Filters, Sort) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService
load(Filters, Sort) - Method in interface ubic.gemma.persistence.service.FilteringDao: Load entities matching the given filters.
load(Filters, Sort) - Method in interface ubic.gemma.persistence.service.FilteringService
load(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
load(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
load(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
load(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
load(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService
load(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.FilteringDao: Load a slice of entities matching the given filters.
load(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.FilteringService
load(Filters, Sort, int, int) - Method in interface ubic.gemma.rest.util.Responders.FilterMethod
loadAccessions(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService: Accessions for a set of preboarded ids, in ONE query.
loadAccessions(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl
loadAclInfoFor(Session, Collection, Class) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Batched post-fetch of ACL info (object identity + owner SID) for a set of entity ids of a given Securable type.
loadAlignments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
loadAlignments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
loadAll() - Method in interface ubic.gemma.core.security.authentication.BaseUserService: Retrieves a list of users
loadAll() - Method in interface ubic.gemma.core.security.authentication.UserManager
loadAll() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
loadAll() - Method in interface ubic.gemma.core.security.authentication.UserReadService
loadAll() - Method in class ubic.gemma.core.security.authentication.UserReadServiceImpl
loadAll() - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
loadAll() - Method in class ubic.gemma.persistence.service.AbstractDao
loadAll() - Method in class ubic.gemma.persistence.service.AbstractService
loadAll() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
loadAll() - Method in interface ubic.gemma.persistence.service.BaseDao: Loads all entities of type T from the persistent storage.
loadAll() - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
loadAll() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
loadAll() - Method in interface ubic.gemma.persistence.service.common.description.DatabaseEntryReadService
loadAll() - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryReadServiceImpl
loadAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
loadAll(int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Load a slice of FactorValues.
loadAll(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
loadAll(int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService
loadAll(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
loadAll(int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Load a slice of FactorValues.
loadAll(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
loadAll(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
loadAll(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
loadAll(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
loadAll(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
loadAll(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
loadAll(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadAll(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
loadAll(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
loadAll(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
loadAll(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
loadAllExperimentSetsWithTaxon() - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
loadAllExperimentSetsWithTaxon() - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
loadAllExperimentSetsWithTaxon() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: Security at DAO level.
loadAllExperimentSetsWithTaxon() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
loadAllExperimentSetValueObjects(boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: Security filtering is handled by the call to load the set entities ubic.gemma.model.analysis.expression.ExpressionExperimentSetService.loadAllExperimentSetsWithTaxon()
loadAllExperimentSetValueObjects(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
loadAllGenericGenePlatforms() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
loadAllGenericGenePlatforms() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
loadAllGenericGenePlatforms() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
loadAllGenericGenePlatforms() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
loadAllGenericGenePlatforms() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Load *generic* gene-based platforms.
loadAllGenericGenePlatforms() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadAllIdentifiers() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Load all possible identifiers for all experiments.
loadAllIdentifiers() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadAllIdentifiersAndName(boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadAllIdentifiersAndName(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadAllIdentifiersAndName(boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load all possible identifiers for experiments.
loadAllIdentifiersAndName(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAllIds() - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Load all factor value IDs.
loadAllIds() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
loadAllIds() - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService
loadAllIds() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
loadAllIds() - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Load all factor value IDs.
loadAllIds() - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
loadAllIds(int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Load a slice of the factor values IDs.
loadAllIds(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
loadAllIds(int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService
loadAllIds(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
loadAllIds(int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Load a slice of the factor values IDs.
loadAllIds(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
loadAllMetaAnalyses() - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperService: Load all meta-analyses.
loadAllMetaAnalyses() - Method in class ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperServiceImpl
loadAllReferences() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadAllReferences() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadAllReferences() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load references for all experiments.
loadAllReferences() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAllTaxaWithGenes() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonReadService
loadAllTaxaWithGenes() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonReadServiceImpl
loadAllTaxaWithGenes() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
loadAllTaxaWithGenes() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
loadAllUniqueByName() - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolDao: Load all protocols that are unique by name.
loadAllUniqueByName() - Method in class ubic.gemma.persistence.service.common.protocol.ProtocolDaoImpl
loadAllUniqueByName() - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolReadService
loadAllUniqueByName() - Method in class ubic.gemma.persistence.service.common.protocol.ProtocolReadServiceImpl
loadAllUniqueByName() - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolService
loadAllUniqueByName() - Method in class ubic.gemma.persistence.service.common.protocol.ProtocolServiceImpl
loadAllValueObjects() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadAllValueObjects() - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao: Should be overridden for any entity that requires special handling of larger amounts of VOs.
loadAllValueObjects() - Method in class ubic.gemma.persistence.service.AbstractVoEnabledService
loadAllValueObjects() - Method in interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadAllValueObjects() - Method in interface ubic.gemma.persistence.service.BaseVoEnabledService: Loads value objects representing all the entities of specific type.
loadAllValueObjects() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService
loadAllValueObjects() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
loadAllValueObjects() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadAllValueObjects(boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
loadAllValueObjects(boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
loadAllWithAuditTrail() - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseReadService
loadAllWithAuditTrail() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseReadServiceImpl
loadAllWithAuditTrail() - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
loadAllWithAuditTrail() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
loadAndInitializeSingleCellDimensions(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Load an experiment for the single-cell data loader path.
loadAndInitializeSingleCellDimensions(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
loadAndThaw(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
loadAndThaw(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
loadAndThaw(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
loadAndThaw(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadAndThaw(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadAndThaw(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadAndThaw(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load an experiment and thaw it as per ExpressionExperimentService.thaw(ExpressionExperiment).
loadAndThaw(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAndThawLite(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadAndThawLite(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadAndThawLite(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadAndThawLite(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAndThawLiteOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadAndThawLiteOrFail(Long, Function) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadAndThawLiteOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadAndThawLiteOrFail(Long, Function) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAndThawLiteOrFail(Long, Function, String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
loadAndThawLiteOrFail(Long, Function, String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
loadAndThawLiteOrFail(Long, Function, String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Load a platform by ID and thaw it with ArrayDesignService.thawLite(ArrayDesign)
loadAndThawLiteOrFail(Long, Function, String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadAndThawLiteOrFail(Long, Function, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadAndThawLiteOrFail(Long, Function, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadAndThawLiteOrFail(Long, Function, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load an experiment and thaw it as per ExpressionExperimentService.thawLite(ExpressionExperiment) or fail with the supplied exception and message.
loadAndThawLiteOrFail(Long, Function, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAndThawLiterOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadAndThawLiterOrFail(Long, Function) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadAndThawLiterOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadAndThawLiterOrFail(Long, Function) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAndThawLiteWithRefreshCacheMode(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadAndThawLiteWithRefreshCacheMode(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadAndThawLiteWithRefreshCacheMode(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load an experiment without cache and thaw it as per ExpressionExperimentService.thaw(ExpressionExperiment) with CacheMode.REFRESH.
loadAndThawLiteWithRefreshCacheMode(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAndThawOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadAndThawOrFail(Long, Function) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadAndThawOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load an experiment and thaw it as per ExpressionExperimentService.thawLite(ExpressionExperiment) or fail with the supplied exception and message.
loadAndThawOrFail(Long, Function) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAndThawOrFail(Long, Function, String) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService: Load a BioMaterial by ID and thaw it eagerly, or throw the supplied exception if no such biomaterial exists.
loadAndThawOrFail(Long, Function, String) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
loadAndThawOrFail(Long, Function, String) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
loadAndThawOrFail(Long, Function, String) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
loadAsMap(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Load a batch of ArrayDesigns by ID and return them keyed by ID for O(1) per-id lookup.
loadAsMap(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
loadBestMatrix(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService: Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix.
loadBestMatrix(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: No need for ACL_VALUE_OBJECT_COLLECTION_READ because the filtering is done in the query.
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Cursor-mode counterpart to ArrayDesignDao.loadBlacklistedValueObjects(Filters, Sort, int, int): keyset pagination over the blacklisted platforms, applying the same shortName/accession blacklist filter that the offset-mode variant composes — see CURSOR_PAGINATION_STEP1_PLAN.md step 1h.
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService: Cursor-mode counterpart to ArrayDesignReadService.loadBlacklistedValueObjects(Filters, Sort, int, int).
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Cursor-mode counterpart to ArrayDesignService.loadBlacklistedValueObjects(Filters, Sort, int, int) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1h.
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Cursor-mode counterpart to ExpressionExperimentDao.loadBlacklistedValueObjects(Filters, Sort, int, int): keyset pagination over the blacklisted-experiment view.
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService: Cursor-mode counterpart to ExpressionExperimentReadService.loadBlacklistedValueObjects(Filters, Sort, int, int).
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Cursor-mode counterpart to ExpressionExperimentService.loadBlacklistedValueObjects(Filters, Sort, int, int).
loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadByExperimentalDesignWithCharacteristics(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Load all FactorValues belonging to the given ExperimentalDesign with their characteristics (and measurement, which is mapped fetch="join" so it is loaded with the FV itself) fetched in a single round-trip.
loadByExperimentalDesignWithCharacteristics(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
loadById(Long, ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
loadById(Long, ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
loadById(Long, ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
loadById(Long, ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
loadById(Long, ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
loadById(Long, ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
loadByIdAndVectorType(Long, ExpressionExperiment, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Load a QT from an experiment by ID and vector type.
loadByIdAndVectorType(Long, ExpressionExperiment, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
loadByIdAndVectorType(Long, ExpressionExperiment, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
loadByIdAndVectorType(Long, ExpressionExperiment, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
loadByIdAndVectorType(Long, ExpressionExperiment, Class) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService: Find a quantitation type by ID and vector type.
loadByIdAndVectorType(Long, ExpressionExperiment, Class) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
loadCellTypeAssignments(ExpressionExperiment, SingleCellDataLoaderConfig) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderService: Load the cell type assignments, the data type is automatically detected.
loadCellTypeAssignments(ExpressionExperiment, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl
loadCellTypeAssignments(ExpressionExperiment, SingleCellDataType, SingleCellDataLoaderConfig) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderService: Load the cell type assignments.
loadCellTypeAssignments(ExpressionExperiment, SingleCellDataType, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl
loadClasspathConfig(String) - Static method in class ubic.gemma.core.util.ConfigUtils: Load a properties configuration from a classpath resource.
loadCompositeSequences(ArrayDesign, int, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
loadCompositeSequences(ArrayDesign, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
loadDetailsValueObjects(Collection, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Special method for front-end access.
loadDetailsValueObjects(Collection, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadDetailsValueObjects(Collection, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadDetailsValueObjects(Collection, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadDetailsValueObjects(Collection, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadDetailsValueObjects(Collection, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadDetailsValueObjectsByIds(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Like ExpressionExperimentDao.loadDetailsValueObjects(Collection, Taxon, Sort, int, int), but returning a list.
loadDetailsValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadDetailsValueObjectsByIds(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadDetailsValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadDetailsValueObjectsByIds(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadDetailsValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadDetailsValueObjectsByIdsWithCache(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
loadDetailsValueObjectsByIdsWithCache(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadDetailsValueObjectsByIdsWithCache(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadDetailsValueObjectsByIdsWithCache(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadDetailsValueObjectsByIdsWithCache(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadDetailsValueObjectsByIdsWithCache(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadDetailsValueObjectsByIdsWithCache(Collection, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
loadDetailsValueObjectsByIdsWithCache(Collection, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadDetailsValueObjectsWithCache(Collection, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadDetailsValueObjectsWithCache(Collection, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadDetailsValueObjectsWithCache(Collection, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadDetailsValueObjectsWithCache(Collection, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loaded - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject
Loaded - Enum constant in enum class ubic.gemma.model.expression.experiment.WorkflowState
loadedCount - Variable in class ubic.gemma.rest.AdminWebService.OntologiesResponse
LoadExpressionDataCli - Class in ubic.gemma.apps: Simple command line to load expression experiments, either singly or in batches defined on the command line or in a file.
LoadExpressionDataCli() - Constructor for class ubic.gemma.apps.LoadExpressionDataCli
loadForExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadService
loadForExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadServiceImpl
loadForExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
loadForExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl
loadFromDirectory(File) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedService
loadFromSoftFile(String, String, boolean, boolean, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService: Load from a SOFT file.
loadFromSoftFile(String, String, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
loadFullMatrix(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService: Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.
loadFullMatrix(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
loadFullyPopulatedValueObject(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService: Returns a detailVO for a geneDd This method may be unnecessary now that we have put all the logic into the GeneService
loadFullyPopulatedValueObject(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
loadGroupAuthorities(User) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
loadGroupAuthorities(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
loadGroupAuthorities(User) - Method in interface ubic.gemma.core.security.authentication.UserReadService
loadGroupAuthorities(User) - Method in class ubic.gemma.core.security.authentication.UserReadServiceImpl
loadGroupAuthorities(User) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.UserDao
loadGroupAuthorities(User) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
loadGroups(User) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.UserDao
loadGroups(User) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
loadIdentifiers(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Load identifiers for the given experiments only.
loadIdentifiers(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadIdentifiers(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService: Resolve the short name and name of the given experiments, for callers that hold ids and need something a person can read.
loadIdentifiers(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadIdentifiers(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadIdentifiers(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadIds(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
loadIds(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadIds(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
loadIds(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
loadIds(Filters, Sort) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService
loadIds(Filters, Sort) - Method in interface ubic.gemma.persistence.service.FilteringDao: Load IDs of entities matching the given filters.
loadIds(Filters, Sort) - Method in interface ubic.gemma.persistence.service.FilteringService
loadIdsWithCache(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
loadIdsWithCache(Filters, Sort) - Method in interface ubic.gemma.persistence.service.CachedFilteringDao
loadIdsWithCache(Filters, Sort) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadIdsWithCache(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadIdsWithCache(Filters, Sort) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadIdsWithCache(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadIdsWithNumberOfOldStyleCharacteristics(Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Deprecated.
loadIdsWithNumberOfOldStyleCharacteristics(Set) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl: Deprecated.
loadIdsWithNumberOfOldStyleCharacteristics(Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService: Deprecated.
do not use, this is only for migrating old-style characteristics to statements and will be removed
loadIdsWithNumberOfOldStyleCharacteristics(Set) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
loadIdsWithNumberOfOldStyleCharacteristics(Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Deprecated.
do not use, this is only for migrating old-style characteristics to statements and will be removed
loadIdsWithNumberOfOldStyleCharacteristics(Set) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl: Deprecated.
loadIgnoreAcls(Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService: Load FactorValues by IDs, ignoring ACLs.
loadIgnoreAcls(Set) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
loadIgnoreAcls(Set) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Load FactorValues by IDs, ignoring ACLs.
loadIgnoreAcls(Set) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
loadKnownGenes(Taxon) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
loadKnownGenes(Taxon) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
loadLackingFactors() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
loadLackingFactors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadLackingFactors() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadLackingFactors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadLackingFactors() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadLackingFactors() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadLackingTags() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
loadLackingTags() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadLackingTags() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadLackingTags() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadLackingTags() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadLackingTags() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadMicroRNAs(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
loadMicroRNAs(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
loadMicroRNAs(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
loadMicroRNAs(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
loadModel(boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService: Delegates the call as to load the model into memory or leave it on disk.
loadModel(boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.ClasspathOntologyService
loadModel(boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.TdbOntologyService
loadModel(boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.UrlOntologyService
loadModel(boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.providers.ChebiOntologyService
loadModel(boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService
loadModelFromStream(InputStream, boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService: Load a model from a given input stream.
loadModelFromStream(InputStream, boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.ClasspathOntologyService
loadModelFromStream(InputStream, boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.TdbOntologyService
loadModelFromStream(InputStream, boolean, OntologyService.LanguageLevel, OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.UrlOntologyService
loadMpsNames() - Method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize
loadMyGeneSets() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
loadMyGeneSets() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
loadMyGeneSets() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Returns the GeneSets for the currently logged in User - i.e, ones for which the current user has specific read permissions on (as opposed to data sets which are public).
loadMyGeneSets() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
loadMyGeneSets(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
loadMyGeneSets(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
loadMyGeneSets(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
loadMyGeneSets(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
loadMySetValueObjects(boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: load the user's sets
loadMySetValueObjects(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
loadMySharedGeneSets(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
loadMySharedGeneSets(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
loadMySharedGeneSets(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
loadMySharedGeneSets(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
loadOrFail(Long) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Long) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Load an entity of fail with a NullPointerException if it does not exist in the persistent storage.
loadOrFail(Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
loadOrFail(Long, Function) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Load an entity or fail with the supplied exception if it does not exist in the persistent storage.
loadOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
loadOrFail(Long, Function, String) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Long, Function, String) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Load an entity or fail with the supplied exception and message.
loadOrFail(Long, Function, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
loadOrFail(Long, Supplier) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Long, Supplier) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Load an entity or fail with the supplied exception if it does not exist in the persistent storage.
loadOrFail(Long, Supplier) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
loadOrFail(Collection) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Collection) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Load multiple objects or fail with a NullPointerException if any of the objects does not exist in the persistent storage.
loadOrFail(Collection, Function) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Collection, Function) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
loadOriginalPlatformValueObjectsForEE(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.
loadOriginalPlatformValueObjectsForEE(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
loadOriginalPlatformValueObjectsForEE(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService: Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.
loadOriginalPlatformValueObjectsForEE(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
loadOriginalPlatformValueObjectsForEE(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.
loadOriginalPlatformValueObjectsForEE(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadOtherCellLevelCharacteristics(ExpressionExperiment, SingleCellDataLoaderConfig) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderService: Load other cell-level characteristics (i.e.
loadOtherCellLevelCharacteristics(ExpressionExperiment, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl
loadOtherCellLevelCharacteristics(ExpressionExperiment, SingleCellDataType, SingleCellDataLoaderConfig) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderService: Load other cell-level characteristics (i.e.
loadOtherCellLevelCharacteristics(ExpressionExperiment, SingleCellDataType, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl
loadPlatformOnly - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest
loadPvalueDistribution(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Obtain the stored histogram of the P-value distribution for a given result set.
loadPvalueDistribution(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
loadPvalueDistribution(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
loadPvalueDistribution(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
loadReference(Long) - Method in class ubic.gemma.persistence.service.AbstractDao
loadReference(Long) - Method in interface ubic.gemma.persistence.service.BaseDao: Load reference for an entity.
loadReference(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadReference(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadReference(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadReference(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadReference(Collection) - Method in class ubic.gemma.persistence.service.AbstractDao
loadReference(Collection) - Method in interface ubic.gemma.persistence.service.BaseDao: Load references of entities of type T for all the given IDs.
loadReferences(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadReferences(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadReferences(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load references for the given experiment IDs.
loadReferences(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadRegressedMatrix(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService: Load the regressed coexpression matrix for the given experiment.
loadRegressedMatrix(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
loadResult(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
loadResult(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl: loads a neDifferentialExpressionMetaAnalysisResult
loadResultIdToGenesMap(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
loadResultIdToGenesMap(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
loadResultToGenesMap(ExpressionAnalysisResultSet, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Load a DifferentialExpressionAnalysisResult to Gene multi-map.
loadResultToGenesMap(ExpressionAnalysisResultSet, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
loadSequencingMetadata(ExpressionExperiment, SingleCellDataLoaderConfig) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderService: Load sequencing metadata.
loadSequencingMetadata(ExpressionExperiment, SingleCellDataLoaderConfig) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl
LoadSimpleExpressionDataCli - Class in ubic.gemma.apps: Command Line tools for loading the expression experiment in flat files
LoadSimpleExpressionDataCli() - Constructor for class ubic.gemma.apps.LoadSimpleExpressionDataCli
loadSubSet(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Load a subset by ID, without initializing collections.
loadSubSet(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
loadSubSetWithBioAssays(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService: Load a subset by ID with its bio-assays initialized.
loadSubSetWithBioAssays(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl
loadTermsInNameSpace(InputStream, boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
loadTermsInNameSpace(InputStream, boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService: Deprecated.
loadTermsInNameSpace(InputStream, boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService: Deprecated.
loadTermsInNameSpace(InputStream, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Deprecated.
use OntologyService.initialize(InputStream, boolean) instead and possibly OntologyService.cancelInitializationThread() prior to get any running initialization thread out of the way
loadThawed(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
loadThawed(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
loadThawed(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService: Load with objects already thawed.
loadThawed(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
loadThawed(Collection) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
loadThawed(Collection) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
loadThawedLiter(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
loadThawedLiter(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
loadThawedLiter(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
loadThawedLiter(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
loadThawedLiter(Collection) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
loadThawedLiter(Collection) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
loadTroubledIds() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
loadTroubledIds() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao: Load IDs of troubled entities.
loadTroubledIds() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDaoImpl
loadTroubledIds() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadTroubledIds() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadTroubledIds() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load troubled experiment IDs.
loadTroubledIds() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadUserByUsername(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
loadUsersByUsername(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
loadValueObject(C) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService
loadValueObject(Long, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
loadValueObject(Long, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
loadValueObject(Long, boolean) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Load a ticket and project it to a TicketValueObject inside the same transaction, force-initializing the reporter + assignee + targets (and events + each event's actor when includeEvents=true) so the projection doesn't raise LazyInitializationException once the transaction ends and the JAX-RS handler reads the returned VO.
loadValueObject(Long, boolean) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
loadValueObject(O) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadValueObject(O) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao
loadValueObject(O) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledService
loadValueObject(O) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledDao: Load a value object corresponding to an entity
loadValueObject(O) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledService
loadValueObject(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
loadValueObject(SearchResult) - Method in interface ubic.gemma.core.search.SearchService: Convert a SearchResult to its VO flavour.
loadValueObject(SearchResult) - Method in class ubic.gemma.core.search.SearchServiceImpl
loadValueObject(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObject(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledService
loadValueObjectById(Long) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadValueObjectById(Long) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledService
loadValueObjectById(Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
loadValueObjectById(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObjectById(Long, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: Get a value object for the id param.
loadValueObjectById(Long, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
loadValueObjectByIdLite(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
loadValueObjectByIdLite(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObjectByIdLite(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
loadValueObjectByIdLite(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
loadValueObjectByIdLite(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
loadValueObjectByIdLite(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
loadValueObjects(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService
loadValueObjects(Collection, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
loadValueObjects(Collection, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
loadValueObjects(Collection) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadValueObjects(Collection) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao: The default implementation calls AbstractVoEnabledDao.loadValueObject(Identifiable) for each entity and filters out nulls.
loadValueObjects(Collection) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledService
loadValueObjects(Collection) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledDao: Load value objects corresponding to entities
loadValueObjects(Collection) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledService: Loads value objects for all given entities.
loadValueObjects(Collection) - Method in interface ubic.gemma.core.search.SearchService: Convert a collection of SearchResult to their VO flavours.
loadValueObjects(Collection) - Method in class ubic.gemma.core.search.SearchServiceImpl
loadValueObjects(Collection, Map, Map, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
loadValueObjects(Collection, Map, Map, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
loadValueObjects(Collection, Map, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
loadValueObjects(Collection, Map, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
loadValueObjects(Collection, Map, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
loadValueObjects(Collection, Map, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
loadValueObjects(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObjects(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
loadValueObjects(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadValueObjects(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
loadValueObjects(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
loadValueObjects(Filters, Sort) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService
loadValueObjects(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadValueObjects(Filters, Sort) - Method in interface ubic.gemma.persistence.service.FilteringVoEnabledDao: Load VOs with minimal ordering and filtering.
loadValueObjects(Filters, Sort) - Method in interface ubic.gemma.persistence.service.FilteringVoEnabledService
loadValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
loadValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
loadValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
loadValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService
loadValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.FilteringVoEnabledDao: Load VOs with ordering, filtering and offset/limit.
loadValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.FilteringVoEnabledService
loadValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
loadValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in interface ubic.gemma.persistence.service.FilteringVoEnabledDao: Load VOs by keyset (cursor) pagination.
loadValueObjectsByCursor(Filters, Sort, Cursor, int) - Method in interface ubic.gemma.persistence.service.FilteringVoEnabledService: Keyset (cursor) pagination — service-layer pass-through to FilteringVoEnabledDao.loadValueObjectsByCursor(Filters, Sort, Cursor, int).
loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao: Cursor-paged listing of BioAssayValueObjects for a single ExpressionExperiment, sorted by ascending id — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService: Cursor-mode counterpart to the legacy unpaginated BioAssayDao EE-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao: Cursor-paged listing of BioAssayValueObjects for a single ExpressionExperimentSubSet, sorted by ascending id — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u (the subset-scoped twin of step 1k).
loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService: Cursor-mode counterpart to the legacy unpaginated subset-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u.
loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
loadValueObjectsByCursorWithCache(Filters, Sort, Cursor, int) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao: Cursor-paged sister of AbstractQueryFilteringVoEnabledDao.loadValueObjectsWithCache(Filters, Sort, int, int).
loadValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao
loadValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledService
loadValueObjectsByIds(Collection) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadValueObjectsByIds(Collection) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledService: Load value objects by a given collection of IDs.
loadValueObjectsByIds(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService
loadValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
loadValueObjectsByIds(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
loadValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
loadValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
loadValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObjectsByIds(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
loadValueObjectsByIds(List, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadValueObjectsByIds(List, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadValueObjectsByIds(List, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Variant of BaseVoEnabledService.loadValueObjectsByIds(Collection) that preserve its input order.
loadValueObjectsByIds(List, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadValueObjectsByIdsLite(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
loadValueObjectsByIdsLite(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObjectsByIdsLite(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
loadValueObjectsByIdsLite(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
loadValueObjectsByIdsLite(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
loadValueObjectsByIdsLite(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
loadValueObjectsByIdsLiter(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
loadValueObjectsByIdsLiter(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
loadValueObjectsByIdsLiter(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
loadValueObjectsByIdsLiter(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
loadValueObjectsByIdsWithRelationsAndCache(List) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadValueObjectsByIdsWithRelationsAndCache(List) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadValueObjectsByIdsWithRelationsAndCache(List) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load VOs for the given dataset IDs and initialize their relations like SecurableFilteringVoEnabledService.load(Filters, Sort).
loadValueObjectsByIdsWithRelationsAndCache(List) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadValueObjectsForEE(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
loadValueObjectsForEE(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
loadValueObjectsForEE(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
loadValueObjectsForEE(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
loadValueObjectsForEE(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Loads the Value Objects for array designs used by expression experiment with the given ID
loadValueObjectsForEE(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadValueObjectsForGene(Gene, int, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
loadValueObjectsForGene(Gene, int, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
loadValueObjectsForGeneByCursor(Gene, Cursor, int, boolean) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService: Cursor-mode counterpart to CompositeSequenceService.loadValueObjectsForGene(Gene, int, int, boolean) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1m.
loadValueObjectsForGeneByCursor(Gene, Cursor, int, boolean) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
loadValueObjectsWithCache(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
loadValueObjectsWithCache(Filters, Sort) - Method in interface ubic.gemma.persistence.service.CachedFilteringVoEnabledDao
loadValueObjectsWithCache(Filters, Sort) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
loadValueObjectsWithCache(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
loadValueObjectsWithCache(Filters, Sort) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
loadValueObjectsWithCache(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadValueObjectsWithCache(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
loadValueObjectsWithCache(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.CachedFilteringVoEnabledDao
loadValueObjectsWithCache(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadValueObjectsWithCache(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadValueObjectsWithCache(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadValueObjectsWithCache(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadValueObjectsWithExpressionExperiment(Collection, ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Load QuantitationTypeValueObject in the context of an associated expression experiment.
loadValueObjectsWithExpressionExperiment(Collection, ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
loadValueObjectsWithExpressionExperiment(Collection, ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
loadValueObjectsWithExpressionExperiment(Collection, ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
loadValueObjectsWithExpressionExperiment(Collection, ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
loadValueObjectsWithExpressionExperiment(Collection, ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
loadValueObjectWithGeneMappingSummary(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService: Include gene mapping summary in the CompositeSequenceValueObject.
loadValueObjectWithGeneMappingSummary(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
loadValueObjectWithResults(ExpressionAnalysisResultSet, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Load an analysis result set with its all of its associated results.
loadValueObjectWithResults(ExpressionAnalysisResultSet, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
loadValueObjectWithResults(ExpressionAnalysisResultSet, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
loadValueObjectWithResults(ExpressionAnalysisResultSet, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
loadVectors(Collection, SingleCellDimension, QuantitationType) - Method in class ubic.gemma.core.loader.expression.singleCell.AbstractDelegatingSingleCellDataLoader
loadVectors(Collection, SingleCellDimension, QuantitationType) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
loadVectors(Collection, SingleCellDimension, QuantitationType) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
loadVectors(Collection, SingleCellDimension, QuantitationType) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
loadVectors(Collection, SingleCellDimension, QuantitationType) - Method in interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader: Produces a stream of single-cell expression data vectors for the given QuantitationType.
loadWithAnalysis(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
loadWithAnalysis(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
loadWithAnalysisAndExperimentAnalyzed(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Load a result set with its analysis and the analysis' experimentAnalyzed fully initialized, in a single round-trip.
loadWithAnalysisAndExperimentAnalyzed(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
loadWithAuditTrail(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
loadWithAuditTrail(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
loadWithAuditTrail(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
loadWithAuditTrail(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadWithAuditTrail(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadWithAuditTrail(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadWithAuditTrail(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load an experiment with its audit trail initialized.
loadWithAuditTrail(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadWithBioAssays(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao
loadWithBioAssays(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl
loadWithBioAssays(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
loadWithBioAssays(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
loadWithCache(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
loadWithCache(Filters, Sort) - Method in interface ubic.gemma.persistence.service.CachedFilteringDao
loadWithCache(Filters, Sort) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
loadWithCache(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
loadWithCache(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.CachedFilteringDao
loadWithCharacteristics(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadWithCharacteristics(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadWithCharacteristics(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadWithCharacteristics(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadWithExperimentalFactor(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService: Load a FactorValue by id and eagerly initialize its experimental factor.
loadWithExperimentalFactor(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
loadWithExperimentalFactor(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService
loadWithExperimentalFactor(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
loadWithExperimentalFactorOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService: Load a FactorValue with an initialized experimental factor, or throw the supplied exception if no such factor value exists.
loadWithExperimentalFactorOrFail(Long, Function) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
loadWithExperimentalFactorOrFail(Long, Function) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Load a FactorValue with an initialized experimental factor or fail.
loadWithExperimentalFactorOrFail(Long, Function) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
loadWithExperimentalFactors(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignReadService
loadWithExperimentalFactors(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignReadServiceImpl
loadWithExperimentalFactors(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
loadWithExperimentalFactors(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignServiceImpl
loadWithExperimentAnalyzed(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService: Load an analysis by ID and eagerly initialize its experimentAnalyzed.
loadWithExperimentAnalyzed(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
loadWithExperimentAnalyzed(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
loadWithExperimentAnalyzed(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
loadWithExperimentAnalyzed(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
loadWithExperimentAnalyzed(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
loadWithExternalDatabases(Long) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseReadService
loadWithExternalDatabases(Long) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseReadServiceImpl
loadWithExternalDatabases(Long) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
loadWithExternalDatabases(Long) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
loadWithMeanVarianceRelation(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadWithMeanVarianceRelation(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadWithMeanVarianceRelation(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadWithMeanVarianceRelation(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadWithMembers(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetReadService
loadWithMembers(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl
loadWithMembers(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Load the gene sets with their members initialized.
loadWithMembers(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
loadWithOldStyleCharacteristics(Long, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Deprecated.
loadWithOldStyleCharacteristics(Long, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl: Deprecated.
loadWithOldStyleCharacteristics(Long, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueReadService: Deprecated.
do not use, this is only for migrating old-style characteristics to statements and will be removed
loadWithOldStyleCharacteristics(Long, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl
loadWithOldStyleCharacteristics(Long, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Deprecated.
do not use this, it is only meant for the purpose of migrating old-style characteristics to statements
loadWithOldStyleCharacteristics(Long, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl: Deprecated.
loadWithPrimaryPublication(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadWithPrimaryPublication(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadWithPrimaryPublication(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadWithPrimaryPublication(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadWithPrimaryPublicationAndOtherRelevantPublications(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
loadWithPrimaryPublicationAndOtherRelevantPublications(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
loadWithPrimaryPublicationAndOtherRelevantPublications(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadWithPrimaryPublicationAndOtherRelevantPublications(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadWithRelationsAndCache(List) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Load datasets by IDs with the same relation as ExpressionExperimentDao.loadWithCache(Filters, Sort).
loadWithRelationsAndCache(List) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadWithResultId(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
loadWithResultId(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl: loads a DifferentialExpressionMetaAnalysis containing a specific result
loadWithResultsAndContrasts(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Load an analysis result set with its all of its associated results.
loadWithResultsAndContrasts(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
loadWithResultsAndContrasts(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
loadWithResultsAndContrasts(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
loadWithResultsAndContrasts(Long, double, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Load a slice of an analysis result set with a corrected P-value threshold.
loadWithResultsAndContrasts(Long, double, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
loadWithResultsAndContrasts(Long, double, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
loadWithResultsAndContrasts(Long, double, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
loadWithResultsAndContrasts(Long, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Load a slice of an analysis result set.
loadWithResultsAndContrasts(Long, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
loadWithResultsAndContrasts(Long, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
loadWithResultsAndContrasts(Long, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
localBasePath - Variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
LocalDatasetFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher: Used for testing, but might have other uses, to fetch GEO data from local files instead of the GEO website.
LocalDatasetFetcher(String) - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.LocalDatasetFetcher
localNameToTermId(String) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Convert an OBO local name (CLO_0007606) to the term-ID form (CLO:0007606).
LocalSeriesFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher: A fetcher that only looks locally for "family" files (GPLXXX_family, GSEXXX_family).
LocalSeriesFetcher(String) - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.LocalSeriesFetcher
locateArrayDesign(String) - Method in interface ubic.gemma.cli.util.EntityLocator
locateArrayDesign(String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
locateBioAssay(ExpressionExperiment, String) - Method in interface ubic.gemma.cli.util.EntityLocator
locateBioAssay(ExpressionExperiment, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
locateBioAssay(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.cli.util.EntityLocator
locateBioAssay(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
locateCellLevelCharacteristics(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.cli.util.EntityLocator
locateCellLevelCharacteristics(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
locateCellTypeAssignment(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.cli.util.EntityLocator
locateCellTypeAssignment(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
Located(String, TermViolation) - Constructor for class ubic.gemma.rest.util.OntologyTermValidationException.Located
locateDiffExAnalysis(ExpressionExperiment, String) - Method in interface ubic.gemma.cli.util.EntityLocator
locateDiffExAnalysis(ExpressionExperiment, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
locateExperimentalFactor(ExpressionExperiment, String) - Method in interface ubic.gemma.cli.util.EntityLocator
locateExperimentalFactor(ExpressionExperiment, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
locateExpressionExperiment(String, boolean) - Method in interface ubic.gemma.cli.util.EntityLocator
locateExpressionExperiment(String, boolean) - Method in class ubic.gemma.cli.util.EntityLocatorImpl: Attempt to locate an experiment using the given identifier.
locateParentAcl(SecuredChild) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice: Called during create.
locatePrimaryReference(ExpressionExperiment) - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder
locatePrimaryReference(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder: Locate the primary reference for an experiment from GEO.
locateProtocol(String) - Method in interface ubic.gemma.cli.util.EntityLocator
locateProtocol(String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
locatePubMedId(String) - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder: As ExpressionExperimentBibRefFinder.locatePubMedIds(String), but only the first id — the primary, matching GeoConverterImpl's first-id-is-primary convention.
locatePubMedIds(String) - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder: Every PubMed id GEO lists for a series, in the order GEO lists them.
locateQuantitationType(ExpressionExperiment, String, Class) - Method in interface ubic.gemma.cli.util.EntityLocator
locateQuantitationType(ExpressionExperiment, String, Class) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
locateQuantitationType(ExpressionExperiment, String, Collection) - Method in interface ubic.gemma.cli.util.EntityLocator
locateQuantitationType(ExpressionExperiment, String, Collection) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
locateTaxon(String) - Method in interface ubic.gemma.cli.util.EntityLocator
locateTaxon(String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl
location(String) - Method in class ubic.gemma.rest.util.WellComposedError.WellComposedErrorBuilder
location(String) - Method in class ubic.gemma.rest.util.WellComposedWarning.WellComposedWarningBuilder
locationType(LocationType) - Method in class ubic.gemma.rest.util.WellComposedError.WellComposedErrorBuilder
locationType(LocationType) - Method in class ubic.gemma.rest.util.WellComposedWarning.WellComposedWarningBuilder
LocationType - Enum Class in ubic.gemma.rest.util
lock - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockBulkResult
lock() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock: Acquire a lock on the cache key.
lock() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLock
LOCK_REQUIRED - Enum constant in enum class ubic.gemma.rest.util.CurationCommitConflictException.Reason: A write was attempted while someone else holds the curation lock.
locked - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockResponse
lockedAt - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockResponse
lockedBy - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockResponse
LockedPath - Interface in ubic.gemma.core.util.locking: A locked path.
LockExpressionDataFileCli - Class in ubic.gemma.apps: This CLI allows one to lock an experiment data or metadata file.
LockExpressionDataFileCli() - Constructor for class ubic.gemma.apps.LockExpressionDataFileCli
lockInterruptibly() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock: Acquire a lock interruptibly on a cache key.
lockInterruptibly() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLock
loessFit(DoubleMatrix2D) - Static method in class ubic.gemma.core.util.math.Smooth
loessFit(DoubleMatrix2D, double) - Static method in class ubic.gemma.core.util.math.Smooth: Computes a loess regression line to fit the data
log - Variable in class ubic.gemma.cli.util.AbstractCLI
log - Static variable in class ubic.gemma.core.goldenpath.GoldenPath
log - Static variable in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
log - Static variable in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
log - Variable in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector
log - Variable in class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer
log - Variable in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractScriptBasedTransformation
log - Variable in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
log - Static variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
log - Variable in class ubic.gemma.core.loader.util.fetcher2.AbstractFetcher
log - Variable in class ubic.gemma.core.loader.util.ftp.AbstractFTPClientAuthenticator
log - Variable in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
log - Variable in class ubic.gemma.core.loader.util.parser.BasicLineParser
log - Static variable in class ubic.gemma.core.loader.util.parser.RecordParser
log - Static variable in class ubic.gemma.core.loader.util.ParserAndLoaderTools
log - Static variable in class ubic.gemma.core.ontology.jena.AbstractOntologyService
log - Variable in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
log - Static variable in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProvider
log - Static variable in class ubic.gemma.core.util.matrix.AbstractMatrixReader
log - Static variable in class ubic.gemma.core.util.matrix.datafilter.AbstractFilter
log - Static variable in class ubic.gemma.persistence.persister.CommonPersister: Shared logger for all persisters.
log - Variable in class ubic.gemma.persistence.service.AbstractDao
log - Static variable in class ubic.gemma.persistence.service.AbstractService
log - Variable in class ubic.gemma.rest.providers.AbstractExceptionMapper
log - Variable in class ubic.gemma.rest.providers.AbstractGzipHeaderDecorator
log - Static variable in class ubic.gemma.rest.TaxaWebService
log(Auditable, AuditEvent) - Method in class ubic.gemma.core.security.audit.AuditLogger: Log a given audit event.
LOG_SUM - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl.SingleCellExpressionAggregationMethod: Equivalent to SingleCellExpressionExperimentAggregateServiceImpl.SingleCellExpressionAggregationMethod.SUM for log-transformed data.
LOG10 - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Data is log-transformed with a base 10 log.
log10ratio - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
LOG1P - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Data is log-transformed as per ln X + 1
LOG1P_SUM - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl.SingleCellExpressionAggregationMethod: Equivalent to SingleCellExpressionExperimentAggregateServiceImpl.SingleCellExpressionAggregationMethod.SUM for data transformed by log 1 + X
LOG2 - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Data is log-transformed with a base 2 log.
log2cpmFromCounts(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
log2cpmFromCounts(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.core.loader.expression.DataUpdaterImpl: RNA-seq: For back filling log2cpm when only counts are available.
log2FoldChange - Variable in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneDiffExStats
log2Ratio - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
Log4jConfig - Class in ubic.gemma.core.logging.log4j
Log4jConfig() - Constructor for class ubic.gemma.core.logging.log4j.Log4jConfig
Log4jConfigurer - Class in ubic.gemma.cli.logging.log4j: Implementation of LoggingConfigurer for Log4j.
Log4jConfigurer() - Constructor for class ubic.gemma.cli.logging.log4j.Log4jConfigurer
LOGBASEUNKNOWN - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Data is log-transformed, but the base is unknown.
logERatio - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
loggedIn() - Method in interface ubic.gemma.core.security.authentication.UserDetailsManager
loggedIn() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
LoggerCompletionSource - Class in ubic.gemma.cli.completion
LoggerCompletionSource(LoggingConfigurer) - Constructor for class ubic.gemma.cli.completion.LoggerCompletionSource
LoggingBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch: Task summary writer that logs the result of a batch task to a logger.
LoggingBatchTaskSummaryWriter(String) - Constructor for class ubic.gemma.cli.batch.LoggingBatchTaskSummaryWriter
LoggingBatchTaskSummaryWriter(String, boolean) - Constructor for class ubic.gemma.cli.batch.LoggingBatchTaskSummaryWriter
LoggingConfigurer - Interface in ubic.gemma.cli.logging: Simple interface for configuring logging levels.
LoggingProgressReporter - Class in ubic.gemma.core.util: Report progress to a specific log category.
LoggingProgressReporter(Object, String) - Constructor for class ubic.gemma.core.util.LoggingProgressReporter
Logical expressions - Section in class ubic.gemma.rest.util.args.FilterArg
logIds(String, Collection) - Method in class ubic.gemma.core.ontology.GoMetricImpl
login(AuthWebService.LoginRequest) - Method in class ubic.gemma.rest.AuthWebService: Verify credentials, mint a new opaque bearer token, and return both the token and the canonical user shape (mirrors GET /rest/v2/users/me).
LoginDetailsValueObject - Class in ubic.gemma.core.security.authentication
LoginDetailsValueObject() - Constructor for class ubic.gemma.core.security.authentication.LoginDetailsValueObject
LoginRequest() - Constructor for class ubic.gemma.rest.AuthWebService.LoginRequest
LoginResponse(String, RootWebService.UserValueObject) - Constructor for class ubic.gemma.rest.AuthWebService.LoginResponse
logout(HttpServletRequest) - Method in class ubic.gemma.rest.AuthWebService: Revoke the bearer token presented in the Authorization header.
logRatio - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
logTransform(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixStats: Log-transform the values in a matrix (log base 2).
logTransformMatrix(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder: Log-transform the values in the matrix (base 2).
LONG - Enum constant in enum class ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType
LONG - Enum constant in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType
longArrayToBytes(long[]) - Method in class ubic.gemma.persistence.util.ByteArrayConverter
longArrayToBytes(long[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
lookup(String) - Static method in class ubic.gemma.core.ontology.ValueStringToOntologyMapping: Deprecated.

Lookup a value across all categories.
lookup(String) - Method in class ubic.gemma.rest.security.TokenStore: Look up the Authentication previously associated with this token, refreshing the sliding-TTL clock.
lookup(String, String) - Static method in class ubic.gemma.core.ontology.ValueStringToOntologyMapping: Deprecated.

Lookup a value for a given category.
lookupStrategy(DataSource, AclCache, AclAuthorizationStrategy, PermissionGrantingStrategy) - Method in class ubic.gemma.core.security.acl.GemmaAclConfiguration
LOOM - Enum constant in enum class ubic.gemma.core.loader.expression.singleCell.SingleCellDataType: Loom
LoomSingleCellDetector - Class in ubic.gemma.core.loader.expression.geo.singleCell: Detects Loom files in series and samples.
LoomSingleCellDetector() - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.LoomSingleCellDetector
LOW - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketPriority
lowDistinctValueCut() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the lowDistinctValueCut record component.
lowExpressionCut() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the lowExpressionCut record component.
lowVarianceCut() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the lowVarianceCut record component.
LowVarianceFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Filter rows with low variance by keeping those with variance above a given cut-off.
LowVarianceFilter() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.LowVarianceFilter
LowVarianceFilter(double) - Constructor for class ubic.gemma.core.analysis.preprocess.filter.LowVarianceFilter
LuceneOrderRankingStrategy - Class in ubic.gemma.rest.ranking: No-op default — returns the input list unchanged (as a defensive copy).
LuceneOrderRankingStrategy() - Constructor for class ubic.gemma.rest.ranking.LuceneOrderRankingStrategy
LuceneParseSearchException - Exception Class in ubic.gemma.core.search.lucene
LuceneParseSearchException(String, String, ParseException) - Constructor for exception class ubic.gemma.core.search.lucene.LuceneParseSearchException
LuceneParseSearchException(String, String, ParseException, LuceneParseSearchException) - Constructor for exception class ubic.gemma.core.search.lucene.LuceneParseSearchException
LuceneParseSearchException(String, ParseException) - Constructor for exception class ubic.gemma.core.search.lucene.LuceneParseSearchException
LuceneQueryUtils - Class in ubic.gemma.core.search.lucene: Utilities for parsing search queries using Lucene.
LuceneQueryUtils() - Constructor for class ubic.gemma.core.search.lucene.LuceneQueryUtils
LUIGI - Enum constant in enum class ubic.gemma.model.pipeline.SchedulerKind
LuigiPipelineScheduler - Class in ubic.gemma.core.pipeline: Luigi-backed scheduler.
LuigiPipelineScheduler() - Constructor for class ubic.gemma.core.pipeline.LuigiPipelineScheduler
lumenOf - Static variable in class ubic.gemma.core.ontology.jena.RO
luminalSpaceOf - Static variable in class ubic.gemma.core.ontology.jena.RO

M

M_1_PI - Static variable in class ubic.gemma.core.util.math.Constants
M_1_SQRT_2 - Static variable in class ubic.gemma.core.util.math.Constants
M_1_SQRT_2PI - Static variable in class ubic.gemma.core.util.math.Constants
m_cellSize - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_colorPalette - Variable in class ubic.gemma.core.util.graphics.ColorMap
m_columnLabelHeight - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_currentColorMap - Variable in class ubic.gemma.core.util.graphics.ColorMap
m_defaultResolution - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_defaultSuggestedNumberOfColors - Static variable in class ubic.gemma.core.util.graphics.ColorMap
m_fontGutter - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_fontSize - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_isShowLabels - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_isShowScale - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_labelFont - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_labelGutter - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
M_LN_2 - Static variable in class ubic.gemma.core.util.math.Constants
M_LN_SQRT_2PI - Static variable in class ubic.gemma.core.util.math.Constants
M_LN_SQRT_PI - Static variable in class ubic.gemma.core.util.math.Constants
M_LN_SQRT_PId2 - Static variable in class ubic.gemma.core.util.math.Constants
M_LOG10_2 - Static variable in class ubic.gemma.core.util.math.Constants
m_maxColumnLength - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_maxFontSize - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
M_PI_2 - Static variable in class ubic.gemma.core.util.math.Constants
M_PI_4 - Static variable in class ubic.gemma.core.util.math.Constants
M_PI_half - Static variable in class ubic.gemma.core.util.math.Constants
m_ratioWidth - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_resolution - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_rowKeys - Variable in class ubic.gemma.core.util.graphics.ColorMatrix: to be able to sort the rows by an arbitrary key
m_rowLabelWidth - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
M_SQRT_2 - Static variable in class ubic.gemma.core.util.math.Constants
M_SQRT_2dPI - Static variable in class ubic.gemma.core.util.math.Constants
M_SQRT_PI - Static variable in class ubic.gemma.core.util.math.Constants
m_textSize - Variable in class ubic.gemma.core.util.graphics.MatrixDisplay
m_totalColumns - Variable in class ubic.gemma.core.util.graphics.ColorMatrix
m_totalRows - Variable in class ubic.gemma.core.util.graphics.ColorMatrix
mad(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the median absolute deviation from the median.
MailEngine - Interface in ubic.gemma.core.mail
MailEngineImpl - Class in ubic.gemma.core.mail
MailEngineImpl() - Constructor for class ubic.gemma.core.mail.MailEngineImpl
mailSender(String, String, String, String) - Method in class ubic.gemma.core.config.DataSourceConfig
MailService - Interface in ubic.gemma.core.mail: High-level service for sending mails.
MailServiceImpl - Class in ubic.gemma.core.mail
MailServiceImpl() - Constructor for class ubic.gemma.core.mail.MailServiceImpl
main(String[]) - Static method in class ubic.gemma.cli.main.GemmaCLI
mainStemOf - Static variable in class ubic.gemma.core.ontology.jena.RO
makeContrasts() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix: In limma, the contrasts are built by referring to the coefficients by name, which isn't what we want.
makeDataMatrix(ObjectMatrix, DoubleMatrix) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Convert the data into a string-keyed matrix.
makeDatasetPrivate(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI workflow-step endpoint: raw ACL flip to make a dataset private.
makeDatasetPublic(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI workflow-step endpoint: raw ACL flip to make a dataset publicly readable.
makeEditableByGroup(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService: Adds write (and read) permissions.
makeEditableByGroup(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
MakeExperimentPrivateCli - Class in ubic.gemma.apps
MakeExperimentPrivateCli() - Constructor for class ubic.gemma.apps.MakeExperimentPrivateCli
MakeExperimentsPublicCli - Class in ubic.gemma.apps: Make data sets public.
MakeExperimentsPublicCli() - Constructor for class ubic.gemma.apps.MakeExperimentsPublicCli
makeNames(String) - Static method in class ubic.gemma.core.util.StringUtil: Mimics the make.names method in R for a single string.
makeNames(String[], boolean) - Static method in class ubic.gemma.core.util.StringUtil: Mimics the make.names method in R.
makeObjectIdentity(Securable) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice: Forms the object identity to be inserted in acl_object_identity table.
makeOwnedByUser(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService: Administrative method to allow a user to get access to an object.
makeOwnedByUser(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
makePreferred(boolean) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder: Make the resulting QT preferred.
makePrivate(Collection) - Method in interface ubic.gemma.core.security.SecurityService: Make a collection of objects private.
makePrivate(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
makePrivate(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Makes the object private.
makePrivate(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
MakePrivateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicate that an entity has been made private.
MakePrivateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.MakePrivateEvent
makePublic(Collection) - Method in interface ubic.gemma.core.security.SecurityService: Make a collection of objects public.
makePublic(Collection) - Method in class ubic.gemma.core.security.SecurityServiceImpl
makePublic(Securable) - Method in interface ubic.gemma.core.security.SecurityService: Makes the object public
makePublic(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
MakePublicEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicate that an entity has been made public.
MakePublicEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.MakePublicEvent
makeReadableByGroup(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService: Adds read permission for a given group.
makeReadableByGroup(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
makeTitle(String, String) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl: Form title (will be experiment name) and ensure is valid length
makeUneditableByGroup(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService: Remove write permissions.
makeUneditableByGroup(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
makeUnique(String[]) - Static method in class ubic.gemma.core.util.StringUtil: Mimics the make.unique method in R.
makeUnreadableByGroup(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService: Remove read permissions; also removes write permissions.
makeUnreadableByGroup(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
MalformedArgException - Exception Class in ubic.gemma.rest.util: Specialized error for malformed Arg The recommended HTTP status for this exception is 400 Bad Request.
MalformedArgException(String) - Constructor for exception class ubic.gemma.rest.util.MalformedArgException
MalformedArgException(String, Throwable) - Constructor for exception class ubic.gemma.rest.util.MalformedArgException
MalformedArgException(Throwable) - Constructor for exception class ubic.gemma.rest.util.MalformedArgException
MalformedArgExceptionMapper - Class in ubic.gemma.rest.providers
MalformedArgExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.MalformedArgExceptionMapper
MammalianPhenotypeOntologyService - Class in ubic.gemma.core.ontology.providers: Mammalian Phenotype Ontology
MammalianPhenotypeOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.MammalianPhenotypeOntologyService
mammalianPhenotypeOntologyServiceOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
Managing security on entities - Section in package ubic.gemma.core.security
manhattanDistance(DoubleArrayList, DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Distance: Calculate the Manhattan distance between two vectors.
ManifestUtils - Class in ubic.gemma.core.util
ManifestUtils() - Constructor for class ubic.gemma.core.util.ManifestUtils
MANUAL - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketMode
ManualAnnotationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
ManualAnnotationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ManualAnnotationEvent
ManualAuthenticationService - Interface in ubic.gemma.core.security.authentication
ManualAuthenticationServiceBasedSecurityContextFactory - Class in ubic.gemma.core.security.authentication: Creates a security context using manual authentication.
ManualAuthenticationServiceBasedSecurityContextFactory() - Constructor for class ubic.gemma.core.security.authentication.ManualAuthenticationServiceBasedSecurityContextFactory
ManualAuthenticationServiceImpl - Class in ubic.gemma.core.security.authentication: Process authentication requests that come from outside a web context.
ManualAuthenticationServiceImpl(AuthenticationManager, String) - Constructor for class ubic.gemma.core.security.authentication.ManualAuthenticationServiceImpl
map(Function) - Method in class ubic.gemma.persistence.util.CursorPage
map(Function) - Method in class ubic.gemma.persistence.util.Slice
MapBasedDesignElementMapper - Class in ubic.gemma.core.loader.util.mapper
MapBasedDesignElementMapper(String, Map) - Constructor for class ubic.gemma.core.loader.util.mapper.MapBasedDesignElementMapper
MapBasedEntityMapper<T> - Class in ubic.gemma.core.loader.util.mapper: A simple implementation of EntityMapper that uses a Map to store association between identifiers and entities.
MapBasedEntityMapper(String, Map) - Constructor for class ubic.gemma.core.loader.util.mapper.MapBasedEntityMapper
mapFromGene2GO(String) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser: Note that "-" means a missing value, which in practice only occurs in the "qualifier" and "pubmed" columns.
Mapping - Class in ubic.gemma.core.loader.util.anndata: Represents an AnnData mapping.
Mapping(H5Group) - Constructor for class ubic.gemma.core.loader.util.anndata.Mapping
Mapping (read side) - Section in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService
MappingStatistics(double, double) - Constructor for class ubic.gemma.core.loader.util.mapper.EntityMapper.MappingStatistics: Creates a new MappingStatistics instance.
mapValuesToColors() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
mark - Variable in class ubic.gemma.rest.DatasetsWebService.BatchOutlierRequest
markAsMissing(Collection) - Method in interface ubic.gemma.core.analysis.service.OutlierFlaggingService: This does not actually remove the sample; rather, it sets all values to "missing" in the processed data.
markAsMissing(Collection) - Method in class ubic.gemma.core.analysis.service.OutlierFlaggingServiceImpl
markAsNeedsAttention(FactorValue, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionService: Mark a given factor value as needs attention.
markAsNeedsAttention(FactorValue, String) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceImpl
markDatasetSampleOutlier(DatasetArg, Long, DatasetsWebService.SampleOutlierRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Mark (or unmark) a BioAssay as a sample outlier.
MarkdownUtils - Class in ubic.gemma.core.util: Utilities for handling Markdown text.
MarkdownUtils() - Constructor for class ubic.gemma.core.util.MarkdownUtils
markedCount - Variable in class ubic.gemma.rest.DatasetsWebService.BatchOutlierResponse
Marker - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser.model
Marker() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
markFactorValueNeedsAttention(DatasetArg, Long, DatasetsWebService.FactorValueNeedsAttentionRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Open a "needs attention" ticket against a factor value.
markQuantitationTypeAsPreferred(boolean) - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder: Mark the QT as preferred.
markQuantitationTypeAsRecomputedFromRawData(boolean) - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder: Mark the quantitation type as recomputed from raw data.
markSingleCellTypeAssignmentAsPreferred(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: If only one CTA is present, mark it as preferred.
marshal(Date) - Method in class ubic.gemma.core.loader.expression.sra.model.SraDateParser
mask - Variable in class ubic.gemma.core.loader.util.anndata.NullableArray
mask() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload: Returns the value of the mask record component.
mask(CellLevelCharacteristics) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder: Categorical mask to use on data.
MASK - Static variable in class ubic.gemma.model.common.description.Categories: Represent a mask for a set of data.
maskColumns(ExpressionDataMatrix, boolean[], T) - Static method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix: Mask whole columns of the given matrix.
maskedCells() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns the value of the maskedCells record component.
MaskedExpressionDataMatrix<T> - Class in ubic.gemma.core.datastructure.matrix: A wrapper for an ExpressionDataMatrix that applies a mask to the data, allowing selective access to the underlying matrix.
maskElements(ExpressionDataMatrix, boolean[][], T) - Static method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix: Mask individual elements of the given matrix.
maskElements(ExpressionDataMatrix, int[], int[], T) - Static method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix: Mask individual elements of the given matrix at the specified coordinates.
maskMissing(DoubleMatrix2D, DoubleMatrix2D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
maskOutliers() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the maskOutliers record component.
maskRows(ExpressionDataMatrix, boolean[], T) - Static method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix: Mask whole rows of the given matrix.
MASS - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementKind
MATCH_BY_ACCESSION_SCORE - Static variable in class ubic.gemma.core.search.source.DatabaseSearchSource
MATCH_BY_ID_SCORE - Static variable in class ubic.gemma.core.search.source.DatabaseSearchSource: Score when a result is matched exactly by numerical ID.
MATCH_BY_NAME_SCORE - Static variable in class ubic.gemma.core.search.source.DatabaseSearchSource
MATCH_BY_NCBI_ID_SCORE - Static variable in class ubic.gemma.core.search.source.DatabaseSearchSource
MATCH_BY_SHORT_NAME_SCORE - Static variable in class ubic.gemma.core.search.source.DatabaseSearchSource
matchAll(String) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper.StatefulEntityMapper: Match the identifier to all the matching candidates.
matchAll(Collection) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper.StatefulEntityMapper: Map each identifier to all the matching candidate.
matchAll(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.ChainedEntityMapper
matchAll(Collection, String) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper: Match the identifier to all the candidates.
matchAll(Collection, Collection) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper: Match each identifier to all the candidates.
matchAll(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
matchAll(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper
matchAll(Collection, Collection) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
matchAllInternal(Collection, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoBioAssayMapper
matchAllInternal(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
matchAllInternal(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.SimpleBioAssayMapper
matchBioAssayToCelFileName(Map, String) - Static method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize
matchDescriptionIgnoreCase(String, String) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
matchedCriteria - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
matchedEvidence - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate: Why each criterion fired, keyed by matcher name — e.g.
matches(CriteriaBuilder, From, Contact) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, Characteristic) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, Gene2GOAssociation) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, QuantitationType) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, ArrayDesign) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, BioAssay) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, BioMaterial) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, ExperimentalFactor) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, BioSequence) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, Chromosome) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, Gene, boolean) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CriteriaBuilder, From, Taxon) - Static method in class ubic.gemma.persistence.util.BusinessKey
matches(CharSequence, String) - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder
matches(TypeDescriptor, TypeDescriptor) - Method in class ubic.gemma.persistence.util.ServiceBasedEntityConverter
matches(TypeDescriptor, TypeDescriptor) - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverter
matchId(Long, String) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
matchingCriteria(DoubleMatrix1D, DoubleFunction) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
matchName(String, String) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
matchNameIgnoreCase(String, String) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
matchOne(String) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper.StatefulEntityMapper: Map the identifier to a matching candidate.
matchOne(Collection) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper.StatefulEntityMapper: Map each identifier to a matching candidate.
matchOne(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.ChainedEntityMapper
matchOne(Collection, String) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper: Map the identifier to a single candidate.
matchOne(Collection, Collection) - Method in interface ubic.gemma.core.loader.util.mapper.EntityMapper: Match each identifier to a single candidate.
matchOne(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
matchOne(Collection, String) - Method in class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper
matchOne(Collection, Collection) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
MatchResult(boolean, String, double) - Constructor for class ubic.gemma.core.geoscrape.GeoRecordMatcher.MatchResult
matchWithFunction(Collection, Function, BiFunction, String, Collection) - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
MathUtil - Class in ubic.gemma.core.util.math: Small numeric helpers.
MathUtil() - Constructor for class ubic.gemma.core.util.math.MathUtil
matmat_j(double[][], double[][], double[][], int, int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method multiplies an n x p matrix by a p x r matrix.
Matrix - Interface in ubic.gemma.core.loader.util.anndata: Represents an AnnData matrix.
Matrix2D<R,C,V> - Interface in ubic.gemma.core.util.matrix: Represents a matrix with index columns and rows.
MatrixDisplay<R,C> - Class in ubic.gemma.core.util.graphics: A visual component for displaying a color matrix
MatrixDisplay(ColorMatrix) - Constructor for class ubic.gemma.core.util.graphics.MatrixDisplay
MatrixDisplay(DoubleMatrix) - Constructor for class ubic.gemma.core.util.graphics.MatrixDisplay
MatrixMarketUtils - Class in ubic.gemma.core.loader.util: Utilities for reading MatrixMarket format.
MatrixMarketUtils() - Constructor for class ubic.gemma.core.loader.util.MatrixMarketUtils
MatrixNormalizer<R,C> - Class in ubic.gemma.core.util.math
MatrixNormalizer() - Constructor for class ubic.gemma.core.util.math.MatrixNormalizer
MatrixRowStats - Class in ubic.gemma.core.util.math: Convenience functions for getting row statistics from matrices.
MatrixSection() - Constructor for class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection
MatrixStats - Class in ubic.gemma.core.util.math
MatrixStats - Class in ubic.gemma.core.util: Extends MatrixStats.
MatrixStats() - Constructor for class ubic.gemma.core.util.math.MatrixStats
MatrixStats() - Constructor for class ubic.gemma.core.util.MatrixStats
MatrixUtil - Class in ubic.gemma.core.util.matrix
MatrixUtil() - Constructor for class ubic.gemma.core.util.matrix.MatrixUtil
MatrixWriter - Class in ubic.gemma.core.datastructure.matrix.io: Writes BulkExpressionDataMatrix to a tabular format.
MatrixWriter<R,C> - Class in ubic.gemma.core.util.matrix: Class for writing matrices to disk
MatrixWriter(OutputStream) - Constructor for class ubic.gemma.core.util.matrix.MatrixWriter
MatrixWriter(OutputStream, Format) - Constructor for class ubic.gemma.core.util.matrix.MatrixWriter
MatrixWriter(OutputStream, Format, String) - Constructor for class ubic.gemma.core.util.matrix.MatrixWriter
MatrixWriter(Writer) - Constructor for class ubic.gemma.core.util.matrix.MatrixWriter
MatrixWriter(Writer, String) - Constructor for class ubic.gemma.core.util.matrix.MatrixWriter
MatrixWriter(Writer, Format) - Constructor for class ubic.gemma.core.util.matrix.MatrixWriter
MatrixWriter(Writer, Format, String) - Constructor for class ubic.gemma.core.util.matrix.MatrixWriter
MatrixWriter(String, Format) - Constructor for class ubic.gemma.core.util.matrix.MatrixWriter
MatrixWriter(String, Format, String) - Constructor for class ubic.gemma.core.util.matrix.MatrixWriter
MatrixWriter(EntityUrlBuilder, BuildInfo) - Constructor for class ubic.gemma.core.datastructure.matrix.io.MatrixWriter
mattran_j(double[][], double[][], int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method obtains the transpose of an n x p matrix.
matvec_j(double[][], double[], double[], int, int) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method multiplies an n x p matrix by a p x 1 vector.
max - Enum constant in enum class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod
max - Variable in class ubic.gemma.core.util.graphics.ColorMatrix
max() - Method in class ubic.gemma.core.util.math.distribution.Histogram
max(double[]) - Static method in class ubic.gemma.core.util.math.MathUtil
max(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing
max(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixStats: Compute the maximum value in the matrix.
max(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
max(SingleCellExpressionDataVector, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
max(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
max(SingleCellExpressionDataVector, CellLevelCharacteristics) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
MAX - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
MAX_BATCH_CONFOUND_LENGTH - Static variable in class ubic.gemma.model.expression.experiment.ExpressionExperiment
MAX_CARDINALITY - Enum constant in enum class ubic.gemma.core.ontology.model.OntologyCardinalityRestriction.CardinalityType
MAX_CLAUSES - Static variable in class ubic.gemma.rest.util.args.FilterArg: Maximum number of clauses that can appear in a filter expression.
MAX_DETAIL_LENGTH - Static variable in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
MAX_LIMIT - Static variable in class ubic.gemma.rest.CompletionsWebService: Hard cap on limit; requests above this are clamped down.
MAX_NAME_LENGTH - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssay
MAX_NAME_LENGTH - Static variable in class ubic.gemma.model.expression.biomaterial.BioMaterial
MAX_NAME_LENGTH - Static variable in class ubic.gemma.model.expression.experiment.ExpressionExperiment
MAX_NAME_LENGTH - Static variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet: Maximum length of the name of a subset.
MAX_NOTE_LENGTH - Static variable in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
MAX_PARAMETER_LIST_SIZE - Static variable in class ubic.gemma.persistence.util.QueryUtils: Largest parameter list size for which QueryUtils.optimizeParameterList(Collection) should be used.
MAX_QUEUING_MILLIS - Static variable in class ubic.gemma.core.job.TaskCommand: How long we will queue a task before giving up and cancelling it (default value)
MAX_ROWS_TO_PRINT - Static variable in class ubic.gemma.core.util.matrix.AbstractMatrix
MAX_RUNTIME_MILLIS - Static variable in class ubic.gemma.core.job.TaskCommand
MAX_SAFE_INMEMORY_SC_MATRIX_SAMPLES - Static variable in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl: Sample-count ceiling above which SingleCellExpressionExperimentServiceImpl.getSingleCellExpressionDataMatrix(ExpressionExperiment, List, QuantitationType) refuses to materialize.
MAX_SEARCH_RESULTS - Static variable in class ubic.gemma.rest.SearchWebService: Maximum number of search results.
MAX_WARNINGS - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
maxAge() - Element in annotation interface ubic.gemma.rest.annotations.CacheControl
maxBytes - Variable in class ubic.gemma.rest.AdminWebService.MemoryBlock: -1 when the JVM does not define a maximum (e.g.
maxExecutionTimeMillis - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
maxExecutionTimeOf(String) - Static method in class ubic.gemma.core.config.DataSourceConfig: Read back the statement timeout DataSourceConfig.withMaxExecutionTime(String, String) composed, in milliseconds, or null when the list carries none.
MAXIMUM - Static variable in class ubic.gemma.rest.util.args.LimitArg: This is the default maximum used for LimitArg.getValue().
maximumObjectBreadth(int) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery: Drop relations whose object relates to more than this many distinct subjects.
maximumPoolSize - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
maximumSubjectBreadth(int) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery: Drop relations whose subject relates to more than this many distinct objects under the same predicate.
maxLifetimeMillis - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
maxRecords - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeRequest: Hard cap on number of GEO records examined, counted from the HEAD of the result set.
maxResults(int) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Limit for the number of results per result type.
maxResults(int) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
maxStringPixelWidth(String[], FontMetrics) - Static method in class ubic.gemma.core.util.graphics.text.Util
maxtrix - Variable in class ubic.gemma.core.util.graphics.ColorMatrix
maybeBackground(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
maybeDerivedSignal(String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
maybeMeasuredSignal(String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
maybeRatio(String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
MayBeUninitialized - Annotation Interface in ubic.gemma.model.annotations: Indicate that a collection or an entity may be intentionally uninitialized.
MDB_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy: 🛑 Spelled MDB rather than MBD.
me() - Method in class ubic.gemma.rest.AuthWebService: Convenience alias for GET /rest/v2/users/me; the curation-UI SPA's useMe() hook points at /rest/v2/me verbatim, so we mirror the shape here rather than asking the SPA to track the longer path.
mean - Enum constant in enum class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod
mean(double[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
mean(float[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
mean(int[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
mean(long[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
mean(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing
mean(DoubleArrayList, int) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Special mean calculation where we use the effective size as an input.
mean(DataVector) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive: Calculate the mean of the data in the vector.
mean(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive: Calculate the mean of each assay for a given vector.
mean(SingleCellExpressionDataVector, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
mean(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
mean(SingleCellExpressionDataVector, BioAssay) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive: Calculate the mean of a given assay.
MEAN - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
meanAboveQuantile(int, double[], int) - Static method in class ubic.gemma.core.util.math.Stats: calculate the mean of the values above (NOT greater or equal to) a particular index rank of an array.
meanAboveQuantile(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Calculate the mean of the values above to a particular quantile of an array.
MeanDifferenceMetaAnalysis - Class in ubic.gemma.core.util.math.metaanalysis: Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
MeanDifferenceMetaAnalysis(boolean) - Constructor for class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
means(DoubleMatrix2D) - Static method in class ubic.gemma.core.util.math.MatrixRowStats: Calculate the means of a matrix's rows
means(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixRowStats: Calculates the means of a matrix's rows.
MeanVarianceEstimator - Class in ubic.gemma.core.util.math.linearmodels: Estimate mean-variance relationship and use this to compute weights for least squares fitting.
MeanVarianceEstimator(DoubleMatrix2D) - Constructor for class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator: Generic method for calculating mean and variance, as a data diagnostic.
MeanVarianceEstimator(DesignMatrix, DoubleMatrix2D, DoubleMatrix1D) - Constructor for class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator: Executes voom() to calculate weights.
MeanVarianceEstimator(DesignMatrix, DoubleMatrix, DoubleMatrix1D) - Constructor for class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator: Preferred interface if you want control over how the design is set up.
MeanVarianceFailureException - Exception Class in ubic.gemma.core.analysis.expression.diff: Exception raised when MeanVarianceEstimator fails.
MeanVarianceFailureException(DifferentialExpressionAnalysisConfig, Exception) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.MeanVarianceFailureException
MeanVarianceRelation - Class in ubic.gemma.model.expression.bioAssayData
MeanVarianceRelation() - Constructor for class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
MeanVarianceRelation.Factory - Class in ubic.gemma.model.expression.bioAssayData
MeanVarianceService - Interface in ubic.gemma.core.analysis.preprocess: Responsible for returning the coordinates of the experiment's Mean-Variance relationship.
MeanVarianceServiceHelper - Interface in ubic.gemma.core.analysis.preprocess
MeanVarianceServiceImpl - Class in ubic.gemma.core.analysis.preprocess: Manage the mean-variance relationship.
MeanVarianceServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.MeanVarianceServiceImpl
MeanVarianceUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
MeanVarianceUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.MeanVarianceUpdateEvent
MeanVarianceValueObject(MeanVarianceRelation) - Constructor for class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject: Rounded to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits with no opt-out, as on DatasetsWebService.SimpleSVDValueObject.
MeanVarianceWriter - Class in ubic.gemma.core.datastructure.matrix.io
MeanVarianceWriter(BuildInfo, EntityUrlBuilder) - Constructor for class ubic.gemma.core.datastructure.matrix.io.MeanVarianceWriter
measuredRegion(StopWatch) - Static method in class ubic.gemma.core.profiling.StopWatchUtils: Create a measured region by a StopWatch, which can be used with a try-with-resource statement to StopWatch.start() and StopWatch.suspend() when entering and leaving the region.
Measurement - Class in ubic.gemma.model.common.measurement
Measurement - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Represents a factor value Measurement.
Measurement() - Constructor for class ubic.gemma.model.common.measurement.Measurement
Measurement.Factory - Class in ubic.gemma.model.common.measurement
measurement2double(Measurement) - Static method in class ubic.gemma.model.common.measurement.MeasurementUtils: Convert a measurement to a double.
MeasurementKind - Enum Class in ubic.gemma.model.common.measurement
measurementOf - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Inverse of TGFVO.hasMeasurement.
MeasurementRef() - Constructor for class ubic.gemma.rest.DatasetsWebService.MeasurementRef
MeasurementType - Enum Class in ubic.gemma.model.common.measurement
MeasurementUtils - Class in ubic.gemma.model.common.measurement: Utilities for Measurement.
MeasurementUtils() - Constructor for class ubic.gemma.model.common.measurement.MeasurementUtils
MeasurementValueObject - Class in ubic.gemma.model.common.measurement
MeasurementValueObject() - Constructor for class ubic.gemma.model.common.measurement.MeasurementValueObject
MeasurementValueObject(Measurement) - Constructor for class ubic.gemma.model.common.measurement.MeasurementValueObject
median(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the median.
median(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive: Calculate the median of each assay for a given vector.
median(SingleCellExpressionDataVector, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
median(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
MEDIAN - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
MEDIAN_COMPARATOR - Static variable in class ubic.gemma.core.analysis.preprocess.OutlierDetails: Compare outliers by median correlation Note: this comparator imposes orderings that are inconsistent with equals
mediaTypes() - Element in annotation interface ubic.gemma.rest.annotations.GZIP: If non-empty, only contents compatible with any of the specified media type will be compressed.
MediaTypeUtils - Class in ubic.gemma.rest.util: Utilities for MediaType.
MediaTypeUtils() - Constructor for class ubic.gemma.rest.util.MediaTypeUtils
MedicalSubjectHeading - Class in ubic.gemma.model.common.description: Hibernate Search 7 mapping: indexed root for MeSH terms attached to a BibliographicReference.
MedicalSubjectHeading() - Constructor for class ubic.gemma.model.common.description.MedicalSubjectHeading
MedicalSubjectHeading.Factory - Class in ubic.gemma.model.common.description
MedicOntologyService - Class in ubic.gemma.core.ontology.providers: Deprecated.
MedicOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.MedicOntologyService: Deprecated.
MEDIP_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
MemberAddRequest() - Constructor for class ubic.gemma.rest.GroupsWebService.MemberAddRequest
memberOf - Static variable in class ubic.gemma.core.ontology.jena.RO
MemInfo - Record Class in ubic.gemma.core.util.runtime: Information about system memory.
MemInfo(long) - Constructor for record class ubic.gemma.core.util.runtime.MemInfo: Creates an instance of a MemInfo record class.
MemoryBlock() - Constructor for class ubic.gemma.rest.AdminWebService.MemoryBlock
MemoryBlock(long, long, long) - Constructor for class ubic.gemma.rest.AdminWebService.MemoryBlock
merge(ArrayDesign, Collection, String, String, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeService: Merge array designs based on their sequence content.
merge(ArrayDesign, Collection, String, String, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceImpl
MergeDuplicateBibRefsCli - Class in ubic.gemma.apps: Merge duplicate BibliographicReference rows that share a PubMed accession.
MergeDuplicateBibRefsCli() - Constructor for class ubic.gemma.apps.MergeDuplicateBibRefsCli
mergeQuantitationTypes(Collection) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils: Merge a given collection of quantitation types.
mergeVectors(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.VectorMergingService: Merge the raw data vectors of a given experiment.
mergeVectors(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.VectorMergingServiceImpl
MESH_TERMS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
meshDiseaseSynonymOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig: Extra search strings for MONDO disease terms, not a vocabulary of its own — the URI prefix is MONDO's, which also fences the table to MONDO URIs should the builder ever emit anything else.
MeshDiseaseSynonymOntologyService - Class in ubic.gemma.core.ontology.providers: MeSH entry terms served as extra search strings for MONDO disease terms.
MeshDiseaseSynonymOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService
meshHeadings - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
meshHeadings(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig.GeoRetrieveConfigBuilder: Fill MeSH headings.
message() - Element in annotation interface ubic.gemma.core.security.audit.Audited: Optional plain (non-SpEL) note string.
message() - Element in annotation interface ubic.gemma.core.security.audit.AuditedConditional: Optional plain (non-SpEL) note string.
message() - Element in annotation interface ubic.gemma.core.security.audit.AuditedOnError: Optional plain (non-SpEL) note string.
message(String) - Method in class ubic.gemma.rest.util.WellComposedError.WellComposedErrorBuilder
message(String) - Method in class ubic.gemma.rest.util.WellComposedErrorBody.WellComposedErrorBodyBuilder
message(String) - Method in class ubic.gemma.rest.util.WellComposedWarning.WellComposedWarningBuilder
MessagesConfig - Class in ubic.gemma.persistence.util
MessagesConfig() - Constructor for class ubic.gemma.persistence.util.MessagesConfig
messageSource() - Method in class ubic.gemma.persistence.util.MessagesConfig: Message source for this context, loaded from localized "messages_xx" files
messageSpel() - Element in annotation interface ubic.gemma.core.security.audit.Audited: Optional SpEL expression evaluated against the join-point.
messageSpel() - Element in annotation interface ubic.gemma.core.security.audit.AuditedConditional: Optional SpEL expression for the note, evaluated only when AuditedConditional.when() is true.
messageSpel() - Element in annotation interface ubic.gemma.core.security.audit.AuditedOnError: Optional SpEL expression for the note, evaluated against the post-throw context.
MetaAnalysis - Class in ubic.gemma.core.util.math.metaanalysis: Statistics for meta-analysis.
MetaAnalysis() - Constructor for class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis
metabolism - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
metadata() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTerm: Returns the value of the metadata record component.
METADATA - Enum constant in enum class ubic.gemma.cli.util.CLI.CommandGroup
metaFEWeights(DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: Weights under a fixed effects model.
MetaField - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser.model
MetaField() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
MetaFieldType - Enum Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser.model
metaRESampleVariance(DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: CH sample variance under random effects model, equation 18-20
metaREVariance(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: CH equation 18-23.
metaREWeights(DoubleArrayList, double) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: Under a random effects model, CH eqn.
metaVariance(DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: CH 18-3.
metaVariance(DoubleArrayList, DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: CH 18-3 version 2 for quality weighted.
metaZscore(double, double) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: Test statistic for H0: effectSize == 0.
meterRegistry() - Method in class ubic.gemma.core.config.MetricsConfig
MeterRegistryCliConfigurer - Class in ubic.gemma.cli.metrics: This configurer adds two tags: environment='cli' and user to the given meter registry.
MeterRegistryCliConfigurer(MeterRegistry) - Constructor for class ubic.gemma.cli.metrics.MeterRegistryCliConfigurer
meterRegistryJCacheConfigurer(MeterRegistry, CacheManager) - Method in class ubic.gemma.core.config.MetricsConfig: Per-cache JSR-107 metrics (Ehcache 3 / JCache backend, see EhcacheConfig).
MeterRegistryJCacheConfigurer - Class in ubic.gemma.core.metrics: Bind per-cache JSR-107 (JCache) metrics from a CacheManager to a MeterRegistry.
MeterRegistryJCacheConfigurer(MeterRegistry, CacheManager) - Constructor for class ubic.gemma.core.metrics.MeterRegistryJCacheConfigurer
Method security - Section in package ubic.gemma.core.security
MethodSecurityConfig - Class in ubic.gemma.core.security: Method-security configuration for Gemma, replacing the deprecated XML <s:global-method-security> block in applicationContext-security.xml.
MethodSecurityConfig() - Constructor for class ubic.gemma.core.security.MethodSecurityConfig
METHYLATION_PROFILING_BY_GENOME_TILING_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
METHYLATION_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
MetricDefinition(String, String, String, String, String, Double, Double, boolean) - Constructor for class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition: Creates a new MetricDefinition instance.
METRICS - Static variable in class ubic.gemma.core.context.EnvironmentProfiles: Independent feature toggles.
MetricsApplicationEventListener - Class in ubic.gemma.rest.providers
MetricsApplicationEventListener() - Constructor for class ubic.gemma.rest.providers.MetricsApplicationEventListener
MetricsConfig - Class in ubic.gemma.core.config: Phase 3 XML->Java migration: replaces the <beans profile="metrics"> block from applicationContext-serviceBeans.xml.
MetricsConfig() - Constructor for class ubic.gemma.core.config.MetricsConfig
MetricsWebService - Class in ubic.gemma.rest.monitoring: Prometheus-format metrics scrape endpoint at /rest/v2/metrics.
MetricsWebService() - Constructor for class ubic.gemma.rest.monitoring.MetricsWebService
MEX - Enum constant in enum class ubic.gemma.core.analysis.service.ExpressionExperimentDataFileType
MEX - Enum constant in enum class ubic.gemma.core.loader.expression.singleCell.SingleCellDataType: MEX format
MEX_SC_DATA_SUFFIX - Static variable in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
MexBundlerProvider - Class in ubic.gemma.rest.providers
MexBundlerProvider() - Constructor for class ubic.gemma.rest.providers.MexBundlerProvider
MexDetector - Class in ubic.gemma.core.loader.expression.geo.singleCell: Detects MEX data from GEO series and samples.
MexDetector() - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
MexMatrixBundler - Class in ubic.gemma.core.datastructure.matrix.io: Bundles a directory containing MEX files into a TAR archive.
MexMatrixBundler() - Constructor for class ubic.gemma.core.datastructure.matrix.io.MexMatrixBundler
MexMatrixWriter - Class in ubic.gemma.core.datastructure.matrix.io: Writes SingleCellExpressionDataMatrix to the 10x MEX format.
MexMatrixWriter() - Constructor for class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter
MexSingleCellDataLoader - Class in ubic.gemma.core.loader.expression.singleCell: Load single cell data from 10X Genomics MEX format.
MexSingleCellDataLoader(List, List, List, List) - Constructor for class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
MexSingleCellDataLoaderConfig - Class in ubic.gemma.core.loader.expression.singleCell
MexSingleCellDataLoaderConfig(MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder) - Constructor for class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig
MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C,B> - Class in ubic.gemma.core.loader.expression.singleCell
MexSingleCellDataLoaderConfigBuilder() - Constructor for class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder
MexSingleCellDataLoaderConfigurer - Class in ubic.gemma.core.loader.expression.singleCell: Configure a MexSingleCellDataLoader for a given directory and collection of BioAssays.
MexSingleCellDataLoaderConfigurer(Path, Collection, BioAssayMapper, SingleCellDataTransformationFactory, GeoSeries) - Constructor for class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer
MGI - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
mgiRelationProducer(List, AnnotationRelationDao, PlatformTransactionManager, TaxonService) - Method in class ubic.gemma.core.ontology.OntologyConfig: MGI's genotype-to-disease reports as EXTERNAL relations.
MgiRelationProducer - Class in ubic.gemma.core.ontology.relation: Turns MGI's genotype-to-disease reports into AnnotationRelationBasis.EXTERNAL relations: which mutant alleles MGI's curators say model which diseases, and which they say do not.
MgiRelationProducer(List, AnnotationRelationDao, TransactionTemplate, TaxonService) - Constructor for class ubic.gemma.core.ontology.relation.MgiRelationProducer
mgiStrainOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
MgiStrainOntologyService - Class in ubic.gemma.core.ontology.providers: MGI (Mouse Genome Informatics) mouse strains as a flat lexical strain name-resolution source, to annotate the complicated mouse strains/genotypes that EFO/TGEMO don't enumerate (the ~84k coisogenic + ~17k congenic mutant strains).
MgiStrainOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.MgiStrainOntologyService
MICRO - Enum constant in enum class ubic.gemma.core.ontology.providers.OntologyService.InferenceMode: Very limited inference.
MICROARRAY - Static variable in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType: Enumeration of microarray platforms.
MIDDLE - Enum constant in enum class ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod
MightFix - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdict: Worth doing eventually; not now.
min - Variable in class ubic.gemma.core.util.graphics.ColorMatrix
min() - Method in class ubic.gemma.core.util.math.distribution.Histogram
min(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing
min(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixStats: Find the minimum of the entire matrix.
min(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
min(SingleCellExpressionDataVector, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
min(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
min(SingleCellExpressionDataVector, CellLevelCharacteristics) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
MIN - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
MIN_CARDINALITY - Enum constant in enum class ubic.gemma.core.ontology.model.OntologyCardinalityRestriction.CardinalityType
MIN_PARSED_LINES_FOR_UPDATE - Static variable in interface ubic.gemma.core.loader.util.parser.LineParser
MINI - Enum constant in enum class ubic.gemma.core.ontology.providers.OntologyService.InferenceMode: Limited inference.
MINIMAL - Static variable in class ubic.gemma.apps.GeoGrabberCli: Preset when seeking records.
MINIML - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoFormat
MINIMUM_DESIGN_ELEMENTS - Static variable in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter: How many design elements a dataset has to have before we consider analyzing it.
MINIMUM_SAMPLES - Static variable in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter: How many samples a dataset has to have before we consider analyzing it.
MinimumCellsFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Filter that removes samples that do not meet a minimum number of cells requirement.
MinimumCellsFilter() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter
minimumIdle - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
minimumSpecificity(double) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery: Off by default, deliberately: no threshold has been tuned against curator judgement, and the shape of the distribution is worth seeing before one is fixed in the API.
minimumSupport(int) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
minPresentCount() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the minPresentCount record component.
minPresentFraction() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the minPresentFraction record component.
MIRNA_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
MISC - Enum constant in enum class ubic.gemma.cli.util.CLI.CommandGroup
MISCRNA - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
miss() - Static method in class ubic.gemma.core.geoscrape.GeoRecordMatcher.MatchResult
misses - Variable in class ubic.gemma.rest.AdminWebService.CacheStatRow
missingColor - Variable in class ubic.gemma.core.util.graphics.ColorMatrix
MissingEncodingAttributeException - Exception Class in ubic.gemma.core.loader.util.anndata: Exception raised when a HDF5 file/group/dataset is lacking a encoding-type and/or encoding-version attribute.
MissingEncodingAttributeException(String) - Constructor for exception class ubic.gemma.core.loader.util.anndata.MissingEncodingAttributeException
MissingResult - Class in ubic.gemma.persistence.service.analysis.expression.diff: Represents a gene that was not tested.
MissingResult(Long, Long) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.MissingResult
MissingValueAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Computing missing values for an expression experiment
MissingValueAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.MissingValueAnalysisEvent
mixed - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
MIXED - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType
mkdir() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher: Like mkdir(accession) but for cases where there is no accession.
mkdir(String) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher: Create a directory according to the current accession number and set path information, including any non-existing parent directories.
MNASE_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
MOCK - Enum constant in enum class ubic.gemma.model.pipeline.SchedulerKind: In-JVM mock used for local-mode smoke testing.
MockPipelineScheduler - Class in ubic.gemma.core.pipeline: In-JVM mock scheduler for local-mode smoke testing of the admin pipeline UI without a real Luigi/Nextflow wired.
MockPipelineScheduler() - Constructor for class ubic.gemma.core.pipeline.MockPipelineScheduler
mode(SearchSettings.SearchMode) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Indicate the search mode to use.
model - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
model - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
model - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
model - Variable in class ubic.gemma.rest.AnnotationSetsWebService.ProvenanceRequest
model - Variable in class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
model - Variable in class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest
ModelUtils - Class in ubic.gemma.model.util: Utilities for working with Gemma models.
ModelUtils() - Constructor for class ubic.gemma.model.util.ModelUtils
ModelUtils.EqualityOutcome - Enum Class in ubic.gemma.model.util
modeNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
ModeratedTstat - Class in ubic.gemma.core.util.math.linearmodels: Implements methods described in
ModeratedTstat() - Constructor for class ubic.gemma.core.util.math.linearmodels.ModeratedTstat
MOLECULAR_FUNCTION - Enum constant in enum class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect
moment(DoubleArrayList, int, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the moment of k -th order with constant c of a data sequence, which is Sum( (data[i]-c)k ) / data.size().
MondoOntologyService - Class in ubic.gemma.core.ontology.providers: Mondo Disease Ontology
MondoOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.MondoOntologyService
mondoOntologyServiceOntologyService(OntologySlimExtractor, MondoSeedResolver, boolean) - Method in class ubic.gemma.core.ontology.OntologyConfig: MONDO, parallel to OntologyConfig.chebiOntologyService(OntologySlimExtractor, ChebiSeedResolver).
MondoSeedResolver - Class in ubic.gemma.core.ontology.providers.mondo: MONDO counterpart of ChebiSeedResolver: every MONDO URI currently used as Characteristic.valueUri anywhere in the gemd corpus.
MondoSeedResolver(SessionFactory) - Constructor for class ubic.gemma.core.ontology.providers.mondo.MondoSeedResolver
MOUSE - Enum constant in enum class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat.BlattableGenome
MouseDevelopmentOntologyService - Class in ubic.gemma.core.ontology.providers: Mouse Developmental Anatomy Ontology
MouseDevelopmentOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.MouseDevelopmentOntologyService
mouseDevelopmentOntologyServiceOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
movingAverage(DoubleMatrix1D, int) - Static method in class ubic.gemma.core.util.math.Smooth: Simple moving average that sums the points "backwards".
MPSS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType
MPSS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
MPSS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
MRE_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
mRNA - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType
MS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
MultiAssayBulkExpressionDataMatrix<T> - Interface in ubic.gemma.core.datastructure.matrix: An interface for bulk matrices that supports multiple BioAssay per BioMaterial.
Multifunctionality - Class in ubic.gemma.model.genome.gene
Multifunctionality() - Constructor for class ubic.gemma.model.genome.gene.Multifunctionality
MULTIFUNCTIONALITY - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
Multifunctionality.Factory - Class in ubic.gemma.model.genome.gene
MultifunctionalityCli - Class in ubic.gemma.apps
MultifunctionalityCli() - Constructor for class ubic.gemma.apps.MultifunctionalityCli
MultifunctionalityRecomputeResponse() - Constructor for class ubic.gemma.rest.AdminWebService.MultifunctionalityRecomputeResponse
MultifunctionalityTask - Interface in ubic.gemma.core.tasks.maintenance
MultifunctionalityTaskCommand - Class in ubic.gemma.core.tasks.maintenance: Task command for recomputing per-gene multifunctionality scores for a single taxon.
MultifunctionalityTaskCommand(Taxon) - Constructor for class ubic.gemma.core.tasks.maintenance.MultifunctionalityTaskCommand
MultifunctionalityTaskImpl - Class in ubic.gemma.core.tasks.maintenance: Async port of MultifunctionalityCli: recompute per-gene multifunctionality scores for a single taxon (or all taxa, if taxon == null).
MultifunctionalityTaskImpl() - Constructor for class ubic.gemma.core.tasks.maintenance.MultifunctionalityTaskImpl
MultipleBaselinesRequireSubsetException - Exception Class in ubic.gemma.core.analysis.expression.diff: Raised when a factor carries more than one explicitly marked baseline and the analysis was not configured with a subset factor.
MultipleBaselinesRequireSubsetException(String, DifferentialExpressionAnalysisConfig) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.MultipleBaselinesRequireSubsetException
MultipleTestCorrection - Class in ubic.gemma.core.util.math: Methods for p-value correction of sets of hypothesis tests.
MultipleTestCorrection() - Constructor for class ubic.gemma.core.util.math.MultipleTestCorrection
MULTIQC_REPORT - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType: Deprecated.
kept for backward-compatibility since we expose this for addMetadataFile --file-type.
multWithMissing(DoubleMatrix1D, DoubleMatrix2D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
multWithMissing(DoubleMatrix2D, DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
multWithMissing(DoubleMatrix2D, DoubleMatrix2D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil: Multiple two matrices, tolerate missing values.
mungeFileName(String) - Static method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl: Remove file separators (e.g., "/") from the file names.
MustFix - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdict: Act on this.
MyQueueResponse() - Constructor for class ubic.gemma.rest.TicketsWebService.MyQueueResponse
MyQueueSummaryResponse() - Constructor for class ubic.gemma.rest.TicketsWebService.MyQueueSummaryResponse
MySQL57InnoDBDialect - Class in ubic.gemma.persistence.hibernate: Gemma's MySQL dialect, pinned to MySQL 5.7 / InnoDB semantics.
MySQL57InnoDBDialect() - Constructor for class ubic.gemma.persistence.hibernate.MySQL57InnoDBDialect

N

NA - Static variable in class ubic.gemma.core.util.TsvUtils: Indicator used for a missing value (e.g.
name - Variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
name - Variable in class ubic.gemma.rest.AdminWebService.CacheStatRow
name - Variable in class ubic.gemma.rest.AdminWebService.OntologyRefreshResponse
name - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject: The ontology's dc:title; null when it doesn't declare one or isn't loaded yet.
name - Variable in class ubic.gemma.rest.ExperimentSetsWebService.ExperimentSetRequest
name() - Method in class ubic.gemma.core.geoscrape.BrainKeywordMatcher
name() - Method in interface ubic.gemma.core.geoscrape.GeoRecordMatcher: Short, stable identifier — surfaces in REST request bodies (the criteria selector), the watermark's criteriaApplied column, and the preboarded's matchedCriteria JSON.
name() - Method in class ubic.gemma.core.geoscrape.SingleCellBrainMatcher
name() - Method in class ubic.gemma.core.geoscrape.TfPerturbationMatcher
NAME - Static variable in class ubic.gemma.rest.ranking.CommonalityRankingStrategy
NAME - Static variable in class ubic.gemma.rest.ranking.CompositeRankingStrategy
NAME - Static variable in class ubic.gemma.rest.ranking.LuceneOrderRankingStrategy
NAME - Static variable in class ubic.gemma.rest.ranking.TokenCoverageRankingStrategy
NAME - Static variable in class ubic.gemma.rest.ranking.UsageWeightedRankingStrategy
NAME_COMPARATOR - Static variable in class ubic.gemma.model.common.DescribableUtils: Comparator that sorts Describable objects by name, case-insensitively, with nulls last.
NAME_DELIMITER - Static variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet: Delimiter used to separate the source experiment name from the subset name.
NAMED_LEVELS - Static variable in interface ubic.gemma.cli.logging.LoggingConfigurer
nameForR(BioMaterial) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Create a name for a sample suitable for R.
nameForR(CompositeSequence) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
nameForR(ExperimentalFactor) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Create a name for the factor that is suitable for R.
nameForR(FactorValue, boolean) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: Create a name for the factor value that is suitable for R.
names - Variable in class ubic.gemma.rest.AdminWebService.CacheListResponse: Names only — preserved for backward compat with pre-stats clients.
nanStatusMatrix(double[][]) - Static method in class ubic.gemma.core.util.math.MatrixStats
NARROW - Enum constant in enum class ubic.gemma.core.ontology.model.OntologyXref.Strength: The foreign term names something narrower than the declaring term.
NARROW_SYNONYM - Enum constant in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia
NAS - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
Native callers: explicit id column (HQL_SQL_AUDIT C5) - Section in class ubic.gemma.persistence.util.AclQueryUtils
NCBI_URI_PREFIX - Static variable in class ubic.gemma.model.genome.Gene: URI prefix for fake ontology terms used in Gemma (e.g.
NCBIGene2Accession - Class in ubic.gemma.core.loader.genome.gene.ncbi.model: See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README
NCBIGene2Accession() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
NcbiGene2AccessionParser - Class in ubic.gemma.core.loader.genome.gene.ncbi: Class to parse the NCBI gene2accession files.
NcbiGene2AccessionParser() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
NCBIGene2GOAssociationLoader - Class in ubic.gemma.core.loader.association
NCBIGene2GOAssociationLoader() - Constructor for class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
NCBIGene2GOAssociationLoaderCLI - Class in ubic.gemma.apps: Load GO -> gene associations from NCBI.
NCBIGene2GOAssociationLoaderCLI() - Constructor for class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI
NCBIGene2GOAssociationParser - Class in ubic.gemma.core.loader.association: This parses GO annotations from NCBI.
NCBIGene2GOAssociationParser(Collection) - Constructor for class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
NcbiGeneConverter - Class in ubic.gemma.core.loader.genome.gene.ncbi: Convert NCBIGene2Accession objects into Gemma Gene objects with associated GeneProducts.
NcbiGeneConverter() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
NcbiGeneData - Class in ubic.gemma.core.loader.genome.gene.ncbi: Simple helper data structure that stores an NcbiGeneInfo and its associated NcbiGene2Accession elements.
NcbiGeneData() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
NcbiGeneDomainObjectGenerator - Class in ubic.gemma.core.loader.genome.gene.ncbi: Combines information from the gene2accession and gene_info files from NCBI Gene.
NcbiGeneDomainObjectGenerator(Collection) - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
NcbiGeneEnsemblFileParser - Class in ubic.gemma.core.loader.genome.gene.ncbi
NcbiGeneEnsemblFileParser() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
NCBIGeneFileFetcher - Class in ubic.gemma.core.loader.genome.gene.ncbi: Class to download files for NCBI gene.
NCBIGeneFileFetcher() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
NcbiGeneHistory - Class in ubic.gemma.core.loader.genome.gene.ncbi.model: Represents the information from the "gene_history" file from NCBI (for one gene's history).
NcbiGeneHistory(String) - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
NcbiGeneHistoryParser - Class in ubic.gemma.core.loader.genome.gene.ncbi: Parse the NCBI "gene_history" file.
NcbiGeneHistoryParser() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
NCBIGeneInfo - Class in ubic.gemma.core.loader.genome.gene.ncbi.model: See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README
NCBIGeneInfo() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
NCBIGeneInfo.GeneType - Enum Class in ubic.gemma.core.loader.genome.gene.ncbi.model: See http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn unknown (0) , 36
NCBIGeneInfo.NomenclatureStatus - Enum Class in ubic.gemma.core.loader.genome.gene.ncbi.model
NcbiGeneInfoParser - Class in ubic.gemma.core.loader.genome.gene.ncbi: Class to parse the gene_info file from NCBI Gene.
NcbiGeneInfoParser() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
NcbiGeneLoader - Class in ubic.gemma.core.loader.genome.gene.ncbi: Load or update information about genes from the NCBI Gene database.
NcbiGeneLoader() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
NcbiGeneLoaderCLI - Class in ubic.gemma.apps: Command line interface to gene parsing and loading
NcbiGeneLoaderCLI() - Constructor for class ubic.gemma.apps.NcbiGeneLoaderCLI
NcbiGeneUtils - Class in ubic.gemma.core.loader.genome.gene.ncbi
NcbiGeneUtils() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneUtils
NcbiIdDesignElementMapper - Class in ubic.gemma.core.loader.util.mapper: Match design elements using the NCBI ID.
NcbiIdDesignElementMapper(Map) - Constructor for class ubic.gemma.core.loader.util.mapper.NcbiIdDesignElementMapper
ncbiTaxonId() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata.Taxon: Returns the value of the ncbiTaxonId record component.
NCBIUtil - Class in ubic.gemma.core.loader.genome.gene.ncbi
NCBIUtil() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NCBIUtil
NCRNA - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
NCRNA_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
ND - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
NEEDS_MORE_INFO - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.FindingDisposition: Neither yet — ruling on this finding is blocked until someone supplies something the finding does not carry.
needsAttention() - Method in record class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject.LastEventTriple: Returns the value of the needsAttention record component.
needsAttention(Curatable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService: Deprecated.

Convenience overload — resolves target type from the entity.
needsAttention(Curatable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImpl
needsAttention(TicketTargetType, Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService: Deprecated.

Whether the given target has at least one open ticket of a type that historically tripped curationDetails.needsAttention=true (i.e.
needsAttention(TicketTargetType, Long) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImpl
NeedsAttentionAlteringEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
see CurationDetailsEvent — the needs-attention flag is being replaced by open GENERIC / BATCH_INFO_NEEDED tickets.
NeedsAttentionAlteringEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionAlteringEvent: Deprecated.
NeedsAttentionEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
open a GENERIC ticket (or TicketType.BATCH_INFO_NEEDED when the trigger is missing batch information) via TicketService.openTicket(Contact, TicketType, String, Collection) instead. See CurationDetailsEvent for the full migration map.
NeedsAttentionEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionEvent: Deprecated.
needToRun(Date, ArrayDesign, Class) - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli: Override to do additional checks to make sure the array design is in a state of readiness for probe mapping.
needToRun(Date, ArrayDesign, Class) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
negative - Enum constant in enum class ubic.gemma.rest.DatasetsWebService.PcLoadingDirection
NegativeEvidenceValueObject(String, boolean, List, boolean) - Constructor for class ubic.gemma.rest.AnnotationsWebService.NegativeEvidenceValueObject
NegativeEvidenceValueObject(String, boolean, List, boolean, AnnotationsWebService.ExternalIdentificationValueObject) - Constructor for class ubic.gemma.rest.AnnotationsWebService.NegativeEvidenceValueObject
negotiate(HttpHeaders, MediaType...) - Static method in class ubic.gemma.rest.util.MediaTypeUtils: Perform content negotiation of a given set of HTTP headers against a list of possible media types.
NEITHER - Enum constant in enum class ubic.gemma.model.common.description.RelationInferenceDirection: Neither end implies the other.
NEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
NEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
NEQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
netDataSourceUtil - Variable in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
NetDatasourceUtil - Class in ubic.gemma.core.util: Helper methods to get FTP connection.
NetDatasourceUtil() - Constructor for class ubic.gemma.core.util.NetDatasourceUtil
NetUtils - Class in ubic.gemma.core.util: Network / transfer-rate helpers.
NetUtils() - Constructor for class ubic.gemma.core.util.NetUtils
neuroBehaviorOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
NeuroBehaviorOntologyService - Class in ubic.gemma.core.ontology.providers: Neuro Behavior Ontology — behavioural processes and the paradigms used to elicit them.
NeuroBehaviorOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.NeuroBehaviorOntologyService
newAgilentDateFormat() - Static method in class ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractor: Each call returns a fresh SimpleDateFormat: SDF is not thread-safe and was previously a shared mutable static field (with per-call setLenient(true)) — a latent race when multiple platform loads ran concurrently.
newBufferedReader(Path) - Method in interface ubic.gemma.core.util.locking.FileLockManager
newBufferedReader(Path) - Method in class ubic.gemma.core.util.locking.FileLockManagerImpl
newBufferedWriter(Path, OpenOption...) - Method in interface ubic.gemma.core.util.locking.FileLockManager
newBufferedWriter(Path, OpenOption...) - Method in class ubic.gemma.core.util.locking.FileLockManagerImpl
newBuilder() - Static method in class ubic.gemma.core.logging.log4j.ProgressUpdateAppender
newBuilder() - Static method in class ubic.gemma.core.logging.log4j.SlackAppender
newCachedThreadPool() - Static method in class ubic.gemma.core.util.concurrent.Executors
newCompRowMatrix(int, int, int[], int[], double[]) - Static method in class ubic.gemma.core.datastructure.sparse.CompRowMatrixUtils: Create a compressed row matrix from its internal arrays using reflection.
NEWEST_FIRST - Static variable in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition: Most recent first, id breaking a same-millisecond tie.
NEWEST_FIRST - Static variable in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision: Most recent first, id breaking a same-millisecond tie — the same ordering the DAO applies in SQL.
newFactorKey(String) - Static method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
newFixedThreadPool(int) - Static method in class ubic.gemma.core.util.concurrent.Executors
newFixedThreadPool(int, ThreadFactory) - Static method in class ubic.gemma.core.util.concurrent.Executors
newInputStream(Path, OpenOption...) - Method in interface ubic.gemma.core.util.locking.FileLockManager
newInputStream(Path, OpenOption...) - Method in class ubic.gemma.core.util.locking.FileLockManagerImpl
newInstance() - Static method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.diff.ContrastResult.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.diff.HitListSize.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.pca.Eigenvector.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis.Factory
newInstance() - Static method in class ubic.gemma.model.association.ReferenceAssociation.Factory
newInstance() - Static method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail.Factory
newInstance() - Static method in class ubic.gemma.model.common.auditAndSecurity.Contact.Factory
newInstance() - Static method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority.Factory
newInstance() - Static method in class ubic.gemma.model.common.auditAndSecurity.JobInfo.Factory
newInstance() - Static method in class ubic.gemma.model.common.auditAndSecurity.UserGroup.Factory
newInstance() - Static method in class ubic.gemma.model.common.description.BibliographicReference.Factory
newInstance() - Static method in class ubic.gemma.model.common.description.Characteristic.Factory
newInstance() - Static method in class ubic.gemma.model.common.description.DatabaseEntry.Factory
newInstance() - Static method in class ubic.gemma.model.common.description.ExternalDatabase.Factory
newInstance() - Static method in class ubic.gemma.model.common.description.Keyword.Factory
newInstance() - Static method in class ubic.gemma.model.common.description.MedicalSubjectHeading.Factory
newInstance() - Static method in class ubic.gemma.model.common.measurement.Measurement.Factory
newInstance() - Static method in class ubic.gemma.model.common.protocol.Protocol.Factory
newInstance() - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationType.Factory
newInstance() - Static method in class ubic.gemma.model.expression.arrayDesign.AlternateName.Factory
newInstance() - Static method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign.Factory
newInstance() - Static method in class ubic.gemma.model.expression.bioAssay.BioAssay.Factory
newInstance() - Static method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension.Factory
newInstance() - Static method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation.Factory
newInstance() - Static method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector.Factory
newInstance() - Static method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector.Factory
newInstance() - Static method in class ubic.gemma.model.expression.biomaterial.BioMaterial.Factory
newInstance() - Static method in class ubic.gemma.model.expression.biomaterial.Compound.Factory
newInstance() - Static method in class ubic.gemma.model.expression.biomaterial.Treatment.Factory
newInstance() - Static method in class ubic.gemma.model.expression.designElement.CompositeSequence.Factory
newInstance() - Static method in class ubic.gemma.model.expression.experiment.ExperimentalDesign.Factory
newInstance() - Static method in class ubic.gemma.model.expression.experiment.ExperimentalFactor.Factory
newInstance() - Static method in class ubic.gemma.model.expression.experiment.ExpressionExperiment.Factory
newInstance() - Static method in class ubic.gemma.model.expression.experiment.FactorValue.Factory
newInstance() - Static method in class ubic.gemma.model.expression.experiment.Statement.Factory
newInstance() - Static method in class ubic.gemma.model.genome.biosequence.BioSequence.Factory
newInstance() - Static method in class ubic.gemma.model.genome.Chromosome.Factory
newInstance() - Static method in class ubic.gemma.model.genome.Gene.Factory
newInstance() - Static method in class ubic.gemma.model.genome.gene.GeneAlias.Factory
newInstance() - Static method in class ubic.gemma.model.genome.gene.GeneProduct.Factory
newInstance() - Static method in class ubic.gemma.model.genome.gene.GeneSet.Factory
newInstance() - Static method in class ubic.gemma.model.genome.gene.GeneSetMember.Factory
newInstance() - Static method in class ubic.gemma.model.genome.gene.Multifunctionality.Factory
newInstance() - Static method in class ubic.gemma.model.genome.PhysicalLocation.Factory
newInstance() - Static method in class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation.Factory
newInstance() - Static method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation.Factory
newInstance() - Static method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult.Factory
newInstance() - Static method in class ubic.gemma.model.genome.Taxon.Factory
newInstance() - Static method in class ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator.Factory
newInstance(double[]) - Static method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution.Factory
newInstance(double[], double[]) - Static method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation.Factory
newInstance(Boolean, String, Date, Date, Integer, String, String, String, User) - Static method in class ubic.gemma.model.common.auditAndSecurity.JobInfo.Factory
newInstance(Boolean, Date, Integer) - Static method in class ubic.gemma.model.common.auditAndSecurity.JobInfo.Factory
newInstance(Double, Double, Double, Double, FactorValue, FactorValue) - Static method in class ubic.gemma.model.analysis.expression.diff.ContrastResult.Factory
newInstance(Double, Integer, Direction, Integer) - Static method in class ubic.gemma.model.analysis.expression.diff.HitListSize.Factory
newInstance(Double, Gene) - Static method in class ubic.gemma.model.genome.gene.GeneSetMember.Factory
newInstance(Integer, double[]) - Static method in class ubic.gemma.model.analysis.expression.pca.Eigenvector.Factory
newInstance(Integer, Double, Integer, CompositeSequence) - Static method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading.Factory
newInstance(String) - Static method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority.Factory
newInstance(String) - Static method in class ubic.gemma.model.common.auditAndSecurity.User.Factory
newInstance(String) - Static method in class ubic.gemma.model.common.measurement.Unit.Factory
newInstance(String) - Static method in class ubic.gemma.model.expression.arrayDesign.AlternateName.Factory
newInstance(String) - Static method in class ubic.gemma.model.expression.bioAssay.BioAssay.Factory
newInstance(String) - Static method in class ubic.gemma.model.expression.biomaterial.BioMaterial.Factory
newInstance(String) - Static method in class ubic.gemma.model.expression.designElement.CompositeSequence.Factory
newInstance(String) - Static method in class ubic.gemma.model.genome.biosequence.BioSequence.Factory
newInstance(String) - Static method in class ubic.gemma.model.genome.gene.GeneAlias.Factory
newInstance(String) - Static method in class ubic.gemma.model.genome.Taxon.Factory
newInstance(String, String) - Static method in class ubic.gemma.model.common.description.Characteristic.Factory
newInstance(String, String, Integer, boolean) - Static method in class ubic.gemma.model.genome.Taxon.Factory
newInstance(String, String, String) - Static method in class ubic.gemma.model.expression.biomaterial.Compound.Factory
newInstance(String, String, String, String) - Static method in class ubic.gemma.model.common.description.Characteristic.Factory
newInstance(String, String, String, String) - Static method in class ubic.gemma.model.expression.experiment.Statement.Factory
newInstance(String, String, String, String, String, String, GOEvidenceCode) - Static method in class ubic.gemma.model.common.description.Characteristic.Factory
newInstance(String, String, List, int[]) - Static method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics.Factory
newInstance(String, List, int[]) - Static method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment.Factory
newInstance(String, DatabaseType) - Static method in class ubic.gemma.model.common.description.ExternalDatabase.Factory
newInstance(String, ExternalDatabase) - Static method in class ubic.gemma.model.common.description.DatabaseEntry.Factory
newInstance(String, ExternalDatabase, BioSequence, Taxon) - Static method in class ubic.gemma.model.genome.Chromosome.Factory
newInstance(String, ArrayDesign) - Static method in class ubic.gemma.model.expression.designElement.CompositeSequence.Factory
newInstance(String, ArrayDesign, BioMaterial) - Static method in class ubic.gemma.model.expression.bioAssay.BioAssay.Factory
newInstance(String, ArrayDesign, BioSequence) - Static method in class ubic.gemma.model.expression.designElement.CompositeSequence.Factory
newInstance(String, ExpressionExperiment) - Static method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.Factory: Subsets are named by appending the name to the source experiment name, separated by ExpressionExperimentSubSet.NAME_DELIMITER.
newInstance(String, FactorType) - Static method in class ubic.gemma.model.expression.experiment.ExperimentalFactor.Factory
newInstance(String, FactorType, Category) - Static method in class ubic.gemma.model.expression.experiment.ExperimentalFactor.Factory
newInstance(String, Taxon) - Static method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign.Factory
newInstance(String, Taxon) - Static method in class ubic.gemma.model.expression.biomaterial.BioMaterial.Factory
newInstance(String, Taxon) - Static method in class ubic.gemma.model.genome.biosequence.BioSequence.Factory
newInstance(String, Taxon) - Static method in class ubic.gemma.model.genome.Chromosome.Factory
newInstance(Date, AuditAction, String, String, User, AuditEventType) - Static method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent.Factory: Create a new, immutable audit event.
newInstance(Date, AuditAction, String, String, User, AuditEventType, String) - Static method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent.Factory: Create a new audit event with a serialised payload.
newInstance(Date, AuditAction, String, String, User, AuditEventType, String, String) - Static method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent.Factory: As above, naming the curator the action was taken for.
newInstance(List) - Static method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension.Factory
newInstance(Set, Integer, Integer, FactorValue, Set, DifferentialExpressionAnalysis, PvalueDistribution, Set) - Static method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet.Factory
newInstance(ColorMatrix) - Static method in class ubic.gemma.core.util.graphics.MatrixDisplay
newInstance(DoubleMatrix) - Static method in class ubic.gemma.core.util.graphics.ColorMatrix
newInstance(TicketEventType, Contact, String) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent.Factory
newInstance(TicketTargetType, Long) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget.Factory
newInstance(TicketType, String, Contact) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket.Factory
newInstance(Category) - Static method in class ubic.gemma.model.common.description.Characteristic.Factory
newInstance(Category, String, String) - Static method in class ubic.gemma.model.common.description.Characteristic.Factory
newInstance(Category, String, String) - Static method in class ubic.gemma.model.expression.experiment.Statement.Factory
newInstance(Category, Value) - Static method in class ubic.gemma.model.common.description.Characteristic.Factory
newInstance(Characteristic) - Static method in class ubic.gemma.model.common.description.Characteristic.Factory: Create a copy from the given characteristic.
newInstance(Characteristic) - Static method in class ubic.gemma.model.expression.experiment.Statement.Factory
newInstance(ExternalDatabase) - Static method in class ubic.gemma.model.common.description.DatabaseEntry.Factory
newInstance(MeasurementType, String, MeasurementKind, String, PrimitiveType, Unit) - Static method in class ubic.gemma.model.common.measurement.Measurement.Factory
newInstance(MeasurementType, String, PrimitiveType) - Static method in class ubic.gemma.model.common.measurement.Measurement.Factory
newInstance(QuantitationType) - Static method in class ubic.gemma.model.common.quantitationtype.QuantitationType.Factory: Create a new QT with the same spec as the provided one.
newInstance(BioAssayDimension, byte[]) - Static method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix.Factory
newInstance(ExperimentalDesign, String, FactorType) - Static method in class ubic.gemma.model.expression.experiment.ExperimentalFactor.Factory
newInstance(ExperimentalFactor) - Static method in class ubic.gemma.model.expression.experiment.FactorValue.Factory
newInstance(ExperimentalFactor, Characteristic) - Static method in class ubic.gemma.model.expression.experiment.FactorValue.Factory: Create a FactorValue with a single characteristic.
newInstance(ExperimentalFactor, Measurement) - Static method in class ubic.gemma.model.expression.experiment.FactorValue.Factory: Create a FactorValue with a measurement.
newInstance(ExperimentalFactor, Statement) - Static method in class ubic.gemma.model.expression.experiment.FactorValue.Factory: Create a FactorValue with a single statement.
newInstance(ExpressionExperiment, SampleCoexpressionMatrix, SampleCoexpressionMatrix) - Static method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis.Factory
newInstance(Chromosome) - Static method in class ubic.gemma.model.genome.PhysicalLocation.Factory
newInstance(Chromosome, Long, Integer, String, Integer) - Static method in class ubic.gemma.model.genome.PhysicalLocation.Factory
newInstance(Gene, Characteristic, GOEvidenceCode) - Static method in class ubic.gemma.model.association.Gene2GOAssociation.Factory
newInstance(Taxon) - Static method in class ubic.gemma.model.genome.biosequence.BioSequence.Factory
newOutputStream(Path, OpenOption...) - Method in interface ubic.gemma.core.util.locking.FileLockManager
newOutputStream(Path, OpenOption...) - Method in class ubic.gemma.core.util.locking.FileLockManagerImpl
newPassword - Variable in class ubic.gemma.rest.RootWebService.ChangePasswordRequest: The desired new password (minimum 8 characters).
newSingleThreadExecutor() - Static method in class ubic.gemma.core.util.concurrent.Executors
newSingleThreadExecutor(ThreadFactory) - Static method in class ubic.gemma.core.util.concurrent.Executors
newSingleThreadScheduledExecutor() - Static method in class ubic.gemma.core.util.concurrent.Executors
newTaskResult(Serializable) - Method in class ubic.gemma.core.job.AbstractTask: Create a new task result for this command with an answer.
newThread(Runnable) - Method in class ubic.gemma.core.util.concurrent.SimpleThreadFactory
newThread(Runnable) - Static method in class ubic.gemma.core.util.concurrent.ThreadUtils
newThread(Runnable, String) - Static method in class ubic.gemma.core.util.concurrent.ThreadUtils
newVirtualThreadPerTaskExecutorIfAvailable() - Static method in class ubic.gemma.core.util.concurrent.Executors: Returns a virtual-thread-per-task executor when running on a JVM that supports it (JDK 21+), or a cached thread pool fallback on older JVMs (JDK 17).
NEXTFLOW - Enum constant in enum class ubic.gemma.model.pipeline.SchedulerKind
NextflowPipelineScheduler - Class in ubic.gemma.core.pipeline: Nextflow-backed scheduler.
NextflowPipelineScheduler() - Constructor for class ubic.gemma.core.pipeline.NextflowPipelineScheduler
nextOffset - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeDryRunResponse: Absolute offset into the resolved window where this scan stopped.
NO_BATCH_EFFECT_SUCCESS - Enum constant in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that there is no batch effect.
NO_BATCH_INFO - Enum constant in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that there is no batch information available.
NO_PARENTS_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
NoDesignElementsException - Exception Class in ubic.gemma.core.analysis.preprocess.filter: Exception raised when no design elements (rows) are left after filtering the expression data matrix.
NoDesignElementsException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.filter.NoDesignElementsException
NoFactorLeftForAnalysisException - Exception Class in ubic.gemma.core.analysis.expression.diff: Exception raised when suitable factor is left for analysis.
NoFactorLeftForAnalysisException(String, DifferentialExpressionAnalysisConfig) - Constructor for exception class ubic.gemma.core.analysis.expression.diff.NoFactorLeftForAnalysisException
NOME_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
NOMINAL - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode
NOMINAL - Enum constant in enum class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter.Mode: Use nominal values to filter for repetitive values.
NON_CODING_RNA_PROFILING_BY_ARRAY - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
NON_CODING_RNA_PROFILING_BY_HIGH_THROUGHPUT_SEQUENCING - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
NON_REPEAT_NON_SPECIFIC_SITE_THRESHOLD - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig: Sequences which hybridize to this many or more sites in the genome are candidates to be considered non-specific.
NON_SPECIFIC_SITE_THRESHOLD - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig: Sequences which hybridize to this many or more sites in the genome are candidates to be considered non-specific.
None() - Constructor for record class ubic.gemma.core.security.audit.AuditEventPayload.None: Creates an instance of a None record class.
NONE - Enum constant in enum class ubic.gemma.core.ontology.providers.OntologyService.InferenceMode: No inference is supported, only the axioms defined in the ontology are considered.
NONE - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.ExternalIssueSyncState: Not mirrored externally.
NONE - Enum constant in enum class ubic.gemma.persistence.util.SubqueryMode: Produce a clause of the form id not in {subquery}.
NONE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
NONE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
NONE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.QuantifierContext
NONE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
noNeedToRun(T, Class) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Check if the given auditable can be skipped.
noNeedToRun(ExpressionExperiment, Class) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
noneOf(Predicate...) - Static method in class ubic.gemma.cli.util.OptionsUtils: Make sure that none of the given predicates are true.
nonHeap - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse
NonRetainedResult - Class in ubic.gemma.persistence.service.analysis.expression.diff: Represents a gene that was tested, but the result wasn't significant.
NonRetainedResult(Long, Long) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult
NonUniqueCellLevelCharacteristicsByNameException - Exception Class in ubic.gemma.core.loader.expression.singleCell
NonUniqueCellLevelCharacteristicsByNameException(NonUniqueDescribableByNameException) - Constructor for exception class ubic.gemma.core.loader.expression.singleCell.NonUniqueCellLevelCharacteristicsByNameException
NonUniqueCellTypeAssignmentByNameException - Exception Class in ubic.gemma.core.loader.expression.singleCell
NonUniqueCellTypeAssignmentByNameException(NonUniqueDescribableByNameException) - Constructor for exception class ubic.gemma.core.loader.expression.singleCell.NonUniqueCellTypeAssignmentByNameException
NonUniqueDescribableByNameException - Exception Class in ubic.gemma.model.common: An exception that can be raised when trying to create a describable entity or add one to a collection with a name that is already being used.
NonUniqueDescribableByNameException(String) - Constructor for exception class ubic.gemma.model.common.NonUniqueDescribableByNameException
NonUniqueDescribableByNameException(String, Throwable) - Constructor for exception class ubic.gemma.model.common.NonUniqueDescribableByNameException
NonUniqueQuantitationTypeByNameException - Exception Class in ubic.gemma.persistence.service.common.quantitationtype: Exception raised when retrieving a non-unique QT by name.
NonUniqueQuantitationTypeByNameException(String, NonUniqueResultException) - Constructor for exception class ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException
NOOP - Static variable in class ubic.gemma.cli.pipeline.PipelineJobReporter
noParents - Enum constant in enum class ubic.gemma.rest.PlatformsWebService.AnnotationFileType: Directly-assigned GO terms only, without the implied parents.
norm2() - Method in class ubic.gemma.core.util.math.linalg.SingularValueDecomposition
NORMAL - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketPriority
normalize(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Stats: Adjust the elements of an array so they total to 1.0.
normalize(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.Stats: Divide the elements of an array by a given factor.
normalize(DoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.normalize.QuantileNormalizer
normalize(DoubleMatrix, boolean[]) - Method in class ubic.gemma.core.analysis.preprocess.normalize.QuantileNormalizer: Normalize, letting only some columns define the reference distribution.
normalizeCurie(String) - Static method in class ubic.gemma.core.ontology.model.OntologyXref: Normalize a foreign identifier to PREFIX:local.
normalizeTermText(String) - Static method in class ubic.gemma.model.common.description.Characteristic: Collapse whitespace on a free-text term field: strip the ends, and reduce internal runs to a single space.
NoSamplesException - Exception Class in ubic.gemma.core.analysis.preprocess.filter
NoSamplesException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.filter.NoSamplesException
NoSingleCellDataFoundException - Exception Class in ubic.gemma.core.loader.expression.geo.singleCell
NoSingleCellDataFoundException(String) - Constructor for exception class ubic.gemma.core.loader.expression.geo.singleCell.NoSingleCellDataFoundException
not(Filter) - Static method in class ubic.gemma.persistence.util.Filter: Negate the given filter.
NOT_DONE - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetStatus
NOT_EQUAL - Enum constant in enum class ubic.gemma.model.util.ModelUtils.EqualityOutcome
NOT_IN - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
NOT_IN - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
NOT_IN() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
NOT_LIKE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
NOT_LIKE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
NOT_LIKE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
note - Variable in class ubic.gemma.rest.AdminPipelineWebService.SubmitBatchRequest
note - Variable in class ubic.gemma.rest.AnnotationSetsWebService.FinalizeRequest: The curator's closing note on this finalization.
note - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageRequest
note - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageResponse
note - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowHistoryEntry: The audit event NOTE, populated by the @AuditedConditional SpEL expression on WorkflowServiceImpl.advance().
NOTE: design choices (deliberately punted for the MVP — flagged for follow-up) - Section in class ubic.gemma.rest.security.TokenStore
notEq - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
noteUpdate() - Method in record class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject.LastEventTriple: Returns the value of the noteUpdate record component.
notFound(String) - Static method in class ubic.gemma.core.ontology.chembl.ChemblCompound: Sentinel for "ChEMBL was asked and has nothing", so a repeatedly-submitted unknown code is only sent upstream once.
notFound(String) - Static method in class ubic.gemma.core.ontology.ols.OlsTerm: A term OLS could not resolve.
NotFoundExceptionMapper - Class in ubic.gemma.rest.providers: This mapper ensures that raised NotFoundException throughout the API contain well-formed ResponseErrorObject entity.
NotFoundExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.NotFoundExceptionMapper
notIn - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
notInSubquery - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
notLike - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator
notNearlyZeroIndices(DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
NotTroubledStatusFlagEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
resolve the open QUALITY_REVIEW ticket(s) via TicketService.transition(Ticket, TicketState, Contact, String) instead (target state TicketState.RESOLVED). See CurationDetailsEvent for the full migration map.
NotTroubledStatusFlagEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent: Deprecated.

No-arg constructor added to satisfy javabean contract
NR - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
NS - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Namespace used by TGFVO.
nuclearRNA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
nuclearRNA - Enum constant in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule
NULL - Enum constant in enum class ubic.gemma.core.loader.expression.singleCell.SingleCellDataType: This is used as an indicator that no data is being loaded.
NULL_BIOSEQUENCE - Static variable in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService: Used to identify design elements that have no sequence associated with them.
NullableArray<T> - Class in ubic.gemma.core.loader.util.anndata
NullableArray(H5Group, String) - Constructor for class ubic.gemma.core.loader.util.anndata.NullableArray
NullableBoolArray - Class in ubic.gemma.core.loader.util.anndata
NullableBoolArray(H5Group) - Constructor for class ubic.gemma.core.loader.util.anndata.NullableBoolArray
NullableIntArray - Class in ubic.gemma.core.loader.util.anndata
NullableIntArray(H5Group) - Constructor for class ubic.gemma.core.loader.util.anndata.NullableIntArray
nullSafeGet(ResultSet, int, SharedSessionContractImplementor, Object) - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
nullSafeGet(ResultSet, int, SharedSessionContractImplementor, Object) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
nullSafeSet(PreparedStatement, Object, int, SharedSessionContractImplementor) - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
nullSafeSet(PreparedStatement, List, int, SharedSessionContractImplementor) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
NullSingleCellDataLoader - Class in ubic.gemma.core.loader.expression.singleCell: Single-cell data loader used when no data is available.
NullSingleCellDataLoader() - Constructor for class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
NullSingleCellDataLoaderConfigurer - Class in ubic.gemma.core.loader.expression.singleCell
NullSingleCellDataLoaderConfigurer() - Constructor for class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoaderConfigurer
NUMBER_OF_CELLS - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssayCategories
NUMBER_OF_CELLS_BY_DESIGN_ELEMENTS - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssayCategories
NUMBER_OF_DESIGN_ELEMENTS - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssayCategories
NUMBER_OF_PLATFORM_PROBES - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
NUMBER_OF_SAMPLES - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
NUMBERED_LEVELS - Static variable in interface ubic.gemma.cli.logging.LoggingConfigurer
numberOfBins() - Method in class ubic.gemma.core.util.math.distribution.Histogram: Get the number of bins in the histogram.
numberOfBioAssays - Variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
numberOfCells() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns the value of the numberOfCells record component.
numberOfCellsByDesignElements() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns the value of the numberOfCellsByDesignElements record component.
numberOfDesignElements() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns the value of the numberOfDesignElements record component.
numberofDistinctValues(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.Stats
numberofDistinctValuesNonNA(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.Stats
numberOfExperiments(long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
numberOfExperimentsAtBioMaterial(long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
numberOfExperimentsAtFactorValue(long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
numberOfExperimentsAtTag(long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
numberOfExperimentsWithSubject(long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
numberOfMaskedMissingValues() - Method in record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Returns the value of the numberOfMaskedMissingValues record component.
numberOfMaskedOutliers() - Method in record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Returns the value of the numberOfMaskedOutliers record component.
numberOfSecondsBetweenDates(Collection) - Static method in class ubic.gemma.core.util.DateUtil: Compute the number of seconds spanned by the given dates.
numMissing() - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
numMissing() - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Return the number of missing values in the matrix.
numSamples - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject

O

obiService() - Method in class ubic.gemma.core.ontology.OntologyConfig
ObiService - Class in ubic.gemma.core.ontology.providers: Ontology for Biomedical Investigations
ObiService() - Constructor for class ubic.gemma.core.ontology.providers.ObiService
object - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
OBJECT_ALIAS - Static variable in interface ubic.gemma.persistence.service.common.description.DatabaseEntryDao
OBJECT_ALIAS - Static variable in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
OBJECT_ALIAS - Static variable in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
OBJECT_ALIAS - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
OBJECT_ALIAS - Static variable in interface ubic.gemma.persistence.service.genome.GeneDao
OBJECT_ALIAS - Static variable in interface ubic.gemma.persistence.service.genome.taxon.TaxonDao
OBJECT_IMPLIES_SUBJECT - Enum constant in enum class ubic.gemma.model.common.description.RelationInferenceDirection: The object is the specific end: knowing the object tells you the subject.
OBJECT_TO_SUBJECT - Enum constant in enum class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.Direction: Seed terms are objects; return subjects.
objectAlias(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder
objectArrayToBytes(T[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
objectArrayToBytes(T[], Charset) - Method in class ubic.gemma.persistence.util.ByteArrayConverter: Convert an array of Objects into an array of bytes.
objectBreadth(long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
objectCategory(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
objectCategoryUri(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
objectCategoryUris(Collection) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
ObjectIdentityRetrievalStrategyImpl - Class in ubic.gemma.core.security.acl: Customized to know how to deal with SecureValueObject, makes it easier to share code in SecurityService; and doesn't use the default ObjectIdentityImpl.
ObjectIdentityRetrievalStrategyImpl() - Constructor for class ubic.gemma.core.security.acl.ObjectIdentityRetrievalStrategyImpl
objectIsUser(Securable) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice
objectIsUser(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
objectIsUserGroup(Securable) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice
objectIsUserGroup(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
objectMapper() - Method in class ubic.gemma.rest.util.JacksonConfig: Mapper used to generate JSON payloads from the REST API.
ObjectMapperResolver - Class in ubic.gemma.rest.providers
ObjectMapperResolver() - Constructor for class ubic.gemma.rest.providers.ObjectMapperResolver
ObjectMatrix<R,C,V> - Interface in ubic.gemma.core.util.matrix
ObjectMatrixImpl<R,C,V> - Class in ubic.gemma.core.util.matrix: Matrix that can hold any type of object
ObjectMatrixImpl(int, int) - Constructor for class ubic.gemma.core.util.matrix.ObjectMatrixImpl
ObjectProperty - Interface in ubic.gemma.core.ontology.model
objectsPersistedUpdate(int, int, String) - Static method in class ubic.gemma.core.loader.util.ParserAndLoaderTools
ObjectTransientnessRetrievalStrategy - Interface in ubic.gemma.core.security.acl: A strategy to determine if a given domain object is transient.
ObjectTransientnessRetrievalStrategyImpl - Class in ubic.gemma.core.security.acl
ObjectTransientnessRetrievalStrategyImpl() - Constructor for class ubic.gemma.core.security.acl.ObjectTransientnessRetrievalStrategyImpl
objectUri - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
objectValue(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
objectValues(Collection) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
objectValueUri(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
objectValueUris(Collection) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
ObsoleteTermCorrectionResult - Class in ubic.gemma.core.ontology: What an obsolete-term correction run did, or — in a dry run — would do.
ObsoleteTermCorrectionResult() - Constructor for class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
ObsoleteTermCorrectionResult.Resync - Class in ubic.gemma.core.ontology
ObsoleteTermCorrectionResult.TermCorrection - Class in ubic.gemma.core.ontology
ObsoleteTermCorrectionService - Interface in ubic.gemma.core.ontology: Rewrites annotations that use an obsolete ontology term to the successor the ontology asserts.
ObsoleteTermCorrectionServiceImpl - Class in ubic.gemma.core.ontology
ObsoleteTermCorrectionServiceImpl() - Constructor for class ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceImpl
ObsoleteTermCorrectionSubmission() - Constructor for class ubic.gemma.rest.AdminWebService.ObsoleteTermCorrectionSubmission
ObsoleteTermCorrectionTask - Interface in ubic.gemma.core.tasks.maintenance
ObsoleteTermCorrectionTaskCommand - Class in ubic.gemma.core.tasks.maintenance: Rewrite annotations using obsolete ontology terms to the successors their ontologies assert.
ObsoleteTermCorrectionTaskCommand(Collection, boolean, int) - Constructor for class ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskCommand
ObsoleteTermCorrectionTaskImpl - Class in ubic.gemma.core.tasks.maintenance: Async wrapper for ObsoleteTermCorrectionService.apply(Collection, boolean, long, TimeUnit).
ObsoleteTermCorrectionTaskImpl() - Constructor for class ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskImpl
ObsoleteTermUsage - Class in ubic.gemma.core.ontology: One obsolete ontology term that Gemma's annotations still use, together with whatever the owning ontology says should replace it.
ObsoleteTermUsage() - Constructor for class ubic.gemma.core.ontology.ObsoleteTermUsage
occurrentPartOf - Static variable in class ubic.gemma.core.ontology.jena.RO
of(Class) - Static method in class ubic.gemma.cli.util.EnumConverter
of(Class, EnumMap) - Static method in class ubic.gemma.cli.util.EnumConverter
of(String) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCounts: Read the counts off a payload, best-effort.
of(String...) - Static method in class ubic.gemma.cli.util.EnumeratedByCommandStringConverter
of(String...) - Static method in class ubic.gemma.cli.util.EnumeratedStringConverter
of(String, String) - Static method in enum class ubic.gemma.model.common.description.RelationInferenceDirection: Which way the implication runs for this row.
of(String, String) - Static method in enum class ubic.gemma.model.common.description.RelationTopicality: Classify one row.
of(String, String, String) - Static method in enum class ubic.gemma.model.common.description.RelationInferenceDirection: Deprecated.
by omission rather than by policy: a RelationInferenceDirection.TYPED_OBJECT_REQUIRED predicate cannot be answered without the object's category and comes back RelationInferenceDirection.NEITHER here. That fails closed, which is the right way for it to fail, but a caller holding a whole row should pass the fourth argument and get the real answer.
of(String, String, String) - Static method in enum class ubic.gemma.model.common.description.RelationTopicality
of(String, String, String, String) - Static method in enum class ubic.gemma.model.common.description.RelationInferenceDirection
of(String, Filter.Operator, String) - Static method in class ubic.gemma.persistence.service.FilteringDao.ConjunctSpec
of(String, Filter.Operator, Collection) - Static method in class ubic.gemma.persistence.service.FilteringDao.ConjunctSpec
of(Path) - Static method in class ubic.gemma.rest.util.Sendfile: Creates a new Sendfile instance.
of(List) - Static method in class ubic.gemma.core.metrics.CompositeMeterRegistryFactory: Build a composite registry that forwards every recording to each backing registry.
of(Map) - Static method in class ubic.gemma.cli.util.EnumeratedStringConverter
OF_WHAT - Static variable in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg
OF_WHAT - Static variable in class ubic.gemma.rest.util.args.DatabaseEntryArrayArg
OF_WHAT - Static variable in class ubic.gemma.rest.util.args.DatasetArrayArg
OF_WHAT - Static variable in class ubic.gemma.rest.util.args.GeneArrayArg
OF_WHAT - Static variable in class ubic.gemma.rest.util.args.PlatformArrayArg
OF_WHAT - Static variable in class ubic.gemma.rest.util.args.StringArrayArg
OF_WHAT - Static variable in class ubic.gemma.rest.util.args.TaxonArrayArg
OFFICIAL - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus
OFFICIAL_NAME - Enum constant in enum class ubic.gemma.model.common.search.SearchMatchType: Exact match on an official (long) name.
OFFICIAL_NAME_PREFIX - Enum constant in enum class ubic.gemma.model.common.search.SearchMatchType: Inexact match on an official name.
OfficialSymbolDesignElementMapper - Class in ubic.gemma.core.loader.util.mapper: Match design elements using the official symbol of a gene.
OfficialSymbolDesignElementMapper(Map) - Constructor for class ubic.gemma.core.loader.util.mapper.OfficialSymbolDesignElementMapper
offset - Variable in class ubic.gemma.rest.AdminWebService.BlacklistListResponse
OffsetArg - Class in ubic.gemma.rest.util.args: Argument used to represent an offset.
ok(ExperimentalDesignValueObject) - Static method in class ubic.gemma.rest.util.args.DatasetArgService.DesignChangeResult
oldestOpenAgeDays - Variable in class ubic.gemma.rest.AdminWebService.TicketsBlock: Days since the oldest non-terminal, non-SCRATCHPAD ticket was created; null when no open tickets exist.
oldestOpenAgeDays - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueSummaryResponse
OLIGO - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType: Represents a (synthetic) oligonucleotide.
oligonucleotideBeads - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
OlsTerm - Class in ubic.gemma.core.ontology.ols: A term resolved from the EBI Ontology Lookup Service by its IRI.
OlsTerm(String, String) - Constructor for class ubic.gemma.core.ontology.ols.OlsTerm
OlsTermResolver - Interface in ubic.gemma.core.ontology.ols: Resolves an ontology term IRI against the EBI Ontology Lookup Service (ols4).
OlsTermResolverImpl - Class in ubic.gemma.core.ontology.ols: Resolves a term IRI against the EBI OLS4 REST API (GET {base}/api/terms?iri={iri}).
OlsTermResolverImpl() - Constructor for class ubic.gemma.core.ontology.ols.OlsTermResolverImpl
OlsUnavailableException - Exception Class in ubic.gemma.core.ontology.ols: Raised when the EBI Ontology Lookup Service cannot be reached or returns an unexpected response — a transient condition, distinct from OLS successfully reporting that it has no term for an IRI (which is a null return from OlsTermResolver.resolve(String)).
OlsUnavailableException(String) - Constructor for exception class ubic.gemma.core.ontology.ols.OlsUnavailableException
OlsUnavailableException(String, Throwable) - Constructor for exception class ubic.gemma.core.ontology.ols.OlsUnavailableException
onApplicationEvent(ContextClosedEvent) - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextSchedulingTaskExecutor: Spring's pool-backed executors (ExecutorConfigurationSupport, the base of ThreadPoolTaskExecutor/ThreadPoolTaskScheduler) shut their thread pool down on ContextClosedEvent by implementing ApplicationListener.
onApplicationEvent(ContextRefreshedEvent) - Method in class ubic.gemma.cli.config.ConfigurationLinter
onApplicationReady() - Method in class ubic.gemma.rest.startup.SearchIndexBootstrapper: Fires once after the Spring context refreshes.
onAuthenticationFailure(HttpServletRequest, HttpServletResponse, AuthenticationException) - Method in class ubic.gemma.core.security.authentication.AjaxAuthenticationFailureHandler
onAuthenticationSuccess(HttpServletRequest, HttpServletResponse, Authentication) - Method in class ubic.gemma.core.security.authentication.AjaxAuthenticationSuccessHandler
ONECOLOR - Enum constant in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType: Indicates this platform uses one channel and measurements are non-ratiometric (e.g.
onError(RetryContext, RetryCallback, Throwable) - Method in class ubic.gemma.persistence.retry.RetryLogger
One ruling on one finding inside an AnnotationSet. - Section in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
onEvent(ApplicationEvent) - Method in class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
onEvent(ApplicationEvent) - Method in class ubic.gemma.rest.providers.MetricsApplicationEventListener
onEvent(ApplicationEvent) - Method in class ubic.gemma.rest.providers.RequestExceptionLogger
onEvent(RequestEvent) - Method in class ubic.gemma.rest.providers.AnalyticsRequestEventListener
OneWayAnovaResult - Interface in ubic.gemma.core.util.math.linearmodels
onPersist(PersistEvent) - Method in class ubic.gemma.persistence.audit.AuditTrailEventListener
onPersist(PersistEvent, PersistContext) - Method in class ubic.gemma.persistence.audit.AuditTrailEventListener
onPostDelete(PostDeleteEvent) - Method in class ubic.gemma.core.security.acl.AclEventListener
onPostInsert(PostInsertEvent) - Method in class ubic.gemma.core.security.acl.AclEventListener
onPostInsert(PostInsertEvent) - Method in class ubic.gemma.persistence.audit.AuditTrailEventListener
onPreDelete(PreDeleteEvent) - Method in class ubic.gemma.persistence.audit.AuditTrailEventListener
onProgressUpdate(String) - Method in interface ubic.gemma.core.job.progress.ProgressUpdateCallback
onRequest(RequestEvent) - Method in class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
onRequest(RequestEvent) - Method in class ubic.gemma.rest.providers.MetricsApplicationEventListener
onRequest(RequestEvent) - Method in class ubic.gemma.rest.providers.RequestExceptionLogger
ont() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl: Generate a URL for ontologies served by Gemma.
ontologies - Variable in class ubic.gemma.rest.AdminWebService.OntologiesResponse
OntologiesResponse() - Constructor for class ubic.gemma.rest.AdminWebService.OntologiesResponse
ONTOLOGY - Enum constant in enum class ubic.gemma.model.common.description.AnnotationRelationBasis: A loaded ontology asserts it as an OWL restriction — CLO's derives from patient having disease and is disease model for, MONDO's in_taxon, CL's part_of into UBERON.
ONTOLOGY - Enum constant in enum class ubic.gemma.model.common.description.DatabaseType
ONTOLOGY_TERM - Enum constant in enum class ubic.gemma.cli.completion.CompletionType
OntologyAnalyzers - Class in ubic.gemma.core.ontology.search: The single place the ontology Lucene analysis recipe is defined.
OntologyCardinalityRestriction - Interface in ubic.gemma.core.ontology.model
OntologyCardinalityRestriction.CardinalityType - Enum Class in ubic.gemma.core.ontology.model
OntologyClassRestriction - Interface in ubic.gemma.core.ontology.model
OntologyConfig - Class in ubic.gemma.core.ontology
OntologyConfig() - Constructor for class ubic.gemma.core.ontology.OntologyConfig
OntologyDatatypeRestriction - Interface in ubic.gemma.core.ontology.model
ontologyExternalLinks(Environment) - Method in class ubic.gemma.core.ontology.OntologyConfig
OntologyExternalLinks - Class in ubic.gemma.core.ontology: Provides external links for ontology resources based on their URIs and other metadata.
OntologyExternalLinks(boolean) - Constructor for class ubic.gemma.core.ontology.OntologyExternalLinks
OntologyHighlighter - Interface in ubic.gemma.core.search: Highlighter specialized for ontology terms.
OntologyIndividual - Interface in ubic.gemma.core.ontology.model
OntologyIndividualSimple - Class in ubic.gemma.core.ontology.simple
OntologyIndividualSimple(String, String, String, OntologyTermSimple) - Constructor for class ubic.gemma.core.ontology.simple.OntologyIndividualSimple: Create a new simple ontology individual.
OntologyIndividualSimple(String, String, OntologyTermSimple) - Constructor for class ubic.gemma.core.ontology.simple.OntologyIndividualSimple
OntologyLoader - Class in ubic.gemma.core.ontology.jena: Reads ontologies from OWL resources
OntologyLoader() - Constructor for class ubic.gemma.core.ontology.jena.OntologyLoader
OntologyModel - Interface in ubic.gemma.core.ontology.model
OntologyProperty - Interface in ubic.gemma.core.ontology.model
OntologyPropertySimple - Class in ubic.gemma.core.ontology.simple: Simple in-memory implementation of OntologyProperty.
OntologyPropertySimple(String, String) - Constructor for class ubic.gemma.core.ontology.simple.OntologyPropertySimple
OntologyPropertySimple(String, String, String) - Constructor for class ubic.gemma.core.ontology.simple.OntologyPropertySimple
OntologyQueries - Class in ubic.gemma.core.ontology.search: Shared query shaping for the ontology Lucene indexes.
OntologyRefreshResponse() - Constructor for class ubic.gemma.rest.AdminWebService.OntologyRefreshResponse
OntologyRefreshResponse(String, String) - Constructor for class ubic.gemma.rest.AdminWebService.OntologyRefreshResponse
ontologyRelationProducer(List, AnnotationRelationDao, PlatformTransactionManager, TaxonService, OntologyService) - Method in class ubic.gemma.core.ontology.OntologyConfig: Writes the ONTOLOGY rows of ANNOTATION_RELATION — the relations CLO and CHEBI already assert and nothing has ever read.
OntologyRelationProducer - Interface in ubic.gemma.core.ontology.relation: Writes the AnnotationRelationBasis.ONTOLOGY rows of ANNOTATION_RELATION: the relations our loaded ontologies already assert.
OntologyRelationProducerImpl - Class in ubic.gemma.core.ontology.relation: Reads OntologyTerm.getRestrictions() over the sources named in OntologyRelationSource and writes what they assert into ANNOTATION_RELATION.
OntologyRelationProducerImpl(List, AnnotationRelationDao, TransactionTemplate, TaxonService, OntologyService) - Constructor for class ubic.gemma.core.ontology.relation.OntologyRelationProducerImpl
OntologyResource - Interface in ubic.gemma.core.ontology.model
OntologyRestriction - Interface in ubic.gemma.core.ontology.model: Note: this only handle 'someof' and 'allof' restrictions, not cardinality.
OntologySearchException - Exception Class in ubic.gemma.core.ontology.search: Base class for exceptions raised by OntologyService.findTerm(String, int) and others.
OntologySearchException(String, String, Throwable) - Constructor for exception class ubic.gemma.core.ontology.search.OntologySearchException
OntologySearchResult<T> - Class in ubic.gemma.core.ontology.search: Represents a search result from an ontology.
OntologySearchResult(T, double) - Constructor for class ubic.gemma.core.ontology.search.OntologySearchResult
ontologySearchService(boolean, Path) - Method in class ubic.gemma.core.ontology.OntologyConfig: In-Gemma jena-text / Lucene-9 ontology full-text search service (Phase 3 search restoration; see SEARCH_RECCE.md Section 6).
OntologySearchService - Interface in ubic.gemma.core.ontology.search: Full-text search over ontology resources backed by Jena's jena-text (Lucene 9) integration over a TDB dataset.
OntologySearchService.Result - Class in ubic.gemma.core.ontology.search: Lightweight result envelope.
OntologySearchSource - Class in ubic.gemma.core.search.source: Ontology-driven SearchSource for ExpressionExperiment discovery via Characteristic URIs.
OntologySearchSource() - Constructor for class ubic.gemma.core.search.source.OntologySearchSource
OntologyService - Interface in ubic.gemma.core.ontology
OntologyService - Interface in ubic.gemma.core.ontology.providers
OntologyService.InferenceMode - Enum Class in ubic.gemma.core.ontology.providers
OntologyService.LanguageLevel - Enum Class in ubic.gemma.core.ontology.providers
OntologyServiceFactory<T> - Class in ubic.gemma.core.ontology.providers: Factory bean for baseCode's OntologyService.
OntologyServiceFactory(Class) - Constructor for class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Create a factory for an ontology service class.
OntologyServiceFactory(T) - Constructor for class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Create a factory for a pre-existing ontology service.
OntologyServiceImpl - Class in ubic.gemma.core.ontology: Has a static method for finding out which ontologies are loaded into the system and a general purpose find method that delegates to the many ontology services.
OntologyServiceImpl() - Constructor for class ubic.gemma.core.ontology.OntologyServiceImpl
OntologyServiceResolver - Class in ubic.gemma.core.ontology.providers: Resolves user-supplied text (a REST path segment, a CLI argument) to an OntologyService.
OntologyServiceResolver() - Constructor for class ubic.gemma.core.ontology.providers.OntologyServiceResolver
OntologySlimExtractor - Class in ubic.gemma.core.ontology.providers: Module-extract a slim subset of an OWL ontology around a given seed of term URIs.
OntologySlimExtractor() - Constructor for class ubic.gemma.core.ontology.providers.OntologySlimExtractor
OntologySlimExtractor.ExtractResult - Class in ubic.gemma.core.ontology.providers: Summary returned from OntologySlimExtractor.extract(File, Collection, File) for caller bookkeeping (sidecar meta.json, log lines, regression tests).
OntologySlimMeta - Class in ubic.gemma.core.ontology.providers: Sidecar metadata for an *Ontology-slim.owl cache.
OntologySlimMeta() - Constructor for class ubic.gemma.core.ontology.providers.OntologySlimMeta
OntologyStatement - Interface in ubic.gemma.core.ontology.model: Represents a statement triplet in an ontology.
OntologyStatementSimple - Class in ubic.gemma.core.ontology.simple
OntologyStatementSimple(OntologyResource, OntologyProperty, OntologyResource) - Constructor for class ubic.gemma.core.ontology.simple.OntologyStatementSimple
OntologyStatusValueObject() - Constructor for class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject
ontologyTaskExecutor() - Method in class ubic.gemma.core.ontology.OntologyConfig: Executor used for loading ontologies in background.
ontologyTaskExecutorMetrics() - Method in class ubic.gemma.core.ontology.OntologyConfig: Micrometer binder for the OntologyConfig.ontologyTaskExecutor() VT executor.
OntologyTerm - Class in ubic.gemma.core.loader.expression.cellxgene.model
OntologyTerm - Interface in ubic.gemma.core.ontology.model
OntologyTerm() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
OntologyTerm(String, String) - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
OntologyTerm.TaxonConstraint - Class in ubic.gemma.core.ontology.model: A term's declared in_taxon value: the NCBITaxon URI, its numeric id, and its label when the loaded model carries one.
OntologyTermRef() - Constructor for class ubic.gemma.rest.DatasetsWebService.OntologyTermRef
OntologyTermSimple - Class in ubic.gemma.core.ontology.simple: A light-weight version of OntologyTerms.
OntologyTermSimple(String, String) - Constructor for class ubic.gemma.core.ontology.simple.OntologyTermSimple
OntologyTermSimple(String, String, String, String, boolean) - Constructor for class ubic.gemma.core.ontology.simple.OntologyTermSimple
OntologyTermSimpleValueObject(String, String) - Constructor for class ubic.gemma.rest.AnnotationsWebService.OntologyTermSimpleValueObject
OntologyTermSynonymValueObject(String, String) - Constructor for class ubic.gemma.rest.AnnotationsWebService.OntologyTermSynonymValueObject: Creates a new OntologyTermSynonymValueObject instance.
OntologyTermValidationException - Exception Class in ubic.gemma.rest.util: Thrown when one or more submitted ontology terms fail grounding validation on a write.
OntologyTermValidationException(List) - Constructor for exception class ubic.gemma.rest.util.OntologyTermValidationException
OntologyTermValidationException.Located - Class in ubic.gemma.rest.util: A TermViolation paired with the request-body path it was found at (e.g.
OntologyTermValidationExceptionMapper - Class in ubic.gemma.rest.providers: Maps an OntologyTermValidationException to a 400 whose errors[] carries one entry per failing term slot — each with a stable reason code, a human message naming the resolved label, and a location (request-body path + clientRef) — so a client can self-correct without guessing.
OntologyTermValidationExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.OntologyTermValidationExceptionMapper
OntologyTermValidator - Interface in ubic.gemma.core.ontology: Validates the ontology terms carried by a Characteristic (or Statement) against the terms Gemma actually knows about — the last checkpoint before a curator's or an agent's annotation is persisted, so a hallucinated URI or a label that doesn't match its URI is caught here rather than becoming stored data.
OntologyTermValidatorImpl - Class in ubic.gemma.core.ontology: Default OntologyTermValidator: resolves each slot's URI against Gemma's loaded ontologies (OntologyService.getTerm(String, long, TimeUnit)) first, then OLS, and compares labels.
OntologyTermValidatorImpl(OntologyService, OlsTermResolver) - Constructor for class ubic.gemma.core.ontology.OntologyTermValidatorImpl
OntologyTermValueObject(String, String, String, boolean, Integer, List, List, List, List, int, String, AnnotationsWebService.LexicalTermMetadataValueObject, String, String, List, String) - Constructor for class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject: Creates a new OntologyTermValueObject instance.
OntologyTermValueObject(OntologyTerm, Set) - Constructor for class ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
OntologyUtils - Class in ubic.gemma.core.ontology: Utilities for working with ontologies.
OntologyUtils() - Constructor for class ubic.gemma.core.ontology.OntologyUtils
OntologyXref - Class in ubic.gemma.core.ontology.model: One cross-reference an ontology declares from its own term to an identifier in another resource, with the mapping qualifier kept.
OntologyXref(String, String, OntologyXref.Strength) - Constructor for class ubic.gemma.core.ontology.model.OntologyXref
OntologyXref(String, String, OntologyXref.Strength, String) - Constructor for class ubic.gemma.core.ontology.model.OntologyXref
OntologyXref.Strength - Enum Class in ubic.gemma.core.ontology.model: How the foreign identifier stands to the term that declares the cross-reference, read from the declaring term's point of view: OntologyXref.Strength.NARROW means the foreign term is narrower than this one, OntologyXref.Strength.BROAD that it is wider.
OntologyXrefIndex - Class in ubic.gemma.core.ontology.relation: The cross-references of an ontology, read backwards: foreign identifier → the terms that claim it.
OPAQUE - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
open - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueResponse
open(Path) - Static method in class ubic.gemma.core.loader.util.anndata.AnnData
open(Path) - Static method in class ubic.gemma.core.loader.util.hdf5.H5File: Open an HDF5 file.
OPEN - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketState
OPEN - Enum constant in enum class ubic.gemma.model.pipeline.PipelineJobBatch.BatchState
openApi(CustomModelResolver, Environment) - Method in class ubic.gemma.rest.util.OpenApiConfig
OpenApiConfig - Class in ubic.gemma.rest.util
OpenApiConfig() - Constructor for class ubic.gemma.rest.util.OpenApiConfig
OpenApiFactory - Class in ubic.gemma.rest.util: Factory for OpenAPI.
OpenApiFactory(String) - Constructor for class ubic.gemma.rest.util.OpenApiFactory
OpenAPIVisitor - Class in ubic.gemma.rest.util: Visits an OpenAPI specification and perform string value resolution.
OpenAPIVisitor(StringValueResolver) - Constructor for class ubic.gemma.rest.util.OpenAPIVisitor
OpenApiWebService - Class in ubic.gemma.rest: Serve the OpenAPI specification held by the openApi bean.
OpenApiWebService() - Constructor for class ubic.gemma.rest.OpenApiWebService
openCompressedFile(Path) - Static method in class ubic.gemma.core.util.FileUtils: Open a GZIP-compressed file safely.
openCount - Variable in class ubic.gemma.rest.AdminWebService.TicketsBlock: Open tickets, EXCLUDING SCRATCHPAD.
openCount - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueResponse
openCount - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueSummaryResponse
openCountByType - Variable in class ubic.gemma.rest.AdminWebService.TicketsBlock: Open-ticket counts keyed by Enum.name().
OPENED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType
Open items at cutover time - Section in class ubic.gemma.rest.security.RestSecurityConfig
openLimit - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueResponse
openSession() - Method in interface ubic.gemma.core.security.acl.domain.AclDao: Open a session to be used by AclDao.readAclsById(List, Session).
openSession() - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
openSession() - Method in interface ubic.gemma.core.security.acl.domain.AclService: Open an Hibernate session for use with AclService.readAclById(ObjectIdentity, Session)
openSession() - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
openSource(boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService: Open the vocabulary source.
openSource(boolean) - Method in class ubic.gemma.core.ontology.providers.CellosaurusOntologyService
openSource(boolean) - Method in class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService
openSource(boolean) - Method in class ubic.gemma.core.ontology.providers.MgiStrainOntologyService
openStream(URL) - Method in interface ubic.gemma.core.loader.util.ftp.FTPClientFactory: Open an input stream for the given FTP URL.
openStream(URL) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
openSupplementaryFileAsStream(String, int, boolean) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector: Open a supplementary file as an input stream, possibly decompressing it.
openTicket(Contact, TicketType, String, Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Create a new ticket and seed its event log with a single TicketEventType.OPENED event.
openTicket(Contact, TicketType, String, Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
openTicketsForArrayDesign(Long) - Method in class ubic.gemma.rest.TicketsWebService: Public hook for PlatformsWebService so the platform-tickets route can delegate here without duplicating the Ticket→VO mapping logic.
openTicketsForArrayDesignByCursor(Long, Cursor, int) - Method in class ubic.gemma.rest.TicketsWebService: Cursor-mode counterpart to TicketsWebService.openTicketsForArrayDesign(Long) (step 1s of CURSOR_PAGINATION_STEP1_PLAN.md).
openTicketsForExpressionExperiment(Long) - Method in class ubic.gemma.rest.TicketsWebService: Public hook for DatasetsWebService so the dataset-tickets route can delegate here without duplicating the Ticket→VO mapping logic.
openTicketsForExpressionExperimentByCursor(Long, Cursor, int) - Method in class ubic.gemma.rest.TicketsWebService: Cursor-mode counterpart to TicketsWebService.openTicketsForExpressionExperiment(Long) (step 1p of CURSOR_PAGINATION_STEP1_PLAN.md).
openTicketSummariesForExpressionExperiments(Collection) - Method in class ubic.gemma.rest.TicketsWebService: Public hook for DatasetsWebService's bulk POST /datasets/tickets: the same question TicketsWebService.openTicketsForExpressionExperiment(Long) answers for one dataset, asked about a page of them in one query.
OpenTicketSummaryResponse() - Constructor for class ubic.gemma.rest.TicketsWebService.OpenTicketSummaryResponse
operator() - Method in class ubic.gemma.rest.util.args.FilterArgParser
operator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
operator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
OperatorContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
Operators - Section in class ubic.gemma.rest.util.args.FilterArg
OPT_AVG - Static variable in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject
OPT_PICK_MAX - Static variable in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject
OPT_PICK_VAR - Static variable in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject
optimizeIdentifiableParameterList(Collection) - Static method in class ubic.gemma.persistence.util.QueryUtils: Optimize a collection of Identifiable entities by ID.
optimizeParameterList(Collection) - Static method in class ubic.gemma.persistence.util.QueryUtils: Optimize a given parameter list by sorting, removing duplicates and padding to the next power of two.
OptionsUtils - Class in ubic.gemma.cli.util
OptionsUtils() - Constructor for class ubic.gemma.cli.util.OptionsUtils
or(String, String, Class, Filter.Operator, Collection) - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder: Add a sub-clause explicitly.
or(String, String, Class, Filter.Operator, Collection, String) - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder
or(String, String, Class, Filter.Operator, T) - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder: Add a sub-clause explicitly.
or(String, String, Class, Filter.Operator, T, String) - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder
or(Filter) - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder: Add a sub-clause.
order(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Rank: Return a permutation which puts the array in sorted order.
orderByExperimentalDesign(List, Collection, ExperimentalFactor) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
orderByExperimentalDesign(BulkExpressionDataMatrix, Collection, ExperimentalFactor) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
orderByExperimentalDesign(DoubleMatrix, Collection, ExperimentalFactor) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
OrderVectorsByDesignCli - Class in ubic.gemma.apps: Use to change the order of the values to match the experimental design.
OrderVectorsByDesignCli() - Constructor for class ubic.gemma.apps.OrderVectorsByDesignCli
ORF - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType
ORGANISM - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
ORGANISM_PART - Static variable in class ubic.gemma.model.common.description.Categories
organismPart - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
organisms - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
osArch - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse
OsBlock(String, String, String) - Constructor for class ubic.gemma.rest.monitoring.InfoWebService.OsBlock
osName - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse
OSTTEST - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.AnalysisType
osVersion - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse
other - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
other - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
other - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
other - Enum constant in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule
Other - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
OTHER - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoLibrarySource
OTHER - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType
OTHER - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
OTHER - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
OTHER - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
OTHER - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Unsupported/unknown GO evidence code are mapped to this value.
OTHER - Enum constant in enum class ubic.gemma.model.common.description.DatabaseType
OTHER - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementKind
OTHER - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Other scale type.
OTHER - Enum constant in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Use this for all other types including unknown.
OTHER - Enum constant in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType: We don't know
OTHER - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType
OTHER_RELEVANT - Enum constant in enum class ubic.gemma.model.common.description.PublicationAssociationRole: A publication that is relevant to the experiment without being the one that reports it.
otherCellLevelCharacteristicsDefaultValues(List) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Default values to use for the cell-level characteristics.
otherCellLevelCharacteristicsDefaultValueUris(List) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Default value URIs to use for the cell-level characteristics.
otherCellLevelCharacteristicsFile(Path) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: A location where additional cell-level characteristics can be loaded.
otherCellLevelCharacteristicsNames(List) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Name to use for the cell-level characteristics.
out - Variable in class ubic.gemma.core.util.matrix.MatrixWriter
OutlierAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
OutlierAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.OutlierAnalysisEvent
outlierBioAssayIds - Variable in class ubic.gemma.rest.DatasetsWebService.BatchOutlierResponse: Full sorted list of outlier-flagged bioAssay ids in this dataset after the mutation.
OutlierDetails - Class in ubic.gemma.core.analysis.preprocess: Container for details about a proposed outlier.
OutlierDetails(Long) - Constructor for class ubic.gemma.core.analysis.preprocess.OutlierDetails
OutlierDetectionService - Interface in ubic.gemma.core.analysis.preprocess
OutlierDetectionServiceImpl - Class in ubic.gemma.core.analysis.preprocess: Methods to (attempt to) detect outliers in data sets.
OutlierDetectionServiceImpl(CacheManager) - Constructor for class ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceImpl
OutlierFlaggingAuditService - Interface in ubic.gemma.core.analysis.service: Co-bean facade for the SampleRemovalEvent / SampleRemovalReversionEvent audit emissions carried out by OutlierFlaggingServiceImpl.
OutlierFlaggingAuditServiceImpl - Class in ubic.gemma.core.analysis.service: Implementation of OutlierFlaggingAuditService.
OutlierFlaggingAuditServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.OutlierFlaggingAuditServiceImpl
OutlierFlaggingService - Interface in ubic.gemma.core.analysis.service
OutlierFlaggingServiceImpl - Class in ubic.gemma.core.analysis.service: Service for removing sample(s) from an expression experiment.
OutlierFlaggingServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.OutlierFlaggingServiceImpl
OutlierFoundAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
OutlierFoundAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.OutlierFoundAnalysisEvent
OutliersFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Filter that removes outliers from expression data by masking them with Double.NaN.
OutliersFilter() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.OutliersFilter
OutliersNotFoundAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
OutliersNotFoundAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.OutliersNotFoundAnalysisEvent
OUTPUT_DIR_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
OUTPUT_FILE_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
outputDir - Variable in class ubic.gemma.cli.options.DataFileOptionValue: Write the file to the given output directory.
outputFile - Variable in class ubic.gemma.cli.options.DataFileOptionValue: Write the file to the given output file.
outranks(PublicationAssociationSource) - Method in enum class ubic.gemma.model.common.description.PublicationAssociationSource
overallDesign - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
overflow() - Method in class ubic.gemma.core.util.math.distribution.Histogram: The height of the overflow bin.
OWA - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.AnalysisType

P

pad(List, T, int) - Static method in class ubic.gemma.core.util.ListUtils: Pad a collection with the given element.
padToNextPowerOfTwo(List, T) - Static method in class ubic.gemma.core.util.ListUtils: Pad a collection to the next power of 2 with the given element.
paginate(Slice, String[]) - Static method in class ubic.gemma.rest.util.Responders: Paginate results.
paginate(Slice, String, Filters, String[]) - Static method in class ubic.gemma.rest.util.Responders: Paginate results with a filter and a full-text query.
paginate(Slice, Filters, String[]) - Static method in class ubic.gemma.rest.util.Responders: Paginate results with a filter.
paginate(Responders.FilterMethod, Filters, String[], Sort, int, int) - Static method in class ubic.gemma.rest.util.Responders: Paginate results with a filter using a callback to produce the payload.
paginateByCursor(CursorPage, String[]) - Static method in class ubic.gemma.rest.util.Responders: Paginate a CursorPage into the cursor-mode response wrapper.
PaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util: Represents paginated results with offset and limit.
PaginatedResponseDataObject(Slice, String[]) - Constructor for class ubic.gemma.rest.util.PaginatedResponseDataObject
PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject(DifferentialExpressionAnalysisResultSetValueObject, Double, int, int, long) - Constructor for class ubic.gemma.rest.AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
paintComponent(Graphics) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
parallelMap(Function, List, ExecutorService, boolean) - Static method in class ubic.gemma.core.util.concurrent.FutureUtils: Map a function over a collection in parallel.
parallelMapRange(IntFunction, int, int, ExecutorService, boolean) - Static method in class ubic.gemma.core.util.concurrent.FutureUtils: Map a function over a range of integers in parallel.
paramsJson - Variable in class ubic.gemma.rest.AdminPipelineWebService.SubmitBatchRequest
Parent-ACL discovery and the parent stash - Section in class ubic.gemma.core.security.acl.AclEventListener
parentId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
parentId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
parentId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
parentId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.UpsertDraftRequest
ParentIdentityRetrievalStrategy - Interface in ubic.gemma.core.security.authorization.acl: Strategy for locating parent ACL identities.
ParentIdentityRetrievalStrategyImpl - Class in ubic.gemma.core.security.authorization.acl: Use domain-specific logic to resolve parent ACL identities.
ParentIdentityRetrievalStrategyImpl() - Constructor for class ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategyImpl
PARKED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions.Disposition: Curator parked the element; overrides any other classification.
parkedElements - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
parkedElements - Variable in class ubic.gemma.rest.AnnotationSetsWebService.UpsertDraftRequest
parse(File) - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParser
parse(File) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
parse(File) - Method in class ubic.gemma.core.loader.util.parser.BasicLineParser
parse(File) - Method in interface ubic.gemma.core.loader.util.parser.Parser: Parse a File
parse(File) - Method in class ubic.gemma.core.loader.util.parser.RecordParser
parse(File, BlockingQueue, Map) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
parse(InputStream) - Static method in class ubic.gemma.core.loader.entrez.EntrezXmlUtils: Parse an XML reply from Entrez.
parse(InputStream) - Static method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
parse(InputStream) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
parse(InputStream) - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParser
parse(InputStream) - Method in class ubic.gemma.core.loader.expression.sra.SraXmlParser
parse(InputStream) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
parse(InputStream) - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParser
parse(InputStream) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
parse(InputStream) - Method in class ubic.gemma.core.loader.util.parser.BasicLineParser
parse(InputStream) - Method in class ubic.gemma.core.loader.util.parser.LineMapParser
parse(InputStream) - Method in interface ubic.gemma.core.loader.util.parser.Parser: Parse a InputStream.
parse(InputStream) - Method in class ubic.gemma.core.loader.util.parser.RecordParser
parse(InputStream) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService: Parse the vocabulary from a stream into its terms.
parse(InputStream) - Method in class ubic.gemma.core.ontology.providers.CellosaurusOntologyService: Stream-parse a Cellosaurus OBO into lexical terms.
parse(InputStream) - Method in class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService: Read the precomputed table, grouping its rows into one term per MONDO URI.
parse(InputStream) - Method in class ubic.gemma.core.ontology.providers.MgiStrainOntologyService: Parse MGI_Strain.rpt: one strain per line, tab-delimited, with the accession (MGI:<id>) in column 1 and the strain nomenclature in column 2.
parse(InputStream, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezXmlUtils: Parse an XML reply with a specific character encoding.
parse(InputStream, BlockingQueue) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
parse(InputStream, BlockingQueue) - Method in interface ubic.gemma.core.loader.util.QueuingParser: Parse an input stream, storing the results in the passed queue (which can be used by a consumer)
parse(InputStream, BlockingQueue) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
parse(InputStream, BlockingQueue) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
parse(Reader) - Method in class ubic.gemma.core.loader.expression.sra.SraRuninfoParser
parse(String) - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParser
parse(String) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
parse(String) - Method in class ubic.gemma.core.loader.util.parser.BasicLineParser
parse(String) - Method in interface ubic.gemma.core.loader.util.parser.Parser: Parse a file identified by its path.
parse(String) - Method in class ubic.gemma.core.loader.util.parser.RecordParser
parse(String, String, Class, Filter.Operator, String) - Static method in class ubic.gemma.persistence.util.Filter
parse(String, String, Class, Filter.Operator, String, String) - Static method in class ubic.gemma.persistence.util.Filter: Parse filter where the right-hand side is a scalar.
parse(String, String, Class, Filter.Operator, Collection) - Static method in class ubic.gemma.persistence.util.Filter
parse(String, String, Class, Filter.Operator, Collection, String) - Static method in class ubic.gemma.persistence.util.Filter: Parse a filter where the right-hand side is a Collection of scalar right-hand side to be parsed.
parse(Path) - Method in class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapperParser
PARSE_ALERT_FREQUENCY - Static variable in interface ubic.gemma.core.loader.util.parser.Parser
PARSE_ALERT_TIME_FREQUENCY_MS - Static variable in interface ubic.gemma.core.loader.util.parser.LineParser
parseBoolean(String) - Static method in class ubic.gemma.core.util.TsvUtils
parseDouble(String) - Static method in class ubic.gemma.core.util.TsvUtils
parseGenePixDateTime(String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
parseGenericCCHeader(DataInputStream) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractor
parseInt(String) - Static method in class ubic.gemma.core.util.TsvUtils
parseISO8601(String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
parseLong(String) - Static method in class ubic.gemma.core.util.TsvUtils
parseLongFormat(String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
parseMask(CellLevelCharacteristics) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellMaskUtils: Parse a mask from a CellLevelCharacteristics object.
parseMask(CellLevelCharacteristics, boolean) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellMaskUtils
parseOneLine(String) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
parseOneLine(String) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
parseOneLine(String) - Method in class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
parseOneLine(String) - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
parseOneLine(String) - Method in class ubic.gemma.core.loader.genome.BlatResultParser
parseOneLine(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
parseOneLine(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
parseOneLine(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
parseOneLine(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
parseOneLine(String) - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParser
parseOneLine(String) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParser
parseOneLine(String) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser: Method to parse one biomart line, note that there is a many to many relationship between ensemble ids and entrez gene ids.
parseOneLine(String) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
parseOneLine(String) - Method in interface ubic.gemma.core.loader.util.parser.LineParser: Handle the parsing of a single line from the input.
parseOneRecord(String) - Method in class ubic.gemma.core.loader.genome.FastaParser
parseOneRecord(String) - Method in class ubic.gemma.core.loader.genome.gene.SwissProtParser
parseOneRecord(String) - Method in class ubic.gemma.core.loader.util.parser.RecordParser: Handle the parsing of a single record from the input.
Parser<T> - Interface in ubic.gemma.core.loader.util.parser: Interface for classes that allow parsing of files and streams.
ParserAndLoaderTools - Class in ubic.gemma.core.loader.util: Utilities to be used by parsers and loaders.
ParserAndLoaderTools() - Constructor for class ubic.gemma.core.loader.util.ParserAndLoaderTools
parseSafely(String, QueryParser, Consumer) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Safely parse the given search query into a Lucene query, falling back on a query with special characters escaped if necessary.
parseSafely(QueryParser, String) - Static method in class ubic.gemma.core.ontology.search.OntologyQueries: Parse a free-text query, falling back on the Lucene-escaped form when the raw one will not parse.
parseSafely(SearchSettings, QueryParser, Consumer) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Safely parse the given search settings into a Lucene query, falling back on a query with special characters escaped if necessary.
ParseSearchException - Exception Class in ubic.gemma.core.search: An exception that indicate that the search query could not be parsed.
ParseSearchException(String, String, Throwable) - Constructor for exception class ubic.gemma.core.search.ParseSearchException
ParseSearchException(String, String, Throwable, ParseSearchException) - Constructor for exception class ubic.gemma.core.search.ParseSearchException
ParseSearchException(String, Throwable) - Constructor for exception class ubic.gemma.core.search.ParseSearchException
parseStandardFormat(String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
parseSupportingEvidence(String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Parse a characteristic's opaque supportingEvidence JSON into a tree for serialization.
parseTaxonBiomartFile(Taxon, File) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator: Method calls the parse method to parse a biomart file.
parseUri(String) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Extract a factor value ID from a factor value URI.
partOf - Static variable in class ubic.gemma.core.ontology.jena.RO
password - Variable in class ubic.gemma.rest.AuthWebService.LoginRequest
passwordEncoder() - Method in class ubic.gemma.core.security.SecurityConfig: Gemma-specific legacy-aware password encoder.
Password upgrade flow - Section in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider
patchDatasetQuantitationType(DatasetArg, Long, DatasetsWebService.QuantitationTypePatchRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Body-driven PATCH dispatcher for a quantitation type.
patchTicket(Long, TicketsWebService.UpdateTicketRequest) - Method in class ubic.gemma.rest.TicketsWebService: PATCH alias for TicketsWebService.updateTicket(Long, UpdateTicketRequest).
patchUser(String, AdminWebService.UpdateUserRequest) - Method in class ubic.gemma.rest.AdminWebService: Partial update — toggle the enabled flag (lock/unlock) and/or admin role.
PathProvider - Class in ubic.gemma.rest.providers: Allow for reading and writing Path objects.
PathProvider() - Constructor for class ubic.gemma.rest.providers.PathProvider
patoOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
PatoOntologyService - Class in ubic.gemma.core.ontology.providers: Phenotype And Trait Ontology
PatoOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.PatoOntologyService
payloadJson - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
payloadJson - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
payloadJson - Variable in class ubic.gemma.rest.AnnotationSetsWebService.UpsertDraftRequest
payloadJson - Variable in class ubic.gemma.rest.InternalPipelineWebService.PostEventRequest
payloadJson - Variable in class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
payloadJson - Variable in class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest
payloadSize - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
PCAAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
PCAAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PCAAnalysisEvent
PcLoadingsValueObject(int, List, Map) - Constructor for class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject: Creates a new PcLoadingsValueObject instance.
peakCount - Variable in class ubic.gemma.rest.AdminWebService.ThreadBlock
peekState() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry: Helper for tests / queue assembly; never the persisted state.
PENDING - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.ExternalIssueSyncState: A sync is requested but hasn't completed.
PENDING - Enum constant in enum class ubic.gemma.model.pipeline.JobState
PendingAssignment(String, Set) - Constructor for class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan.PendingAssignment
pendingSignupCount - Variable in class ubic.gemma.rest.AdminWebService.UsersListResponse: Users with a signup token outstanding AND not yet enabled (unverified).
percent - Enum constant in enum class ubic.gemma.core.ontology.GoMetric.Metric
PERCENT - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Constrained to be a value between 0 and 100.
PERCENT1 - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Constrained to be a value between 0 and 1.
perform() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation
perform() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedTransformation
perform() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractScriptBasedTransformation
perform() - Method in interface ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformation: Perform the transformation.
perform() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationPipeline
perform(String) - Method in interface ubic.gemma.core.util.GemmaRestApiClient: Access a given REST endpoint.
perform(String) - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
perform(String, String, Object, Object...) - Method in interface ubic.gemma.core.util.GemmaRestApiClient
perform(String, String, Object, Object...) - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
perform(String, MultiValueMap) - Method in interface ubic.gemma.core.util.GemmaRestApiClient: Access a given endpoint REST endpoint with parameters.
perform(String, MultiValueMap) - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
PermissionChangeEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Represents a change in permissions of an Auditable entity.
PermissionChangeEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PermissionChangeEvent
permissionEvaluator(AclService, ObjectProvider, ObjectProvider) - Method in class ubic.gemma.core.security.MethodSecurityConfig: The AclPermissionEvaluator that backs @PreAuthorize("hasPermission(...)") and @PostAuthorize("hasPermission(...)") SpEL.
permissionGrantingStrategy(AuditLogger) - Method in class ubic.gemma.core.security.acl.GemmaAclConfiguration
PermissionsUpdateRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.PermissionsUpdateRequest
persist(Collection) - Method in class ubic.gemma.persistence.persister.CommonPersister
persist(Collection) - Method in interface ubic.gemma.persistence.persister.Persister: Persist all the objects in a collection.
persist(Collection) - Method in class ubic.gemma.persistence.persister.PersisterHelperImpl
persist(T) - Method in class ubic.gemma.persistence.persister.CommonPersister
persist(T) - Method in interface ubic.gemma.persistence.persister.Persister: Persist a single object.
persist(T) - Method in class ubic.gemma.persistence.persister.PersisterHelperImpl: Persister-shrink S2e: PHI owns the FlushMode.MANUAL window on the polymorphic public entry points.
persist(GeneDifferentialExpressionMetaAnalysis) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService
persist(GeneDifferentialExpressionMetaAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceImpl
persist(ExpressionExperiment, Collection) - Method in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValueHelperService
persist(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in interface ubic.gemma.persistence.persister.PersisterHelper
persist(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in class ubic.gemma.persistence.persister.PersisterHelperImpl: Deprecated.
use EeWriteService.create(ExpressionExperiment, ArrayDesignsForExperimentCache) directly. Retained only so test fixtures that hit PersisterHelper.persist(ExpressionExperiment, ArrayDesignsForExperimentCache) keep working.
persistAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService: Made public for testing purposes only.
persistAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl: Made public for testing purposes only.
persistArrayDesign(ArrayDesign) - Method in class ubic.gemma.persistence.persister.ArrayDesignPersister: Persister-shrink S3 public entry point: find an existing ArrayDesign by business key, else create.
persistArrayDesign(ArrayDesign, Map, Map, Map) - Method in class ubic.gemma.persistence.persister.ArrayDesignPersister: Look up an existing ArrayDesign by business key (shortName, alternate names, or name — see BusinessKey.matches(CriteriaBuilder, From, ArrayDesign)); otherwise create a new one along with its full graph.
persistBibliographicReference(BibliographicReference, Map) - Method in class ubic.gemma.persistence.persister.CommonPersister: Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.
persistBioAssay(BioAssay) - Method in class ubic.gemma.persistence.persister.EeWriteServiceImpl: Persister-shrink S4c: public typed entry point for standalone BioAssay persistence.
persistBioAssay(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.experiment.EeWriteService: Persist a standalone BioAssay.
persistBioMaterial(BioMaterial) - Method in class ubic.gemma.persistence.persister.EeWriteServiceImpl: Persister-shrink S4c: public typed entry point for standalone BioMaterial persistence.
persistBioMaterial(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.experiment.EeWriteService: Persist a standalone BioMaterial.
persistBioSequence(BioSequence) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persist a BioSequence: find by business key, else create.
persistBioSequence(BioSequence, Map, Map, Map) - Method in class ubic.gemma.persistence.persister.GenomePersister: Public after S2b: reached by ArrayDesignPersister via @Autowired.
persistBlatAssociation(BlatAssociation) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persist a BlatAssociation.
persistBlatResults(Collection) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persist a collection of BlatResults.
persistChromosome(Chromosome) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persist a Chromosome.
persistDatabaseEntry(DatabaseEntry, Map) - Method in class ubic.gemma.persistence.persister.CommonPersister: Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.
Persister - Interface in ubic.gemma.persistence.persister: Interface defining the ability to create domain objects in bulk or singly.
PersisterHelper - Interface in ubic.gemma.persistence.persister: This interface contains a few extensions to the base Persister interface to handle special cases with ExpressionExperiment.
PersisterHelperImpl - Class in ubic.gemma.persistence.persister: A service that knows how to persist Gemma-domain objects.
PersisterHelperImpl() - Constructor for class ubic.gemma.persistence.persister.PersisterHelperImpl
persistExpressionExperimentSet(ExpressionExperimentSet, Map) - Method in class ubic.gemma.persistence.persister.RelationshipPersister: Persist an ExpressionExperimentSet.
persistExternalDatabase(ExternalDatabase, Map) - Method in class ubic.gemma.persistence.persister.CommonPersister: Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.
persistGene(Gene) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persist a Gene: find by business key, else create.
persistGene(Gene, Map, Map, Map) - Method in class ubic.gemma.persistence.persister.GenomePersister: Public after S2b: reached by RelationshipPersister via @Autowired.
persistGene2GOAssociation(Gene2GOAssociation) - Method in class ubic.gemma.persistence.persister.RelationshipPersister: Persister-shrink S3 public entry point: persist a single Gene2GOAssociation.
persistGene2GOAssociation(Gene2GOAssociation, Map) - Method in class ubic.gemma.persistence.persister.RelationshipPersister: Public after S2d so the S2e dispatcher can reach it.
persistGene2GOAssociations(Collection) - Method in class ubic.gemma.persistence.persister.RelationshipPersister: Persister-shrink S3 public entry point: persist a batch of Gene2GOAssociations.
persistGeneProduct(GeneProduct) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persist a GeneProduct.
persistMerging(ArrayDesign, ArrayDesign, Collection, boolean, Collection) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperService: Finalize the assembly and persistence of the merged array design.
persistMerging(ArrayDesign, ArrayDesign, Collection, boolean, Collection) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperServiceImpl
persistOrUpdate(T) - Method in class ubic.gemma.persistence.persister.CommonPersister
persistOrUpdate(T) - Method in interface ubic.gemma.persistence.persister.Persister: Persist or update a single object.
persistOrUpdate(T) - Method in class ubic.gemma.persistence.persister.PersisterHelperImpl
persistOrUpdateBioSequence(BioSequence) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persist-or-update a BioSequence: equivalent to the persistOrUpdate(BioSequence) arm formerly routed through PersisterHelperImpl.persistOrUpdate(T).
persistOrUpdateGene(Gene) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persist-or-update a Gene: equivalent to the persistOrUpdate(Gene) arm formerly routed through PersisterHelperImpl.persistOrUpdate(T).
persistStub(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperService
persistStub(DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceImpl
persistTaxon(Taxon) - Method in class ubic.gemma.persistence.persister.GenomePersister: Persist a Taxon: find by business key, else create.
persistTaxon(Taxon, Map) - Method in class ubic.gemma.persistence.persister.GenomePersister: Public after S2b: reached by ArrayDesignPersister and EeWriteServiceImpl via @Autowired.
Person - Class in ubic.gemma.model.common.auditAndSecurity: Deprecated.
not needed
Person() - Constructor for class ubic.gemma.model.common.auditAndSecurity.Person: Deprecated.
PersonDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity: Deprecated.
as Person is deprecated
PersonDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity: Deprecated.
as Person is deprecated
PersonDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.PersonDaoImpl: Deprecated.
PerturbedGeneStat() - Constructor for class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat
PerturbedGeneStat(String, String, long) - Constructor for class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat
phenotype - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
phyper(int, int, int, int, boolean) - Static method in class ubic.gemma.core.util.math.SpecFunc: Ported from R phyper.c
PhysicalLocation - Class in ubic.gemma.model.genome
PhysicalLocation() - Constructor for class ubic.gemma.model.genome.PhysicalLocation
PhysicalLocation.Factory - Class in ubic.gemma.model.genome
PhysicalLocationValueObject - Class in ubic.gemma.model.genome: A very simple value object to represent a physical location
PhysicalLocationValueObject() - Constructor for class ubic.gemma.model.genome.PhysicalLocationValueObject
PhysicalLocationValueObject(PhysicalLocation) - Constructor for class ubic.gemma.model.genome.PhysicalLocationValueObject
pipeline - Variable in class ubic.gemma.rest.AdminPipelineWebService.SubmitBatchRequest
PipelineBatchCancelledEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Curator requested cancellation of a batch (or of one job mid-batch — the latter still emits a batch-level event so the timeline reads as one stream).
PipelineBatchCancelledEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PipelineBatchCancelledEvent
PipelineBatchClosedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: All child jobs in a batch reached a terminal state and the batch moved to CLOSED.
PipelineBatchClosedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PipelineBatchClosedEvent
PipelineBatchEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Abstract base for audit events that live on a PipelineJobBatch's audit trail.
PipelineBatchEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PipelineBatchEvent
PipelineBatchSubmittedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Curator submitted a new pipeline batch.
PipelineBatchSubmittedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PipelineBatchSubmittedEvent
PipelineJob - Class in ubic.gemma.model.pipeline: One pipeline run against one experiment, dispatched to an external scheduler.
PipelineJob() - Constructor for class ubic.gemma.model.pipeline.PipelineJob
PipelineJobBatch - Class in ubic.gemma.model.pipeline: One curator-initiated submission of a pipeline against a set of experiments.
PipelineJobBatch() - Constructor for class ubic.gemma.model.pipeline.PipelineJobBatch
PipelineJobBatch.BatchState - Enum Class in ubic.gemma.model.pipeline: Coarse batch lifecycle.
PipelineJobBatchDao - Interface in ubic.gemma.persistence.service.pipeline
PipelineJobBatchDaoImpl - Class in ubic.gemma.persistence.service.pipeline
PipelineJobBatchDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.pipeline.PipelineJobBatchDaoImpl
PipelineJobBatchService - Interface in ubic.gemma.persistence.service.pipeline: Curator-driven pipeline batch submissions.
PipelineJobBatchServiceImpl - Class in ubic.gemma.persistence.service.pipeline
PipelineJobBatchServiceImpl() - Constructor for class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl
PipelineJobDao - Interface in ubic.gemma.persistence.service.pipeline
PipelineJobDaoImpl - Class in ubic.gemma.persistence.service.pipeline
PipelineJobDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.pipeline.PipelineJobDaoImpl
PipelineJobEvent - Class in ubic.gemma.model.pipeline: One progress / state / log record reported by the scheduler-side pipeline.
PipelineJobEvent() - Constructor for class ubic.gemma.model.pipeline.PipelineJobEvent
PipelineJobEventDao - Interface in ubic.gemma.persistence.service.pipeline
PipelineJobEventDaoImpl - Class in ubic.gemma.persistence.service.pipeline
PipelineJobEventDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.pipeline.PipelineJobEventDaoImpl
PipelineJobReporter - Class in ubic.gemma.cli.pipeline: Reports CLI progress to the Gemma pipeline framework when this process was launched as a child of a pipeline job.
pipelineRegistry() - Method in class ubic.gemma.rest.AdminPipelineWebService
PipelineRunEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: A pipeline job reached terminal success on an experiment.
PipelineRunEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PipelineRunEvent
PipelineScheduler - Interface in ubic.gemma.core.pipeline: Abstraction over an external pipeline scheduler (Luigi or Nextflow today; a different impl tomorrow if needed).
PipelineSchedulerException - Exception Class in ubic.gemma.core.pipeline: Wraps any scheduler-side failure (network, auth, HTTP non-2xx, malformed response, etc.).
PipelineSchedulerException(String) - Constructor for exception class ubic.gemma.core.pipeline.PipelineSchedulerException
PipelineSchedulerException(String, Throwable) - Constructor for exception class ubic.gemma.core.pipeline.PipelineSchedulerException
PipelineStatusBulkRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.PipelineStatusBulkRequest
PipelineStatusValueObject - Class in ubic.gemma.rest: Snapshot of every preprocessing/analysis pipeline step for a single experiment.
PipelineStatusValueObject() - Constructor for class ubic.gemma.rest.PipelineStatusValueObject
PipelineStatusValueObject.PipelineStepValueObject - Class in ubic.gemma.rest
PipelineStepValueObject() - Constructor for class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject
PipelineStepValueObject(String, String, Date, String, String) - Constructor for class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject
PipelineStepValueObject(String, String, Date, String, String, SampleCorrelationAnalysisPayload, ProcessedVectorComputationPayload) - Constructor for class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject
platform - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject: Semicolon-delimited platform accessions (e.g.
PLATFORM - Enum constant in enum class ubic.gemma.cli.completion.CompletionType
PLATFORM - Enum constant in enum class ubic.gemma.cli.util.CLI.CommandGroup
PLATFORM - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoRecordType
PLATFORM - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoScope
PLATFORM_TECHNOLOGY_TYPE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
PlatformArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for dataset (ExpressionExperiment) API.
PlatformArg(String, Class, T) - Constructor for class ubic.gemma.rest.util.args.PlatformArg
PlatformArgService - Class in ubic.gemma.rest.util.args
PlatformArgService(ArrayDesignService, ExpressionExperimentService, CompositeSequenceService, CompositeSequenceArgService) - Constructor for class ubic.gemma.rest.util.args.PlatformArgService
PlatformArrayArg - Class in ubic.gemma.rest.util.args
platformConstraint(ArrayDesign) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Constraint results to be related to the given platform.
PlatformFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher: Fetch GEO "GPLXXX_family.soft.gz" files
PlatformFetcher() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.PlatformFetcher
PlatformIdArg - Class in ubic.gemma.rest.util.args: Long argument type for platform API, referencing the platform ID.
PlatformStringArg - Class in ubic.gemma.rest.util.args: String argument type for platform API, referencing the Platform short name.
PlatformsWebService - Class in ubic.gemma.rest: RESTful interface for platforms.
PlatformsWebService() - Constructor for class ubic.gemma.rest.PlatformsWebService
PlatformsWebService.AnnotationFileType - Enum Class in ubic.gemma.rest: Which of the three annotation-file flavours written by ArrayDesignAnnotationService.create(ArrayDesign, Boolean, boolean) to serve.
PlatformSwitchRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.PlatformSwitchRequest
plot() - Method in class ubic.gemma.core.util.math.distribution.Histogram: Provide graph for JFreePlot; counts expressed as a fraction.
Pointcuts - Class in ubic.gemma.persistence.util: General-purpose pointcuts to recognize CRUD operations etc.
Pointcuts() - Constructor for class ubic.gemma.persistence.util.Pointcuts
POLICY - Enum constant in enum class ubic.gemma.model.annotations.WithheldFromApi.Reason: Withheld by curation or editorial policy rather than by a technical hazard.
poll(SchedulerHandle) - Method in class ubic.gemma.core.pipeline.LuigiPipelineScheduler
poll(SchedulerHandle) - Method in class ubic.gemma.core.pipeline.MockPipelineScheduler
poll(SchedulerHandle) - Method in class ubic.gemma.core.pipeline.NextflowPipelineScheduler
poll(SchedulerHandle) - Method in interface ubic.gemma.core.pipeline.PipelineScheduler: Best-effort fetch of current scheduler-side state.
polyARNA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
polyARNA - Enum constant in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule
PolymerType - Enum Class in ubic.gemma.model.genome.biosequence
POOLCLONE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
poolName - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
populate() - Method in class ubic.gemma.cli.logging.log4j.UserDetailsThreadContextPopulator
populate() - Method in class ubic.gemma.core.logging.log4j.BuildInfoThreadContextPopulator
populate() - Method in interface ubic.gemma.core.logging.log4j.ThreadContextPopulator: Populate the ThreadContext.
populate(Connection) - Method in class ubic.gemma.persistence.initialization.CreateDatabasePopulator
populate(Connection) - Method in class ubic.gemma.persistence.initialization.DatabaseSchemaUpdatePopulator
populate(Connection) - Method in class ubic.gemma.persistence.initialization.InitialDataPopulator
populateAclInfo(ExpressionExperimentValueObject, AclObjectIdentity, AclSid) - Static method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Apply ACL-derived flags (isPublic, userCanWrite, isShared, userOwned) onto an existing VO.
populateAliases(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService: Populate GeneValueObject.getAliases() for each VO in the given collection.
populateAliases(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
populateAssociatedExperimentCount(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService: Populate GeneValueObject.getAssociatedExperimentCount() for each VO in the given collection by counting distinct experiments that reference the gene's synthetic NCBI URI in a characteristic.
populateAssociatedExperimentCount(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl: Looks up all gene URIs in a single CharacteristicReadService.findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean, boolean) call, then assigns the distinct-EE counts back to each VO.
populateBMFMap(Map, BioMaterial) - Static method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl: Retrieve relationships between factors, biomaterials and factor values.
populateEventInformation(Collection) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService
populateEventInformation(Collection) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl: Fills in event and security information from the database.
populateFactorValues(Collection, ExperimentalFactor, Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils: As above, over a given set of samples rather than every sample of the experiment or subset.
populateFactorValuesFromBASet(BioAssaySet, ExperimentalFactor, Collection) - Static method in class ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
populateOutliers(ExpressionExperiment, Collection) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Set BioAssayValueObject.getPredictedOutlier() from the median-correlation algorithm.
populateReportInformation(Collection) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: Fills in link analysis and differential expression analysis summaries, and other info from the report.
populateReportInformation(Collection) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
population - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
positive - Enum constant in enum class ubic.gemma.rest.DatasetsWebService.PcLoadingDirection
postEvent(Long, String, InternalPipelineWebService.PostEventRequest) - Method in class ubic.gemma.rest.InternalPipelineWebService
PostEventRequest() - Constructor for class ubic.gemma.rest.InternalPipelineWebService.PostEventRequest
postProcessAfterInitialization(Object, String) - Method in class ubic.gemma.core.logging.log4j.TaskExecutorThreadContextInheritPostProcessor
postProcessAfterInitialization(Object, String) - Method in class ubic.gemma.core.security.concurrent.TaskExecutorSecurityContextDelegatePostProcessor
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ubic.gemma.core.config.BaseCodeConfigurer
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ubic.gemma.core.context.LazyInitByDefaultPostProcessor
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
postProcessBeforeInitialization(Object, String) - Method in class ubic.gemma.core.logging.log4j.TaskExecutorThreadContextInheritPostProcessor
postProcessBeforeInitialization(Object, String) - Method in class ubic.gemma.core.security.concurrent.TaskExecutorSecurityContextDelegatePostProcessor
postprocessExpressionExperiments(Collection) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Post-process ExpressionExperiments that were processed by the CLI.
postprocessExpressionExperiments(Collection) - Method in class ubic.gemma.apps.UpdateEe2AdCli
postprocessExpressionExperiments(Collection) - Method in class ubic.gemma.apps.UpdateEE2CCli
postProcessValueObjects(List) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
postProcessValueObjects(List) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
postProcessValueObjects(List) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
postProcessValueObjects(List) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
postProcessValueObjects(List) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao: Post-process VOs in bulk.
PRE_COMMIT_SNAPSHOT_RUN_ID_PREFIX - Static variable in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: Run-id prefix on a SNAPSHOT taken by a curation commit to keep the state it displaced, as opposed to one a caller asked for through POST /datasets/{id}/annotation-sets/snapshot.
Preboarded - Enum constant in enum class ubic.gemma.model.expression.experiment.WorkflowState
PREBOARDED_EXPERIMENT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetType: A PreboardedExperiment — a GEO accession Gemma knows about but has not loaded.
PreboardedAlreadyPromotedException(Long) - Constructor for exception class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PreboardedAlreadyPromotedException
PreboardedAuditService - Interface in ubic.gemma.persistence.service.expression.experiment: Co-bean carrying the PreboardedCreatedEvent emission for PreboardedExperimentServiceImpl.createPreboarded(String, String, String).
PreboardedAuditServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of PreboardedAuditService: a thin co-bean that exists so PreboardedAuditServiceImpl.recordPreboardedCreated(PreboardedExperiment, String) is invoked through a Spring proxy and the @Audited aspect can intercept its return path and emit the PreboardedCreatedEvent.
PreboardedAuditServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.PreboardedAuditServiceImpl
PreboardedCreatedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted by POST /preboarded when a PreboardedExperiment is created for a previously-unknown accession.
PreboardedCreatedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PreboardedCreatedEvent
PreboardedExperiment - Class in ubic.gemma.model.expression.experiment: Subclass of Investigation representing a proposed-but-not-yet-loaded dataset.
PreboardedExperiment() - Constructor for class ubic.gemma.model.expression.experiment.PreboardedExperiment
PreboardedExperimentService - Interface in ubic.gemma.persistence.service.expression.experiment: Service surface for PreboardedExperiment CRUD + accession resolution + promotion.
PreboardedExperimentService.AccessionAlreadyExistsException - Exception Class in ubic.gemma.persistence.service.expression.experiment: Thrown by PreboardedExperimentService.createPreboarded(String, String, String) when an existing entity carries the same accession.
PreboardedExperimentService.PreboardedAlreadyPromotedException - Exception Class in ubic.gemma.persistence.service.expression.experiment: Thrown by PreboardedExperimentService.promote(ExpressionExperiment, PreboardedExperiment) when the preboarded has already been promoted.
PreboardedExperimentService.PromotionResult - Class in ubic.gemma.persistence.service.expression.experiment: Return value of PreboardedExperimentService.promote(ExpressionExperiment, PreboardedExperiment).
PreboardedExperimentServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Default PreboardedExperimentService implementation.
PreboardedExperimentServiceImpl(SessionFactory, AnnotationSetService, ExpressionExperimentService, PreboardedAuditService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl
preboardedId - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
preboardedId - Variable in class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
preboardedId - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
preboardedId - Variable in class ubic.gemma.rest.PreboardedWebService.PromoteResponse
PreboardedPromotedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted on POST /preboarded/{id}/promote, when a PreboardedExperiment is promoted to a loaded ExpressionExperiment.
PreboardedPromotedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PreboardedPromotedEvent
PreboardedResponse() - Constructor for class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
PreboardedWebService - Class in ubic.gemma.rest: REST surface for the proposed-experiment workflow.
PreboardedWebService(PreboardedExperimentService, AnnotationSetService, ExpressionExperimentService) - Constructor for class ubic.gemma.rest.PreboardedWebService
PreboardedWebService.AnnotationSetSnapshotResponse - Class in ubic.gemma.rest: Thin annotation-set summary shown inline on the preboarded GET.
PreboardedWebService.AttachAnnotationSetRequest - Class in ubic.gemma.rest: Body of PreboardedWebService.attachAnnotationSet(Long, PreboardedWebService.AttachAnnotationSetRequest).
PreboardedWebService.CreatePreboardedRequest - Class in ubic.gemma.rest: Body of PreboardedWebService.createPreboarded(PreboardedWebService.CreatePreboardedRequest).
PreboardedWebService.PreboardedResponse - Class in ubic.gemma.rest: Response of get/create preboarded.
PreboardedWebService.PromoteRequest - Class in ubic.gemma.rest: Body of PreboardedWebService.promotePreboarded(Long, PreboardedWebService.PromoteRequest).
PreboardedWebService.PromoteResponse - Class in ubic.gemma.rest: Response of promote.
predicate - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
predicate() - Method in class ubic.gemma.rest.util.args.FilterArgParser
predicate() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
predicate(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
predicate(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
PredicateContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
predicateUri - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
predicateUri(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
predicateUris(Collection) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
PREFERRED_LABEL - Enum constant in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia: Query normalises to the term's preferred label exactly.
PreferredCellTypeAssignmentChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when the preferred cell type assignment is changed.
PreferredCellTypeAssignmentChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PreferredCellTypeAssignmentChangedEvent
preferredCellTypeAssignmentName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Name of the CTA to mark as preferred, or null to ignore.
PreferredDataChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when the preferred data for an experiment is changed.
PreferredDataChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PreferredDataChangedEvent
PreferredRawDataChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when the preferred raw data is changed.
PreferredRawDataChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PreferredRawDataChangedEvent
PreferredSingleCellDataChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event emitted when the preferred set of single-cell vectors is changed.
PreferredSingleCellDataChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PreferredSingleCellDataChangedEvent
preferSinglePrecision(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Prefer single-precision for storage, even if the data is available with double-precision.
prefersShortLivedTasks() - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextSchedulingTaskExecutor
Prefetch(Set, FactorValue) - Constructor for class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.Prefetch
prefixWeightedHammingDistance(String, String, double) - Static method in class ubic.gemma.core.util.math.StringDistance: Compute the Hamming distance between two strings of equal length (if they are of unequal length the longer one is trimmed), giving higher weight to characters at the start of the strings, so strings that are similar at the starts are given higher scores (shorter distances) than strings that are similar at the ends.
preflightCuration(DatasetArg, String, DatasetsWebService.CurationDocument) - Method in class ubic.gemma.rest.DatasetsWebService
PRELOAD - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: GEO deep-fetch / metadata pre-population work.
prepare(ExpressionExperiment) - Method in interface ubic.gemma.persistence.persister.PersisterHelper
prepare(ExpressionExperiment) - Method in class ubic.gemma.persistence.persister.PersisterHelperImpl: Deprecated.
use ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) directly. Retained only so test fixtures that hit PersisterHelper.prepare(ExpressionExperiment) keep working.
prepare(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService
prepare(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
prepare(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistService: Call this before calling the persister.
prepare(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistServiceImpl
prepare(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistService
prepare(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistServiceImpl
prepareContext(ApplicationContext) - Static method in class ubic.gemma.core.context.SpringContextUtils: Prepare a given context for prime time.
prepareDatabaseQuery(String, boolean) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils
prepareDatabaseQuery(SearchSettings, boolean, Consumer) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Obtain a query suitable for a database match.
prepareDatabaseQuery(SearchSettings, Consumer) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils
PreparedCoexMatrices - Class in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression: Helper class for sample coexpression analysis.
PreparedCoexMatrices(SampleCoexpressionMatrix, SampleCoexpressionMatrix) - Constructor for class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.PreparedCoexMatrices
PreparedCoexMatrices(SampleCoexpressionMatrix, SampleCoexpressionMatrix, SampleCorrelationAnalysisPayload) - Constructor for class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.PreparedCoexMatrices
prepareStatementCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
prepareTermUriQuery(SearchSettings, Consumer) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils
PreprocessExperimentTask - Interface in ubic.gemma.core.tasks.analysis.expression: A "processed expression data vector create" task
preprocessExpressionExperiments(Collection) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Preprocess the set of ExpressionExperiment before invoking ExpressionExperimentManipulatingCLI.processExpressionExperiments(Collection) or ExpressionExperimentManipulatingCLI.processExpressionExperiment(ExpressionExperiment).
PreprocessingException - Exception Class in ubic.gemma.core.analysis.preprocess: Allows us to catch preprocessing errors and handle them correctly.
PreprocessingException(ExpressionExperiment, String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.PreprocessingException
PreprocessingException(ExpressionExperiment, String, Throwable) - Constructor for exception class ubic.gemma.core.analysis.preprocess.PreprocessingException
PreprocessingException(ExpressionExperiment, Throwable) - Constructor for exception class ubic.gemma.core.analysis.preprocess.PreprocessingException
PreprocessorHelperService - Interface in ubic.gemma.core.analysis.preprocess: Co-bean carrying the processFor* diagnostic steps that PreprocessorServiceImpl.processDiagnostics(ExpressionExperiment) runs as part of the post-load preprocessing pipeline.
PreprocessorHelperServiceImpl - Class in ubic.gemma.core.analysis.preprocess: Implementation of PreprocessorHelperService: a thin co-bean that exists so each processFor* method is invoked through a Spring proxy and the AuditedOnError aspect can intercept its catch path.
PreprocessorHelperServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.PreprocessorHelperServiceImpl
PreprocessorService - Interface in ubic.gemma.core.analysis.preprocess: Encapsulates steps that are done to expression data sets after they are loaded and experimental design curated.
PreprocessorServiceImpl - Class in ubic.gemma.core.analysis.preprocess
PreprocessorServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl
PreprocessTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression: Command object for processing data vectors.
PreprocessTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
PreprocessTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression
PreprocessTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskImpl
PRESENTABSENT - Enum constant in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Indicate if a value is present or absent.
previewDatasetDesignChange(DatasetArg, ExperimentalDesignValueObject) - Method in class ubic.gemma.rest.DatasetsWebService: Dry-run preflight for a proposed design replacement.
previewDesignChange(ExpressionExperiment, ExperimentalDesignValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Predict what would happen if proposed were applied as the experiment's new design via PUT.
previewDesignChange(ExpressionExperiment, ExperimentalDesignValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
previewDesignChange(ExpressionExperiment, ExperimentalDesignValueObject, DesignCommitPlan) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Predict what would happen if proposed were applied, including the bindings a DesignCommitPlan defers to a second apply pass.
previewDesignChange(ExpressionExperiment, ExperimentalDesignValueObject, DesignCommitPlan) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
previewDesignChange(DatasetArg, ExperimentalDesignValueObject) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Run a dry-run preflight for the proposed design replacement.
previewDesignChange(DatasetArg, ExperimentalDesignValueObject, DesignCommitPlan) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Run a dry-run preflight for a design commit, counting the bindings plan defers to a second apply pass.
previousState - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowTransitionResponse
PRIMARY - Enum constant in enum class ubic.gemma.model.common.description.PublicationAssociationRole: The primary citable publication — the paper that reports this experiment.
PrimitiveMatrix<R,C,V> - Interface in ubic.gemma.core.util.matrix: Matrix that holds primitives, with an available object representation of the values.
PrimitiveType - Enum Class in ubic.gemma.model.common.quantitationtype: Primitive storage types for data vectors.
PrincipalComponentAnalysis - Class in ubic.gemma.model.analysis.expression.pca
PrincipalComponentAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
PrincipalComponentAnalysis.Factory - Class in ubic.gemma.model.analysis.expression.pca
PrincipalComponentAnalysisDao - Interface in ubic.gemma.persistence.service.analysis.expression.pca
PrincipalComponentAnalysisDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression.pca
PrincipalComponentAnalysisDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImpl
PrincipalComponentAnalysisReadService - Interface in ubic.gemma.persistence.service.analysis.expression.pca: Read-only retrieval service for PrincipalComponentAnalysis.
PrincipalComponentAnalysisReadServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.pca: Implementation of PrincipalComponentAnalysisReadService.
PrincipalComponentAnalysisReadServiceImpl(PrincipalComponentAnalysisDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadServiceImpl
PrincipalComponentAnalysisService - Interface in ubic.gemma.persistence.service.analysis.expression.pca
PrincipalComponentAnalysisServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.pca
PrincipalComponentAnalysisServiceImpl(PrincipalComponentAnalysisDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl
principalName(Sid) - Static method in class ubic.gemma.core.security.acl.domain.Sids: Principal name (username) carried by the sid, or null if sid is not a principal sid.
principals - Variable in class ubic.gemma.rest.AdminWebService.SessionsResponse
printHelp(PrintWriter, String, Options, String, String) - Static method in class ubic.gemma.cli.util.HelpUtils
printMapping(Map) - Static method in class ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils
printMapping(Map, Appendable) - Static method in class ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils
printResult(CompositeSequence, Collection) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService: Print results to STDOUT
printResult(CompositeSequence, Collection) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
PriorCurationUsage(String, String, long, double) - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicDao.PriorCurationUsage
PriorCurationValueObject(String, String, long, double) - Constructor for class ubic.gemma.rest.AnnotationsWebService.PriorCurationValueObject
ProbeLoading - Class in ubic.gemma.model.analysis.expression.pca: Only stored for some of the probes (e.g.
ProbeLoading() - Constructor for class ubic.gemma.model.analysis.expression.pca.ProbeLoading
ProbeLoading.Factory - Class in ubic.gemma.model.analysis.expression.pca
ProbeMapper - Interface in ubic.gemma.core.analysis.sequence
ProbeMapperConfig - Class in ubic.gemma.core.analysis.sequence: Holds parameters for how mapping should be done.
ProbeMapperConfig() - Constructor for class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
ProbeMapperImpl - Class in ubic.gemma.core.analysis.sequence: Provides methods for mapping sequences to genes and gene products.
ProbeMapperImpl() - Constructor for class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
ProbeMapUtils - Class in ubic.gemma.core.analysis.sequence
ProbeMapUtils() - Constructor for class ubic.gemma.core.analysis.sequence.ProbeMapUtils
ProbeSequenceParser - Class in ubic.gemma.core.loader.genome: Parse probes from a tabular file.
ProbeSequenceParser() - Constructor for class ubic.gemma.core.loader.genome.ProbeSequenceParser
problematic() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Returns the value of the problematic record component.
PROBLEMATIC_BATCH_INFO_FAILURE - Enum constant in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Batch information is problematic.
process(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorService: Preprocess a dataset.
process(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorService: Preprocess a dataset.
process(ExpressionExperiment, boolean, boolean) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorService: Preprocess a dataset.
process(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl
Process - Enum constant in enum class ubic.gemma.model.expression.experiment.WorkflowState
processAffymetrixDesign(ArrayDesign, InputStream, Taxon) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Use this to add sequences to an existing Affymetrix design.
processAffymetrixDesign(ArrayDesign, InputStream, Taxon) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processAllExpressionExperiments() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Process all ExpressionExperiment.
processAllExpressionExperiments() - Method in class ubic.gemma.apps.UpdateEe2AdCli
processAllExpressionExperiments() - Method in class ubic.gemma.apps.UpdateEE2CCli
processArrayDesign(ArrayDesign) - Method in class ubic.gemma.apps.ArrayDesignBlatCli
processArrayDesign(ArrayDesign) - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli
processArrayDesign(ArrayDesign) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
processArrayDesign(ArrayDesign) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService: Do probe mapping, writing the results to the database and using default settings.
processArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
processArrayDesign(ArrayDesign) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService
processArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
processArrayDesign(ArrayDesign, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService: Run blat on all sequences on the array design.
processArrayDesign(ArrayDesign, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
processArrayDesign(ArrayDesign, InputStream, InputStream, SequenceType, Taxon) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Read from FASTA file when the sequence file lacks any way to link the sequences back to the probes.
processArrayDesign(ArrayDesign, InputStream, InputStream, SequenceType, Taxon) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, InputStream, String[], Taxon, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Intended for use with array designs that use sequences that are in genbank, but the accessions need to be assigned after the array is already in the system.
processArrayDesign(ArrayDesign, InputStream, String[], Taxon, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, InputStream, String[], Taxon, boolean, FastaCmd) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
processArrayDesign(ArrayDesign, InputStream, String[], Taxon, boolean, FastaCmd) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, InputStream, SequenceType) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: The sequence file must provide an unambiguous way to associate the sequences with design elements on the array.
processArrayDesign(ArrayDesign, InputStream, SequenceType) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, InputStream, SequenceType, Taxon) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: The sequence file must provide an unambiguous way to associate the sequences with design elements on the array.
processArrayDesign(ArrayDesign, InputStream, SequenceType, Taxon) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, String[], boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: For the case where the sequences are retrieved simply by the GenBank accession.
processArrayDesign(ArrayDesign, String[], boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, String[], boolean, FastaCmd) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Provided primarily for testing.
processArrayDesign(ArrayDesign, String[], boolean, FastaCmd) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, Blat) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService
processArrayDesign(ArrayDesign, Blat) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
processArrayDesign(ArrayDesign, ProbeMapperConfig, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService
processArrayDesign(ArrayDesign, ProbeMapperConfig, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
processArrayDesign(ArrayDesign, Taxon, File, ExternalDatabase, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService: Annotate an array design using a direct source file.
processArrayDesign(ArrayDesign, Taxon, File, ExternalDatabase, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
processArrayDesign(ArrayDesign, Taxon, Collection) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService
processArrayDesign(ArrayDesign, Taxon, Collection) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignBlatCli
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignMergeCli
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignProbeCleanupCLI
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli: See 'configure' for how the other options are handled.
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli
processArrayDesignOptions(CommandLine) - Method in class ubic.gemma.apps.BioSequenceCleanupCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignAuditTrailCleanupCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignBlatCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignMapSummaryCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignMergeCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignProbeCleanupCLI
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignReportCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli
processArrayDesigns(Collection) - Method in class ubic.gemma.apps.BioSequenceCleanupCli
processBlatResults(GoldenPathSequenceAnalysis, Collection) - Method in interface ubic.gemma.core.analysis.sequence.ProbeMapper: Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associatd with; if there are multiple results for a single sequence, these are further analyzed for specificity and redundancy, so that there is a single BlatAssociation between any sequence andy andy gene product.
processBlatResults(GoldenPathSequenceAnalysis, Collection) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
processBlatResults(GoldenPathSequenceAnalysis, Collection, ProbeMapperConfig) - Method in interface ubic.gemma.core.analysis.sequence.ProbeMapper: Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associated with; if there are multiple results for a single sequence, these are further analyzed for specificity and redundancy, so that there is a single BlatAssociation between any sequence andy andy gene product.
processBlatResults(GoldenPathSequenceAnalysis, Collection, ProbeMapperConfig) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
processCompositeSequence(ProbeMapperConfig, Taxon, GoldenPathSequenceAnalysis, CompositeSequence) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService
processCompositeSequence(ProbeMapperConfig, Taxon, GoldenPathSequenceAnalysis, CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
processContributionDate(Node, BibliographicReference) - Static method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
processDataSet(GeoSeries, String, GeoFamilyParser) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator: Process a data set and add it to the series
processDiagnostics(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorService: Create or update the sample correlation, PCA and M-V data.
processDiagnostics(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl
ProcessedDataComputeCLI - Class in ubic.gemma.apps: Prepare the "processed" expression data vectors, and can also do batch correction.
ProcessedDataComputeCLI() - Constructor for class ubic.gemma.apps.ProcessedDataComputeCLI
ProcessedDataDeleterCli - Class in ubic.gemma.apps
ProcessedDataDeleterCli() - Constructor for class ubic.gemma.apps.ProcessedDataDeleterCli
ProcessedExpressionDataVector - Class in ubic.gemma.model.expression.bioAssayData: Represents the processed data that is used for actual analyses.
ProcessedExpressionDataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
ProcessedExpressionDataVector.Factory - Class in ubic.gemma.model.expression.bioAssayData
ProcessedExpressionDataVectorAuditService - Interface in ubic.gemma.persistence.service.expression.bioAssayData: Co-bean facade for the ProcessedVectorComputationEvent success-path audit emission carried out by ProcessedExpressionDataVectorServiceImpl.createProcessedDataVectors(ExpressionExperiment, boolean, boolean).
ProcessedExpressionDataVectorAuditServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData: Implementation of ProcessedExpressionDataVectorAuditService: a thin co-bean whose only purpose is to expose an Audited-annotated method through a Spring proxy.
ProcessedExpressionDataVectorAuditServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorAuditServiceImpl
ProcessedExpressionDataVectorDao - Interface in ubic.gemma.persistence.service.expression.bioAssayData
ProcessedExpressionDataVectorDao.RankMethod - Enum Class in ubic.gemma.persistence.service.expression.bioAssayData
ProcessedExpressionDataVectorDaoImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData
ProcessedExpressionDataVectorDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
ProcessedExpressionDataVectorService - Interface in ubic.gemma.persistence.service.expression.bioAssayData
ProcessedExpressionDataVectorServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData
ProcessedExpressionDataVectorServiceImpl(ProcessedExpressionDataVectorDao) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
processedQuantitationType() - Method in record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Returns the value of the processedQuantitationType record component.
ProcessedVectorComputationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Computation of the "processed" expression data with the ranking (by 'expression level') information filled in, for an Expression Experiment
ProcessedVectorComputationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ProcessedVectorComputationEvent
ProcessedVectorComputationPayload - Record Class in ubic.gemma.core.security.audit.payload: Structured payload for ProcessedVectorComputationEvent writes.
ProcessedVectorComputationPayload(String, String, int, int, boolean, String) - Constructor for record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Creates an instance of a ProcessedVectorComputationPayload record class.
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.AffyDataFromCelCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.DeleteExperimentsCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisWriterCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExperimentalDesignImportCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.GeeqCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.LockExpressionDataFileCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ProcessedDataComputeCLI
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.RefreshExperimentCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ReplaceDataCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.RNASeqDataAddCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataLoaderCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.SplitExperimentCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateEe2AdCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateEE2CCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCli
processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCli
processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.CellLevelMetadataWriterCli
processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.RawExpressionDataWriterCli
processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli
processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataDeleterCli
processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataUpdaterCli
processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataWriterCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.AffyDataFromCelCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.BatchEffectPopulationCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.DeleteDiffExCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.DeleteExperimentsCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisWriterCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExperimentalDesignImportCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionDataCorrMatCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Process an ExpressionExperiment.
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogViewerCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.GeeqCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ListQuantitationTypesCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.LockExpressionDataFileCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.MakeExperimentPrivateCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.MakeExperimentsPublicCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.OrderVectorsByDesignCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ProcessedDataComputeCLI
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ProcessedDataDeleterCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.RawDataDeleterCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.RefreshExperimentCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ReplaceDataCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.RNASeqDataAddCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SingleCellCellTypeFactorCreatorCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SingleCellDataDeleterCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SingleCellDataLoaderCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SingleCellSparsityMetricsUpdaterCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SplitExperimentCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SVDCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.UpdateEe2AdCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.UpdateEE2CCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.UpdateGeoSourceMetadataCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.VectorMergingCli
processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCli
processExpressionExperiments(Collection) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Process multiple ExpressionExperiment.
processExpressionExperiments(Collection) - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli
processExpressionExperiments(Collection) - Method in class ubic.gemma.apps.SingleCellDataLoaderCli
processExpressionExperiments(Collection) - Method in class ubic.gemma.apps.VerifyPublicationEvidenceCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.CellLevelMetadataWriterCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli: Process a set of vectors identified by a QuantitationType.
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.ListQuantitationTypesCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.ProcessedDataDeleterCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.RawDataDeleterCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.RawExpressionDataWriterCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.SingleCellDataDeleterCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.SingleCellDataUpdaterCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.SingleCellDataWriterCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli
processExpressionExperimentVectors(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.apps.DetectQuantitationTypeCli
processForMeanVarianceRelation(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorHelperService: Compute and persist the mean-variance scatter used for the heteroscedasticity diagnostic plot.
processForMeanVarianceRelation(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.PreprocessorHelperServiceImpl: Create the scatter plot to evaluate heteroscedasticity.
processForPca(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorHelperService: Run SVD / PCA for diagnostics.
processForPca(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.PreprocessorHelperServiceImpl
processForSampleCorrelation(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorHelperService: Compute and persist the sample-sample correlation matrix used for the diagnostic heatmap.
processForSampleCorrelation(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.PreprocessorHelperServiceImpl: Create the heatmaps used to judge similarity among samples.
processGbId(GoldenPathSequenceAnalysis, String) - Method in interface ubic.gemma.core.analysis.sequence.ProbeMapper: Given a genbank accession (for a mRNA or EST), find alignment data from GoldenPath.
processGbId(GoldenPathSequenceAnalysis, String) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
processGbIds(GoldenPathSequenceAnalysis, Collection) - Method in interface ubic.gemma.core.analysis.sequence.ProbeMapper
processGbIds(GoldenPathSequenceAnalysis, Collection) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
processIdentifier(String) - Method in class ubic.gemma.core.loader.util.mapper.AbstractGeneIdentifierBasedDesignElementMapper: Extract an identifier from an externally supplied string.
processIdentifier(String) - Method in class ubic.gemma.core.loader.util.mapper.EnsemblIdDesignElementMapper
processIdentifier(String) - Method in class ubic.gemma.core.loader.util.mapper.GeneNameDesignElementMapper
processIdentifier(String) - Method in class ubic.gemma.core.loader.util.mapper.MapBasedEntityMapper: Process the identifier before using it to query the mapping.
processIdentifier(String) - Method in class ubic.gemma.core.loader.util.mapper.NcbiIdDesignElementMapper
processIdentifier(String) - Method in class ubic.gemma.core.loader.util.mapper.OfficialSymbolDesignElementMapper
processImports - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject
PROCESSING_DATE - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssayCategories
processOptions(CommandLine) - Method in class ubic.gemma.apps.AclLinterCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.AffyProbeCollapseCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.BibRefUpdaterCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.BlacklistCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.CellXGeneDataAdderCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.CellXGeneDataDownloaderCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.CellXGeneGrabberCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.CompleteCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.ExperimentalDesignViewCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
processOptions(CommandLine) - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI: This method is called at the end of processCommandLine
processOptions(CommandLine) - Method in class ubic.gemma.apps.FactorValueOntologyWriterCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.FindObsoleteTermsCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator
processOptions(CommandLine) - Method in class ubic.gemma.apps.GeoGrabberCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.GeoSingleCellDataDownloaderCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.IndexGemmaCLI
processOptions(CommandLine) - Method in class ubic.gemma.apps.InitializeDatabaseCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.LoadExpressionDataCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.MergeDuplicateBibRefsCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.MultifunctionalityCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI
processOptions(CommandLine) - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI
processOptions(CommandLine) - Method in class ubic.gemma.apps.ProtocolAdderCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.ProtocolDeleterCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.PubMedLoaderCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.PubMedSearcher
processOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataTransformCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.TaxonLoaderCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateDatabaseCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateExternalRelationsCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateGene2CsCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateOntologyRelationsCli
processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdatePubMedCli
processOptions(CommandLine) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI
processOptions(CommandLine) - Method in class ubic.gemma.cli.util.AbstractCLI: Process command line options.
processPsl(InputStream, Taxon) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat: Process the output of a BLAT search in psl format.
processRepeatMaskerOutput(Collection, Path) - Method in class ubic.gemma.core.analysis.sequence.RepeatScan
processSequence(GoldenPathSequenceAnalysis, BioSequence) - Method in interface ubic.gemma.core.analysis.sequence.ProbeMapper: Get BlatAssociation results for a single sequence.
processSequence(GoldenPathSequenceAnalysis, BioSequence) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
processSequences(GoldenPathSequenceAnalysis, Collection, ProbeMapperConfig) - Method in interface ubic.gemma.core.analysis.sequence.ProbeMapper: Given a collection of sequences, blat them against the selected genome.
processSequences(GoldenPathSequenceAnalysis, Collection, ProbeMapperConfig) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
processSingleAccession(String, String[], boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Update a single sequence in the system.
processSingleAccession(String, String[], boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl: Update a single sequence in the system.
produce() - Method in class ubic.gemma.core.ontology.relation.CellosaurusRelationProducer
produce() - Method in class ubic.gemma.core.ontology.relation.ClInferredLocationProducer
produce() - Method in class ubic.gemma.core.ontology.relation.MgiRelationProducer: Rebuild from the reports as configured, fetching and caching them the way the lexical ontology services do.
produce() - Method in interface ubic.gemma.core.ontology.relation.OntologyRelationProducer: Rebuild every source this producer knows how to read.
produce() - Method in class ubic.gemma.core.ontology.relation.OntologyRelationProducerImpl
produce(InputStream) - Method in class ubic.gemma.core.ontology.relation.CellosaurusRelationProducer: Rebuild every Cellosaurus relation.
produce(InputStream, InputStream) - Method in class ubic.gemma.core.ontology.relation.MgiRelationProducer: Rebuild every MGI relation from the two genotype reports, without the disease report.
produce(InputStream, InputStream, InputStream) - Method in class ubic.gemma.core.ontology.relation.MgiRelationProducer: Rebuild every MGI relation from the three reports.
produce(Collection) - Method in interface ubic.gemma.core.ontology.relation.OntologyRelationProducer: Rebuild a subset of the sources.
produce(Collection) - Method in class ubic.gemma.core.ontology.relation.OntologyRelationProducerImpl
product(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the product of a data sequence, which is Prod( data[i] ).
PRODUCTION - Static variable in class ubic.gemma.core.context.EnvironmentProfiles: Mutually-exclusive environment profiles.
PROFILING - Static variable in class ubic.gemma.core.context.EnvironmentProfiles: Independent feature toggles.
ProfilingConfig - Class in ubic.gemma.core.profiling
ProfilingConfig() - Constructor for class ubic.gemma.core.profiling.ProfilingConfig
progress(int) - Static method in class ubic.gemma.cli.util.AnsiEscapeCodes: Indicate progress.
progress(Integer, String) - Method in class ubic.gemma.cli.pipeline.PipelineJobReporter: Report a progress sample.
ProgressData - Class in ubic.gemma.core.job.progress
ProgressData() - Constructor for class ubic.gemma.core.job.progress.ProgressData
ProgressData(String, int, String) - Constructor for class ubic.gemma.core.job.progress.ProgressData
ProgressData(String, int, String, boolean) - Constructor for class ubic.gemma.core.job.progress.ProgressData
ProgressInputStream - Class in ubic.gemma.core.util
ProgressInputStream(InputStream, ProgressReporter, long) - Constructor for class ubic.gemma.core.util.ProgressInputStream
ProgressReporter - Interface in ubic.gemma.core.util: Report progress.
ProgressReporterFactory - Interface in ubic.gemma.core.util
ProgressUpdateAppender - Class in ubic.gemma.core.logging.log4j: This appender is used by remote tasks to send progress notifications to the webapp.
ProgressUpdateAppender.Builder - Class in ubic.gemma.core.logging.log4j
ProgressUpdateAppender.ProgressUpdateContextImpl - Class in ubic.gemma.core.logging.log4j: Represents a context under which progress update logs are intercepted the ProgressUpdateCallback is invoked.
ProgressUpdateCallback - Interface in ubic.gemma.core.job.progress: Callback used to emit progress updates.
ProgressUpdateContext - Interface in ubic.gemma.core.job.progress
PROJECT - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
prometheus() - Static method in class ubic.gemma.core.metrics.CompositeMeterRegistryFactory: Build a default PrometheusMeterRegistry using PrometheusConfig.DEFAULT.
promote(ExpressionExperiment, PreboardedExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService: Promote the preboarded to a loaded ExpressionExperiment.
promote(ExpressionExperiment, PreboardedExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl
promotedAt - Variable in class ubic.gemma.rest.PreboardedWebService.PromoteResponse
promotePreboarded(Long, PreboardedWebService.PromoteRequest) - Method in class ubic.gemma.rest.PreboardedWebService: Promote a preboarded to a loaded ExpressionExperiment.
PromoteRequest() - Constructor for class ubic.gemma.rest.PreboardedWebService.PromoteRequest
PromoteResponse() - Constructor for class ubic.gemma.rest.PreboardedWebService.PromoteResponse
PromotionResult(Long, Long, int) - Constructor for class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PromotionResult
promptConfirmationOrAbort(String) - Method in class ubic.gemma.cli.util.AbstractCLI: Prompt the user for a confirmation or raise an exception to abort the AbstractCLI.doWork() method.
properPartOf - Static variable in class ubic.gemma.core.ontology.jena.RO: Deprecated.
Properties - Section in class ubic.gemma.rest.util.args.FilterArg
PROPERTY - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
PROPERTY - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
PROPERTY() - Method in class ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
PROPERTY() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
PropertyMapping - Interface in ubic.gemma.persistence.util: Represents a mapping between a query/criteria property and some original property space.
PropertyMappingUtils - Class in ubic.gemma.persistence.util: Utilities for dealing with PropertyMapping.
PropertyMappingUtils() - Constructor for class ubic.gemma.persistence.util.PropertyMappingUtils
propertyName(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder
PropertySourcesConfiguration - Class in ubic.gemma.core.config: Deprecated.
This has been replaced with Spring-based configuration SettingsConfig and usage of Value to inject configurations. You can use @Value("${property}") as replacement.
PropertySourcesConfiguration(PropertySources, DefaultListDelimiterHandler) - Constructor for class ubic.gemma.core.config.PropertySourcesConfiguration: Deprecated.
propertySourcesPlaceholderConfigurer(PropertySources) - Static method in class ubic.gemma.core.config.SettingsConfig: Allow for substitution placeholders with values from the settings.
propertyType(Class) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder
PROPOSAL - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetRole
PROPOSAL - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionScope: A whole proposal at once — reject_all.
PROPOSAL - Enum constant in enum class ubic.gemma.model.expression.experiment.AgentCurationKind
proposalCount - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
proposalCount - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
proposals - Variable in class ubic.gemma.rest.AdminWebService.CurationStatusResponse
ProposalsBlock() - Constructor for class ubic.gemma.rest.AdminWebService.ProposalsBlock
protein - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
protein - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
protein - Enum constant in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule
PROTEIN - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType
PROTEIN - Enum constant in enum class ubic.gemma.model.common.description.DatabaseType
PROTEIN - Enum constant in enum class ubic.gemma.model.genome.biosequence.PolymerType
PROTEINCODING - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
proteinExpressionArraybased - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
proteinExpressionMSBased - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
protocol - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
Protocol - Class in ubic.gemma.model.common.protocol
Protocol() - Constructor for class ubic.gemma.model.common.protocol.Protocol
PROTOCOL - Enum constant in enum class ubic.gemma.cli.completion.CompletionType
Protocol.Factory - Class in ubic.gemma.model.common.protocol
ProtocolAdderCli - Class in ubic.gemma.apps
ProtocolAdderCli() - Constructor for class ubic.gemma.apps.ProtocolAdderCli
ProtocolDao - Interface in ubic.gemma.persistence.service.common.protocol
ProtocolDaoImpl - Class in ubic.gemma.persistence.service.common.protocol: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type Protocol.
ProtocolDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.protocol.ProtocolDaoImpl
ProtocolDeleterCli - Class in ubic.gemma.apps
ProtocolDeleterCli() - Constructor for class ubic.gemma.apps.ProtocolDeleterCli
ProtocolListCli - Class in ubic.gemma.apps
ProtocolListCli() - Constructor for class ubic.gemma.apps.ProtocolListCli
ProtocolReadService - Interface in ubic.gemma.persistence.service.common.protocol: Read-only retrieval service for Protocol.
ProtocolReadServiceImpl - Class in ubic.gemma.persistence.service.common.protocol: Implementation of ProtocolReadService.
ProtocolReadServiceImpl(ProtocolDao) - Constructor for class ubic.gemma.persistence.service.common.protocol.ProtocolReadServiceImpl
ProtocolService - Interface in ubic.gemma.persistence.service.common.protocol
ProtocolServiceImpl - Class in ubic.gemma.persistence.service.common.protocol
ProtocolServiceImpl(ProtocolDao) - Constructor for class ubic.gemma.persistence.service.common.protocol.ProtocolServiceImpl
ProtocolValueObject - Class in ubic.gemma.model.analysis
ProtocolValueObject(Protocol) - Constructor for class ubic.gemma.model.analysis.ProtocolValueObject
PrototypeScopeResolver - Class in ubic.gemma.cli.util
PrototypeScopeResolver() - Constructor for class ubic.gemma.cli.util.PrototypeScopeResolver
ProvenanceRequest() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.ProvenanceRequest
PSEUDO - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
Public - Enum constant in enum class ubic.gemma.model.expression.experiment.WorkflowState
PUBLICATION_DATE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
PUBLICATION_REJECTED - Enum constant in enum class ubic.gemma.rest.util.CurationCommitConflictException.Reason: A paper the commit attaches stands rejected for this dataset by a source the commit does not outrank.
PublicationAssertion - Class in ubic.gemma.persistence.service.common.description: One incoming claim about a publication: the reference, plus who is claiming it and on what basis.
PublicationAssertion(BibliographicReference, PublicationAssociationSource) - Constructor for class ubic.gemma.persistence.service.common.description.PublicationAssertion: A claim with a reference and an authority but no stated basis — what the pre-evidence write path amounts to, and what the plain three-argument ExpressionExperimentService.updatePublications(ExpressionExperiment, BibliographicReference, Collection) produces for its callers.
PublicationAssertion(BibliographicReference, PublicationAssociationSource, String, String, GOEvidenceCode, Double, String) - Constructor for class ubic.gemma.persistence.service.common.description.PublicationAssertion
PublicationAssociation - Class in ubic.gemma.model.common.description: An evidenced claim about whether a BibliographicReference belongs to an Investigation — who says so, on what basis, and whether they are affirming or denying it.
PublicationAssociation() - Constructor for class ubic.gemma.model.common.description.PublicationAssociation
PublicationAssociationConflictException - Exception Class in ubic.gemma.persistence.service.common.description: Thrown when a writer tries to accept a publication that a higher authority has already ruled out for that experiment.
PublicationAssociationConflictException(String, PublicationAssociation) - Constructor for exception class ubic.gemma.persistence.service.common.description.PublicationAssociationConflictException
PublicationAssociationDao - Interface in ubic.gemma.persistence.service.common.description: DAO for PublicationAssociation rows.
PublicationAssociationDaoImpl - Class in ubic.gemma.persistence.service.common.description: Hibernate implementation of PublicationAssociationDao.
PublicationAssociationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.PublicationAssociationDaoImpl
PublicationAssociationRole - Enum Class in ubic.gemma.model.common.description: Which of the two publication slots on an Investigation an accepted PublicationAssociation occupies.
PublicationAssociationService - Interface in ubic.gemma.persistence.service.common.description: Reads and writes the evidenced claims behind an experiment's publication links.
PublicationAssociationServiceImpl - Class in ubic.gemma.persistence.service.common.description: Implementation of PublicationAssociationService.
PublicationAssociationServiceImpl(PublicationAssociationDao) - Constructor for class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
PublicationAssociationSource - Enum Class in ubic.gemma.model.common.description: Who asserted a PublicationAssociation — the authority behind the claim, as distinct from the evidence they gave for it.
PublicationAssociationStatus - Enum Class in ubic.gemma.model.common.description: Whether a PublicationAssociation affirms or denies the link between an experiment and a publication.
PublicationAssociationValueObject - Class in ubic.gemma.model.common.description: Wire form of a PublicationAssociation: why a publication is (or is not) attached to a dataset, and on whose authority.
PublicationAssociationValueObject() - Constructor for class ubic.gemma.model.common.description.PublicationAssociationValueObject
PublicationAssociationValueObject(PublicationAssociation) - Constructor for class ubic.gemma.model.common.description.PublicationAssociationValueObject
PublicationEntry() - Constructor for class ubic.gemma.rest.DatasetsWebService.PublicationEntry
publications(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig.GeoUpdateConfigBuilder
PublicationsUpdateRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.PublicationsUpdateRequest
publishDataset(DatasetArg, String) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI workflow-step endpoint: curator-state-machine transition that publishes a dataset under a named reviewer.
PUBMED - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
pubMedIds - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
PubMedLoaderCli - Class in ubic.gemma.apps: Load PubMed files from XML files -- not used routinely!
PubMedLoaderCli() - Constructor for class ubic.gemma.apps.PubMedLoaderCli
PubMedSearch - Class in ubic.gemma.core.loader.entrez.pubmed: Search PubMed for terms, retrieve document records.
PubMedSearch(String) - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch
PubMedSearcher - Class in ubic.gemma.apps: Simple application to perform pubmed searches from a list of terms, and persist the results in the database.
PubMedSearcher() - Constructor for class ubic.gemma.apps.PubMedSearcher
PubMedService - Class in ubic.gemma.core.loader.entrez.pubmed: Manage the loading of large numbers of pubmed entries into the database.
PubMedService() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedService
PubMedUtils - Class in ubic.gemma.core.loader.entrez.pubmed
PubMedUtils() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedUtils
PubMedXMLParser - Class in ubic.gemma.core.loader.entrez.pubmed: Simple class to parse XML in the format defined by ncbi.
PubMedXMLParser() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
put(Integer, Taxon) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParser
put(String, String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
put(String, Reporter) - Method in class ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
put(String, NcbiGeneHistory) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
put(String, NCBIGeneInfo) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
put(String, BioSequence) - Method in class ubic.gemma.core.loader.genome.ProbeSequenceParser
put(K, T) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
put(K, T) - Method in class ubic.gemma.core.loader.util.parser.LineMapParser
put(CompositeSequence, Collection) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
puts - Variable in class ubic.gemma.rest.AdminWebService.CacheStatRow
pvalue - Variable in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneDiffExStats
pvalue(double, int) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Compute pvalue for the pearson correlation, using the t distribution method.
PVALUE_CLIP_THRESHOLD - Static variable in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService: p values smaller than this will be treated as this value in a meta-analysis.
PVALUE_DIST_SUFFIX - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionFileUtils
pvalueAsByte(double, int) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Convert a p value into a value between 0 and 255 inclusive.
PvalueDistribution - Class in ubic.gemma.model.analysis.expression.diff
PvalueDistribution() - Constructor for class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
PvalueDistribution.Factory - Class in ubic.gemma.model.analysis.expression.diff
PvalueDistributionResponseDataObject(PvalueDistributionValueObject) - Constructor for class ubic.gemma.rest.AnalysisResultSetsWebService.PvalueDistributionResponseDataObject
PvalueDistributionValueObject - Class in ubic.gemma.rest: Wire payload for GET /resultSets/{id}/pvalueDistribution.
PvalueDistributionValueObject(Long, String, long[]) - Constructor for class ubic.gemma.rest.PvalueDistributionValueObject
PvalueDistributionValueObject.Bin - Class in ubic.gemma.rest
PythonBasedSingleCellDataTransformation - Interface in ubic.gemma.core.loader.expression.singleCell.transform: Interface implemented by single-cell data transformation that require Python.
🛑 Pass the id of the object that OWNS the ACEs, not of a SecuredChild - Section in ubic.gemma.persistence.util.AclQueryUtils.formAclRestrictionPredicate(Session, CriteriaBuilder, CommonAbstractCriteria, Expression, Class, Permission)

Q

QcMetricDefinitionValueObject(SequencingQcMetrics.MetricDefinition) - Constructor for class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject
QRDecomposition - Class in ubic.gemma.core.util.math.linalg: QR with pivoting.
QRDecomposition(DoubleMatrix2D) - Constructor for class ubic.gemma.core.util.math.linalg.QRDecomposition
QRDecomposition(DoubleMatrix2D, boolean) - Constructor for class ubic.gemma.core.util.math.linalg.QRDecomposition: Construct the QR decomposition of A.
qStatistic(DoubleArrayList, DoubleArrayList, double) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: The "Q" statistic used to test homogeneity of effect sizes.
qTest(double, double) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: Test for statistical significance of Q.
QTM - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode: Quantitative Trait Measurement (RGD code)
QUALITY_REVIEW - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: General quality-review request (geeq follow-up, suspect outliers, etc.).
quantifier() - Method in class ubic.gemma.rest.util.args.FilterArgParser
quantifier() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
QuantifierContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.QuantifierContext
Quantifiers - Section in class ubic.gemma.rest.util.args.FilterArg
Quantifying a conjunction - Section in class ubic.gemma.rest.util.args.FilterArg
quantile(int, double[], int) - Static method in class ubic.gemma.core.util.math.Stats: Given a double array, calculate the quantile requested.
quantile(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the phi- quantile; that is, an element elem for which holds that phi percent of data elements are less than elem.
quantile(SingleCellExpressionDataVector, double) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
quantile(SingleCellExpressionDataVector, int, double) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
quantile(SingleCellExpressionDataVector, int, CellLevelCharacteristics, int, double) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
quantile(SingleCellExpressionDataVector, CellLevelCharacteristics, int, double) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
quantileInverse(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns how many percent of the elements contained in the receiver are <= element.
quantileNormalize(DoubleMatrix) - Method in class ubic.gemma.core.util.math.MatrixNormalizer: Rows with all missing will not be returned.
quantileNormalize(DoubleMatrix, boolean[]) - Method in class ubic.gemma.core.util.math.MatrixNormalizer: Quantile-normalize, optionally computing the reference distribution from a subset of the columns.
quantileNormalized() - Method in record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Returns the value of the quantileNormalized record component.
QuantileNormalizer<R,C> - Class in ubic.gemma.core.analysis.preprocess.normalize: Perform quantile normalization on a matrix, as described in:
QuantileNormalizer() - Constructor for class ubic.gemma.core.analysis.preprocess.normalize.QuantileNormalizer
quantiles(DoubleArrayList, DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the quantiles of the specified percentages.
QuantitationMismatchException - Exception Class in ubic.gemma.core.analysis.preprocess.detect: Exception raised when an ExpressionDataMatrix does not meet the expectations set by a given QuantitationType.
QuantitationMismatchException(QuantitationType, String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException
QuantitationType - Class in ubic.gemma.model.common.quantitationtype
QuantitationType() - Constructor for class ubic.gemma.model.common.quantitationtype.QuantitationType
QuantitationType.Factory - Class in ubic.gemma.model.common.quantitationtype
QuantitationTypeArg<T> - Class in ubic.gemma.rest.util.args
QuantitationTypeArg(String, Class, T) - Constructor for class ubic.gemma.rest.util.args.QuantitationTypeArg
QuantitationTypeArgService - Class in ubic.gemma.rest.util.args
QuantitationTypeArgService(QuantitationTypeService) - Constructor for class ubic.gemma.rest.util.args.QuantitationTypeArgService
QuantitationTypeByIdArg - Class in ubic.gemma.rest.util.args
QuantitationTypeByNameArg - Class in ubic.gemma.rest.util.args
QuantitationTypeConversionException - Exception Class in ubic.gemma.core.analysis.preprocess.convert: Base class for representing problematic QuantitationType conversion.
QuantitationTypeConversionException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionException
QuantitationTypeConversionRelatedPreprocessingException - Exception Class in ubic.gemma.core.analysis.preprocess
QuantitationTypeConversionRelatedPreprocessingException(ExpressionExperiment, QuantitationTypeConversionException) - Constructor for exception class ubic.gemma.core.analysis.preprocess.QuantitationTypeConversionRelatedPreprocessingException
QuantitationTypeConversionUtils - Class in ubic.gemma.core.analysis.preprocess.convert: Perform various computations on ExpressionDataMatrices (usually in-place).
QuantitationTypeConversionUtils() - Constructor for class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionUtils
QuantitationTypeDao - Interface in ubic.gemma.persistence.service.common.quantitationtype
QuantitationTypeDaoImpl - Class in ubic.gemma.persistence.service.common.quantitationtype: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type QuantitationType.
QuantitationTypeDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
QuantitationTypeDetectionException - Exception Class in ubic.gemma.core.analysis.preprocess.detect
QuantitationTypeDetectionException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionException
QuantitationTypeDetectionRelatedPreprocessingException - Exception Class in ubic.gemma.core.analysis.preprocess: An exception that wraps a QuantitationTypeDetectionException.
QuantitationTypeDetectionRelatedPreprocessingException(ExpressionExperiment, QuantitationTypeDetectionException) - Constructor for exception class ubic.gemma.core.analysis.preprocess.QuantitationTypeDetectionRelatedPreprocessingException
QuantitationTypeDetectionUtils - Class in ubic.gemma.core.analysis.preprocess.detect
QuantitationTypeDetectionUtils() - Constructor for class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtils
quantitationTypeName(String) - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder: Name of the QT to use if more than one is present in the data as per DataLoader.getQuantitationTypes().
quantitationTypeNewName(String) - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder: Override the name of the resulting QT.
quantitationTypeNewScaleType(ScaleType) - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder: Override the scale type of the resulting QT.
quantitationTypeNewType(StandardQuantitationType) - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder: Override the type of the resulting QT.
QuantitationTypeParameterGuesser - Class in ubic.gemma.core.loader.expression.geo: Has the unpleasant task of figuring out what the quantitation type should look like, given a description and name string.
QuantitationTypeParameterGuesser() - Constructor for class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
QuantitationTypePatchRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
QuantitationTypePreferredRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.QuantitationTypePreferredRequest
QuantitationTypeReadService - Interface in ubic.gemma.persistence.service.common.quantitationtype: Read-only retrieval service for QuantitationType.
QuantitationTypeReadServiceImpl - Class in ubic.gemma.persistence.service.common.quantitationtype: Implementation of QuantitationTypeReadService.
QuantitationTypeReadServiceImpl(QuantitationTypeDao) - Constructor for class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
QuantitationTypeService - Interface in ubic.gemma.persistence.service.common.quantitationtype
QuantitationTypeServiceImpl - Class in ubic.gemma.persistence.service.common.quantitationtype
QuantitationTypeServiceImpl(QuantitationTypeDao) - Constructor for class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
QuantitationTypeUtils - Class in ubic.gemma.model.common.quantitationtype: Utilities for working with QuantitationTypes.
QuantitationTypeUtils() - Constructor for class ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils
QuantitationTypeValueObject - Class in ubic.gemma.model.common.quantitationtype: Value object for the QuantitationType.
QuantitationTypeValueObject() - Constructor for class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
QuantitationTypeValueObject(QuantitationType) - Constructor for class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
QuantitationTypeValueObject(QuantitationType, ExpressionExperiment, Class) - Constructor for class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject: Create a QuantitationType VO in the context of an associated experiment.
QUANTITATIVE - Enum constant in enum class ubic.gemma.model.common.quantitationtype.GeneralType: For quantitative data.
QUANTITY - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementKind
quarterRootVariance(LeastSquaresFit) - Method in class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator
QueriedAndFilteredAndCursorPaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util: Cursor-mode counterpart to QueriedAndFilteredAndPaginatedResponseDataObject.
QueriedAndFilteredAndCursorPaginatedResponseDataObject(CursorPage, String, Filters, String[]) - Constructor for class ubic.gemma.rest.util.QueriedAndFilteredAndCursorPaginatedResponseDataObject
QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObject(CursorPage, String, Filters, String[], Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObject
QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObjectExperimentExpressionLevelsValueObject(CursorPage, String, Filters, String[], Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObjectExperimentExpressionLevelsValueObject
QueriedAndFilteredAndInferredAndLimitedResponseDataObject(List, String, Filters, String[], Sort, Integer, Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject
QueriedAndFilteredAndInferredAndPaginatedResponseDataObject(Slice, String, Filters, String[], Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject
QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultByGeneValueObject(Slice, String, Filters, String[], Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultByGeneValueObject
QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectExperimentExpressionLevelsValueObject(Slice, String, Filters, String[], Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectExperimentExpressionLevelsValueObject
QueriedAndFilteredAndInferredResponseDataObject(List, String, Filters, String[], Sort, Collection) - Constructor for class ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredResponseDataObject
QueriedAndFilteredAndLimitedResponseDataObject<T> - Class in ubic.gemma.rest.util: Represents a payload with a limited number of results.
QueriedAndFilteredAndLimitedResponseDataObject(List, String, Filters, String[], Sort, Integer) - Constructor for class ubic.gemma.rest.util.QueriedAndFilteredAndLimitedResponseDataObject
QueriedAndFilteredAndPaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util
QueriedAndFilteredAndPaginatedResponseDataObject(Slice, String, Filters, String[]) - Constructor for class ubic.gemma.rest.util.QueriedAndFilteredAndPaginatedResponseDataObject
QueriedAndFilteredResponseDataObject<T> - Class in ubic.gemma.rest.util
QueriedAndFilteredResponseDataObject(List, String, Filters, String[], Sort) - Constructor for class ubic.gemma.rest.util.QueriedAndFilteredResponseDataObject
query - Variable in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao.CriteriaContext
query(String) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Processed query for performing a search.
QUERY - Enum constant in enum class ubic.gemma.rest.util.LocationType
QueryArg - Class in ubic.gemma.rest.util.args
queryCacheHitCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
queryCacheMissCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
queryCachePutCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
queryExecutionCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
queryExecutionMaxTimeMillis - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
queryExecutionMaxTimeQuery - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
QueryTokens - Class in ubic.gemma.rest.ranking: The one query tokeniser the annotation-search stack uses.
QueryUtils - Class in ubic.gemma.persistence.util: Utilities for Hibernate Query.
QueryUtils() - Constructor for class ubic.gemma.persistence.util.QueryUtils
queue(WorkflowState, String, String, Date, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.WorkflowService: Return datasets currently in state, oldest entry first (so the curator's "what's been waiting longest" view is the natural read).
queue(WorkflowState, String, String, Date, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceImpl
queued - Variable in class ubic.gemma.rest.AdminWebService.JobsListResponse
QUEUED - Enum constant in enum class ubic.gemma.core.job.SubmittedTask.Status
QUEUED - Enum constant in enum class ubic.gemma.model.pipeline.JobState
QueuingParser<T> - Interface in ubic.gemma.core.loader.util: Defines a class that produces object that can be consumed by other classes.
QUICK - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoAmount: Add the first 20 lines of all data tables.
quote(String) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Quote the given Lucene query to be used for an exact match.
QUOTED_STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
QUOTED_STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
QUOTED_STRING() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
quoteIfNecessary(String) - Static method in class ubic.gemma.core.util.ShellUtils
quoteTerm(String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Quote a term if needed in a search query.

R

R - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Read
RAD_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
RAN_AT - Enum constant in enum class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao.SummarySort: When the agent run happened, which is not when it was stored — a queue is ordered by the former.
ranAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
ranAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
ranAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
ranAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.ProvenanceRequest
ranAt - Variable in class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
ranAt - Variable in class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest
randomAnalysis(BioAssaySet, ExperimentalDesign, ArrayDesign) - Static method in class ubic.gemma.model.analysis.expression.diff.RandomDifferentialExpressionAnalysisUtils
RandomDifferentialExpressionAnalysisUtils - Class in ubic.gemma.model.analysis.expression.diff: Utilities for generating random DifferentialExpressionAnalysis for testing purposes.
RandomDifferentialExpressionAnalysisUtils() - Constructor for class ubic.gemma.model.analysis.expression.diff.RandomDifferentialExpressionAnalysisUtils
range(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Stats: Compute the range of an array.
rank() - Method in class ubic.gemma.core.util.math.linalg.SingularValueDecomposition
rank(String, List, Map) - Method in interface ubic.gemma.rest.ranking.AnnotationSearchRankingStrategy: Re-order rawHits according to this strategy.
rank(String, List, Map) - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategy
rank(String, List, Map) - Method in class ubic.gemma.rest.ranking.CompositeRankingStrategy
rank(String, List, Map) - Method in class ubic.gemma.rest.ranking.LuceneOrderRankingStrategy
rank(String, List, Map) - Method in class ubic.gemma.rest.ranking.TokenCoverageRankingStrategy
rank(String, List, Map) - Method in class ubic.gemma.rest.ranking.UsageWeightedRankingStrategy
rank(String, List, Map, Map) - Method in interface ubic.gemma.rest.ranking.AnnotationSearchRankingStrategy: Re-order rawHits with the per-string corpus prior available in addition to the usage counts.
rank(String, List, Map, Map) - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategy
rank(String, List, Map, Map, Map) - Method in interface ubic.gemma.rest.ranking.AnnotationSearchRankingStrategy: Re-order rawHits with the per-URI matched text available in addition to the counts.
rank(String, List, Map, Map, Map) - Method in class ubic.gemma.rest.ranking.CompositeRankingStrategy
Rank - Class in ubic.gemma.core.util.math: Calculate rank statistics for arrays.
Rank() - Constructor for class ubic.gemma.core.util.math.Rank
RANK - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode
RANK - Enum constant in enum class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter.Mode: Use ranks to filter for repetitive values.
RankComputationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
RankComputationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent: Deprecated.
Ranking - Section in class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService
rankInterpolated(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the linearly interpolated number of elements in a list less or equal to a given element.
ranksByColumn(DoubleMatrix) - Static method in class ubic.gemma.core.util.MatrixStats: Calculate the ranks of each value in each column of the matrix.
rankSum(List) - Static method in class ubic.gemma.core.util.math.Rank
rankTransform(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Rank: Rank transform an array.
rankTransform(DoubleArrayList, boolean) - Static method in class ubic.gemma.core.util.math.Rank: Rank transform an array.
rankTransform(Map) - Static method in class ubic.gemma.core.util.math.Rank: Rank transform a map, where the values are Comparable values we wish to rank.
rankTransform(Map, boolean) - Static method in class ubic.gemma.core.util.math.Rank: Ties are broken as for the other methods.
RAT - Enum constant in enum class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat.BlattableGenome
RAW_H5AD - Enum constant in enum class ubic.gemma.core.loader.expression.cellxgene.FileType
RawAndProcessedExpressionDataVectorDao - Interface in ubic.gemma.persistence.service.expression.bioAssayData
RawAndProcessedExpressionDataVectorDaoImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData
RawAndProcessedExpressionDataVectorDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
RawAndProcessedExpressionDataVectorService - Interface in ubic.gemma.persistence.service.expression.bioAssayData
RawAndProcessedExpressionDataVectorServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData
RawAndProcessedExpressionDataVectorServiceImpl(RawAndProcessedExpressionDataVectorDao) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl
RawDataAddedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
RawDataAddedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.RawDataAddedEvent
RawDataDeleterCli - Class in ubic.gemma.apps
RawDataDeleterCli() - Constructor for class ubic.gemma.apps.RawDataDeleterCli
RawDataFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher: Retrieve and unpack the raw data files for GEO series.
RawDataFetcher() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
RawDataRemovedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
RawDataRemovedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.RawDataRemovedEvent
RawDataReplacedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
RawDataReplacedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.RawDataReplacedEvent
RawExpressionDataVector - Class in ubic.gemma.model.expression.bioAssayData: Data for one design element, across one or more bioassays, for a single quantitation type.
RawExpressionDataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
RawExpressionDataVector.Factory - Class in ubic.gemma.model.expression.bioAssayData
RawExpressionDataVectorDao - Interface in ubic.gemma.persistence.service.expression.bioAssayData
RawExpressionDataVectorDaoImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData
RawExpressionDataVectorDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl
RawExpressionDataVectorService - Interface in ubic.gemma.persistence.service.expression.bioAssayData
RawExpressionDataVectorServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData: Provides methods that can be applied to both RawExpressionDataVector and ProcessedExpressionDataVector
RawExpressionDataVectorServiceImpl(RawExpressionDataVectorDao) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorServiceImpl
RawExpressionDataWriterCli - Class in ubic.gemma.apps
RawExpressionDataWriterCli() - Constructor for class ubic.gemma.apps.RawExpressionDataWriterCli
rawQuantitationType() - Method in record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Returns the value of the rawQuantitationType record component.
rbfNormalize(DoubleMatrix, double) - Static method in class ubic.gemma.core.util.math.MatrixStats: Normalize a matrix in place to be a transition matrix.
RCA - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
read() - Method in class ubic.gemma.core.util.ProgressInputStream
read(byte[], int, int) - Method in class ubic.gemma.core.util.ProgressInputStream
read(InputStream) - Method in class ubic.gemma.core.util.matrix.AbstractMatrixReader
read(InputStream) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader
read(InputStream) - Method in class ubic.gemma.core.util.matrix.StringMatrixReader
read(InputStream, int, int) - Method in class ubic.gemma.core.util.matrix.StringMatrixReader
read(InputStream, Collection) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader
read(InputStream, Collection, boolean, int, int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader
read(InputStream, Collection, int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader
read(Reader) - Method in class ubic.gemma.core.datastructure.matrix.CellBrowserTabularMetadataReader: Read single-cell metadata from a UCSC Cell Browser tabular file.
read(String) - Method in class ubic.gemma.core.util.matrix.AbstractMatrixReader
read(String) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader
read(String) - Method in class ubic.gemma.core.util.matrix.StringMatrixReader
read(String, int) - Method in class ubic.gemma.core.util.matrix.AbstractMatrixReader
read(String, int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader
read(String, int) - Method in class ubic.gemma.core.util.matrix.StringMatrixReader
read(String, int, int) - Method in class ubic.gemma.core.util.matrix.StringMatrixReader
read(String, Collection) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader: Read a matrix from a file, subject to filtering criteria.
read(String, Collection, int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrixReader
READ - Static variable in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Aliases, for readability.
readableBy(Securable) - Method in interface ubic.gemma.core.security.SecurityService
readableBy(Securable) - Method in class ubic.gemma.core.security.SecurityServiceImpl
readAclById(ObjectIdentity) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
readAclById(ObjectIdentity, List) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
readAclById(ObjectIdentity, Session) - Method in interface ubic.gemma.core.security.acl.domain.AclService: Read ACLs from a specific Hibernate session.
readAclById(ObjectIdentity, Session) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
readAclsById(List) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
readAclsById(List, List) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
readAclsById(List) - Method in interface ubic.gemma.core.security.acl.domain.AclDao: Read ACLs for the given object identities.
readAclsById(List) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
readAclsById(List, Session) - Method in interface ubic.gemma.core.security.acl.domain.AclDao: Read ACLs for the given object identities from the provided Hibernate session.
readAclsById(List, Session) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl
readAnnotationFile(ArrayDesign) - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService: This tries to read one of the annotation files (noparents, bioprocess or regular) to get the gene information - GO annotations are not part of the result.
readAnnotationFile(ArrayDesign) - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
readChangelog(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileService: Read the content of the changelog file of the given experiment.
readChangelog(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileServiceImpl
readChangelogEntryFromConsole(ExpressionExperiment, String) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Read a changelog entry from the console.
readCount(Long) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata.SequencingMetadataBuilder: The number of reads in the library.
readFrom(File) - Static method in class ubic.gemma.core.ontology.providers.OntologySlimMeta
readFrom(Class, Type, Annotation[], MediaType, MultivaluedMap, InputStream) - Method in class ubic.gemma.rest.providers.PathProvider
readGemmaPropertiesFromManifest() - Static method in class ubic.gemma.core.util.ManifestUtils: Read all the Gemma-related properties from the manifest files.
readHeader(BufferedReader, int) - Method in class ubic.gemma.core.util.matrix.AbstractMatrixReader
readLength(Integer) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata.SequencingMetadataBuilder: The length of the reads.
readListFileToStrings(String) - Static method in class ubic.gemma.cli.util.FileUtils: may be tab-delimited, only first column used, commented (#) lines are ignored.
readListFileToStrings(Path) - Static method in class ubic.gemma.cli.util.FileUtils
readMappingFromFile(CellLevelCharacteristics, ExperimentalFactor, Path) - Static method in class ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils: Create a mapping of cell type assignments to factor values from a file.
readMatrix(Reader, QuantitationType, Map, Map) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixReader: Read a single-cell data matrix from a Cell Browser-compatible format.
readMatrixMarketFromPath(Path) - Static method in class ubic.gemma.core.loader.util.MatrixMarketUtils
REALIGNMENT_NEEDED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: Sequencing data needs to be (re-)aligned — either first-time alignment of uploaded RNA-seq reads, or re-alignment of an existing dataset to a new genome / annotation set.
reason - Variable in class ubic.gemma.rest.AdminWebService.BlacklistRequest: Reason for blacklisting.
reason - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionRequest: Why.
reason - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse
reason - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionRequest: Why.
reason - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
reason - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockBulkResult
reason(String) - Method in class ubic.gemma.rest.util.WellComposedError.WellComposedErrorBuilder
reason(String) - Method in class ubic.gemma.rest.util.WellComposedWarning.WellComposedWarningBuilder
REASON_NEAR_MATCH - Static variable in class ubic.gemma.rest.AnnotationsWebService.RuledOutTermValueObject: Lexically near the query but not naming it — a different entity.
REASON_OUT_OF_CATEGORY - Static variable in class ubic.gemma.rest.AnnotationsWebService.RuledOutTermValueObject: Names the query, but sits in a namespace that is impossible for the stated category.
reauthenticate(String, String) - Method in interface ubic.gemma.core.security.authentication.UserDetailsManager: Sign in the user identified
reauthenticate(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
rebindInvestigation(Investigation, Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao: Rebind every row currently attached to from so it points at to.
rebindInvestigation(Investigation, Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl
rebindInvestigation(Investigation, Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
rebindInvestigation(Investigation, Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
rebindPublication(BibliographicReference, BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationDao: Move every assertion about from onto to, for the duplicate-reference merge.
rebindPublication(BibliographicReference, BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationDaoImpl
rebindPublication(BibliographicReference, BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationService: Move every assertion about from onto to, for the duplicate-reference merge.
rebindPublication(BibliographicReference, BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
rebuild() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix: Refresh the design matrix, for example after releveling.
rebuildOntologySlim(String) - Method in class ubic.gemma.rest.AdminWebService: Rebuild the slim-cache OWL for an ontology that supports it (currently CHEBI only).
recalculateExperimentBatchConfound(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: Recompute the batch confound for ee and persist it; emit a BatchProblemsUpdateEvent only when the value actually changed.
recalculateExperimentBatchConfound(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
recalculateExperimentBatchEffect(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: Recompute the batch effect for ee and persist it; emit a BatchProblemsUpdateEvent only when the effect or its statistics actually changed.
recalculateExperimentBatchEffect(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
recalculateExperimentBatchInfo(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: Recalculates the batch effect and batch confound information for the given dataset.
recalculateExperimentBatchInfo(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
recalculateExperimentBatchInfoAsAdmin(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: Recalculates the batch effect and batch confound information for the given dataset.
recalculateExperimentBatchInfoAsAdmin(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
RecentExperiment() - Constructor for class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
RecentExperiment(Long, String, String, String, Date) - Constructor for class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
recentlyResolved - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueResponse
recentlyResolvedCount - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueResponse
recomputeDatasetGeeq(DatasetArg, GeeqService.ScoreMode) - Method in class ubic.gemma.rest.DatasetsWebService
recomputeDatasetGeeqViaPost(DatasetArg, DatasetsWebService.GeeqRecomputeRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Alias for DatasetsWebService.recomputeDatasetGeeq(DatasetArg, GeeqService.ScoreMode) that exposes the GEEQ recompute under POST /datasets/{id}/geeq/recompute with a JSON body.
recomputeDatasetGeeqViaPostAlias(DatasetArg, DatasetsWebService.GeeqRecomputeRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI compatibility alias for DatasetsWebService.recomputeDatasetGeeqViaPost(DatasetArg, DatasetsWebService.GeeqRecomputeRequest): UI calls POST /datasets/{id}/geeq/recalculate with the same body shape.
reconcile(Investigation, PublicationAssertion, Collection, Collection) - Method in interface ubic.gemma.persistence.service.common.description.PublicationAssociationService: Bring the assertions for investigation into line with a set-replace of its publications, and record any explicit rejections.
reconcile(Investigation, PublicationAssertion, Collection, Collection) - Method in class ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl
record(ExpressionExperiment, QuantitationType, SingleCellDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao: Insert (or no-op if already present) a link row for (ee, qt, scd).
record(ExpressionExperiment, QuantitationType, SingleCellDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl
recordAggregateCreated(ExpressionExperiment, String, SingleCellAggregationPayload) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateAuditService: Emit a DataAddedEvent for ee with the given aggregate payload.
recordAggregateCreated(ExpressionExperiment, String, SingleCellAggregationPayload) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateAuditServiceImpl
recordAlignmentBasedGeneMapping(ArrayDesign, String) - Method in interface ubic.gemma.cli.audit.CliArrayDesignAuditService: Records an AlignmentBasedGeneMappingEvent on the platform.
recordAlignmentBasedGeneMapping(ArrayDesign, String) - Method in class ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl
recordAnalysisPersisted(ExpressionExperiment, String, DifferentialExpressionAnalysisPayload) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerAuditService: Emit a DifferentialExpressionAnalysisEvent for ee with the given payload.
recordAnalysisPersisted(ExpressionExperiment, String, DifferentialExpressionAnalysisPayload) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerAuditServiceImpl
recordAnnotationBasedGeneMapping(ArrayDesign, String) - Method in interface ubic.gemma.cli.audit.CliArrayDesignAuditService: Records an AnnotationBasedGeneMappingEvent on the platform.
recordAnnotationBasedGeneMapping(ArrayDesign, String) - Method in class ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl
recordBatchInformationFetched(ExpressionExperiment, String) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService: Record a BatchInformationFetchingEvent on ee.
recordBatchInformationFetched(ExpressionExperiment, String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl: Record a BatchInformationFetchingEvent on ee.
recordCellTypeFactorCreated(ExpressionExperiment, ExperimentalFactor, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExperimentDesignAuditService: Record an ExperimentalDesignUpdatedEvent against the EE noting the creation of a cell-type factor from a preferred cell-type assignment.
recordCellTypeFactorCreated(ExpressionExperiment, ExperimentalFactor, String) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExperimentDesignAuditServiceImpl: Record an ExperimentalDesignUpdatedEvent against the EE noting the creation of a cell-type factor from a preferred cell-type assignment.
recordCellTypeFactorRemoved(ExpressionExperiment, ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExperimentDesignAuditService: Record an ExperimentalDesignUpdatedEvent against the EE noting the removal of an existing cell-type factor.
recordCellTypeFactorRemoved(ExpressionExperiment, ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExperimentDesignAuditServiceImpl: Record an ExperimentalDesignUpdatedEvent against the EE noting the removal of an existing cell-type factor.
recordCurationDecision(DatasetArg, String, DatasetsWebService.CurationDecisionRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Record a curator's standing ruling that a change must NOT be made -- or, rarely, that one may be.
recordDataReplaced(ExpressionExperiment, String) - Method in interface ubic.gemma.core.loader.expression.DataUpdaterAuditService: Record a DataReplacedEvent against the given experiment with the supplied note.
recordDataReplaced(ExpressionExperiment, String) - Method in class ubic.gemma.core.loader.expression.DataUpdaterAuditServiceImpl: Record a DataReplacedEvent against the given experiment with the supplied note.
recordEvent(Long, String, String) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService: Append an event from the scheduler-side pipeline.
recordEvent(Long, String, String) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl
recordGeeqScoring(ExpressionExperiment, String, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.GeeqAuditService: Record a GeeqEvent against the given experiment with the supplied note and detail string.
recordGeeqScoring(ExpressionExperiment, String, String) - Method in class ubic.gemma.persistence.service.expression.experiment.GeeqAuditServiceImpl: Record a GeeqEvent against the given experiment with the supplied note and detail string.
recordGeoUpdate(ExpressionExperiment, int, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoUpdateAuditService: Record an ExpressionExperimentUpdateFromGEOEvent audit row for ee, but only when the update actually changed something -- either a new characteristic was added or the primary publication was populated.
recordGeoUpdate(ExpressionExperiment, int, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoUpdateAuditServiceImpl
recordMadePrivate(ExpressionExperiment, String) - Method in interface ubic.gemma.cli.audit.CliExpressionExperimentAuditService: Records a MakePrivateEvent on the experiment.
recordMadePrivate(ExpressionExperiment, String) - Method in class ubic.gemma.cli.audit.CliExpressionExperimentAuditServiceImpl
recordMadePublic(ExpressionExperiment, String) - Method in interface ubic.gemma.cli.audit.CliExpressionExperimentAuditService: Records a MakePublicEvent on the experiment.
recordMadePublic(ExpressionExperiment, String) - Method in class ubic.gemma.cli.audit.CliExpressionExperimentAuditServiceImpl
recordMerge(ArrayDesign, String) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeAuditService: Record an ArrayDesignMergeEvent against the given platform with the supplied note.
recordMerge(ArrayDesign, String) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeAuditServiceImpl: Record an ArrayDesignMergeEvent against the given platform with the supplied note.
RecordParser<T> - Class in ubic.gemma.core.loader.util.parser: Abstract record-based parser.
RecordParser() - Constructor for class ubic.gemma.core.loader.util.parser.RecordParser
recordPlatformSwitch(ExpressionExperiment, String) - Method in interface ubic.gemma.core.loader.expression.DataUpdaterAuditService: Record an ExpressionExperimentPlatformSwitchEvent against the given experiment with the supplied note.
recordPlatformSwitch(ExpressionExperiment, String) - Method in class ubic.gemma.core.loader.expression.DataUpdaterAuditServiceImpl: Record an ExpressionExperimentPlatformSwitchEvent against the given experiment with the supplied note.
recordPreboardedCreated(PreboardedExperiment, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.PreboardedAuditService: Record a PreboardedCreatedEvent against the freshly persisted preboarded with a note that interpolates the accession.
recordPreboardedCreated(PreboardedExperiment, String) - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedAuditServiceImpl: Record a PreboardedCreatedEvent against the freshly persisted preboarded with a note that interpolates the accession.
recordPreferredQtChanged(ExpressionExperiment, QuantitationType, QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteAuditService: Audit that the preferred QuantitationType for the given vector type changed to qt.
recordPreferredQtChanged(ExpressionExperiment, QuantitationType, QuantitationType, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteAuditServiceImpl: Audit that the preferred QuantitationType for the given vector type changed to qt.
recordPreferredQtCleared(ExpressionExperiment, QuantitationType, Class) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteAuditService: Audit that the preferred QuantitationType for the given vector type was cleared (the previously-preferred QT is no longer preferred).
recordPreferredQtCleared(ExpressionExperiment, QuantitationType, Class) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteAuditServiceImpl: Audit that the preferred QuantitationType for the given vector type was cleared (the previously-preferred QT is no longer preferred).
recordProbeRenaming(ArrayDesign, String) - Method in interface ubic.gemma.cli.audit.CliArrayDesignAuditService: Records an ArrayDesignProbeRenamingEvent on the platform.
recordProbeRenaming(ArrayDesign, String) - Method in class ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl
recordProcessedVectorComputation(ExpressionExperiment, ProcessedVectorComputationPayload) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorAuditService: Emit a ProcessedVectorComputationEvent for ee with the typed ProcessedVectorComputationPayload.
recordProcessedVectorComputation(ExpressionExperiment, ProcessedVectorComputationPayload) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorAuditServiceImpl
recordReleaseDetailsUpdate(ExternalDatabase, String, ReleaseDetailsUpdatePayload) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseReleaseAuditService: Emit a ReleaseDetailsUpdateEvent for the given external database.
recordReleaseDetailsUpdate(ExternalDatabase, String, ReleaseDetailsUpdatePayload) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseReleaseAuditServiceImpl
recordRepeatAnalysis(ArrayDesign, String) - Method in interface ubic.gemma.cli.audit.CliArrayDesignAuditService: Records an ArrayDesignRepeatAnalysisEvent on the platform.
recordRepeatAnalysis(ArrayDesign, String) - Method in class ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl
records - Variable in class ubic.gemma.rest.AdminWebService.GeoGrabResponse
recordSampleCorrelationAnalysis(ExpressionExperiment, SampleCorrelationAnalysisPayload) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAuditService: Emit a SampleCorrelationAnalysisEvent for ee, carrying the filter attrition recorded while the matrix was built.
recordSampleCorrelationAnalysis(ExpressionExperiment, SampleCorrelationAnalysisPayload) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAuditServiceImpl
recordSampleRemoval(ExpressionExperiment, String, SampleRemovalPayload) - Method in interface ubic.gemma.core.analysis.service.OutlierFlaggingAuditService: Emit a SampleRemovalEvent for ee with the given payload.
recordSampleRemoval(ExpressionExperiment, String, SampleRemovalPayload) - Method in class ubic.gemma.core.analysis.service.OutlierFlaggingAuditServiceImpl
recordSampleRemovalReversion(ExpressionExperiment, String, SampleRemovalPayload) - Method in interface ubic.gemma.core.analysis.service.OutlierFlaggingAuditService: Emit a SampleRemovalReversionEvent for ee with the given payload.
recordSampleRemovalReversion(ExpressionExperiment, String, SampleRemovalPayload) - Method in class ubic.gemma.core.analysis.service.OutlierFlaggingAuditServiceImpl
recordSequenceAnalysis(ArrayDesign, String) - Method in interface ubic.gemma.cli.audit.CliArrayDesignAuditService: Records an ArrayDesignSequenceAnalysisEvent on the platform.
recordSequenceAnalysis(ArrayDesign, String) - Method in class ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl
recordSequenceRemove(ArrayDesign, String) - Method in interface ubic.gemma.cli.audit.CliArrayDesignAuditService: Records an ArrayDesignSequenceRemoveEvent on the platform.
recordSequenceRemove(ArrayDesign, String) - Method in class ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl
recordSequenceUpdate(ArrayDesign, String) - Method in interface ubic.gemma.cli.audit.CliArrayDesignAuditService: Records an ArrayDesignSequenceUpdateEvent on the platform.
recordSequenceUpdate(ArrayDesign, String) - Method in class ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl
recordSingleBatchDetermination(ExpressionExperiment, String) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService: Record a SingleBatchDeterminationEvent on ee.
recordSingleBatchDetermination(ExpressionExperiment, String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl: Record a SingleBatchDeterminationEvent on ee.
recordsMatched - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
recordsScanned - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
recordSubSetsCreated(ExpressionExperiment, String, SingleCellSubSetsCreatedPayload) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetAuditService: Emit a SingleCellSubSetsCreatedEvent for ee carrying the typed SingleCellSubSetsCreatedPayload.
recordSubSetsCreated(ExpressionExperiment, String, SingleCellSubSetsCreatedPayload) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetAuditServiceImpl
recordSubsumeCheck(ArrayDesign, String) - Method in interface ubic.gemma.cli.audit.CliArrayDesignAuditService: Records an ArrayDesignSubsumeCheckEvent on the platform.
recordSubsumeCheck(ArrayDesign, String) - Method in class ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl
recreateCellTypeFactorIfNecessary(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Re-create the cell type factor if necessary.
recycleClient(URL, FTPClient) - Method in interface ubic.gemma.core.loader.util.ftp.FTPClientFactory: Recycle the FTP client so that it might be reused in the future.
recycleClient(URL, FTPClient) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
REDGREEN_COLORMAP - Static variable in class ubic.gemma.core.util.graphics.ColorMap
redoAggregate(ExpressionExperiment, QuantitationType, CellLevelCharacteristics, ExperimentalFactor, Map, BioAssayDimension, QuantitationType, SingleCellAggregationConfig) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateService: Re-aggregate a dataset by any cell-level characteristics.
redoAggregate(ExpressionExperiment, QuantitationType, CellLevelCharacteristics, ExperimentalFactor, Map, BioAssayDimension, QuantitationType, SingleCellAggregationConfig) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl
redoAggregateByCellType(ExpressionExperiment, BioAssayDimension, QuantitationType, SingleCellAggregationConfig) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateService: Re-aggregate a dataset by cell type.
redoAggregateByCellType(ExpressionExperiment, BioAssayDimension, QuantitationType, SingleCellAggregationConfig) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl
redoAnalyses(ExpressionExperiment, Collection, DifferentialExpressionAnalysisConfig, boolean) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService: Redo multiple analyses.
redoAnalyses(ExpressionExperiment, Collection, DifferentialExpressionAnalysisConfig, boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService: Redo an analysis.
redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService: Redo an analysis.
redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
redoDatasetDifferentialAnalysis(DatasetArg, Long) - Method in class ubic.gemma.rest.DatasetsWebService
redoDatasetDifferentialAnalysisAlias(DatasetArg, Long) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI compatibility alias for DatasetsWebService.redoDatasetDifferentialAnalysis(DatasetArg, Long): UI calls POST /datasets/{id}/analyses/differential/{aid}/redo; the canonical handler lives at /tasks/redo/{analysisId}.
REDUNDANT - Enum constant in enum class ubic.gemma.model.annotations.WithheldFromApi.Reason: Nothing is being withheld: this datum is already on the wire under another name, or is trivially derivable from what is.
REFERENCE - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
ReferenceAssociation - Class in ubic.gemma.model.association: An association between a BioSequence and a GeneProduct based on external database identifiers.
ReferenceAssociation() - Constructor for class ubic.gemma.model.association.ReferenceAssociation
ReferenceAssociation.Factory - Class in ubic.gemma.model.association
ReferenceAssociationDao - Interface in ubic.gemma.persistence.service.association
ReferenceAssociationDaoImpl - Class in ubic.gemma.persistence.service.association: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ReferenceAssociation.
ReferenceAssociationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.ReferenceAssociationDaoImpl
refresh() - Method in interface ubic.gemma.core.analysis.report.HomeStatsService: Recompute the snapshot from scratch (anonymous-user perspective), persist to disk, and update the in-memory cache.
refresh() - Method in class ubic.gemma.core.analysis.report.HomeStatsServiceImpl
refresh() - Method in interface ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService: Refresh homologene data.
refresh() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl
refresh(String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
refresh(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
refresh(Investigation, String, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService: Extend the caller's existing lease without taking one they do not hold.
refresh(Investigation, String, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl
refreshDaily() - Method in class ubic.gemma.core.analysis.report.HomeStatsRefresher: Daily refresh.
refreshDataset(DatasetArg, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve a "refreshed" dataset.
refreshDatasetsAnnotations(QueryArg, FilterArg, ExcludeArg, LimitArg, Integer, String, StringArrayArg, Boolean, StringArrayArg, Boolean, Boolean, Boolean, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService
refreshDatasetsPlatforms(QueryArg, FilterArg, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService
RefreshExperimentCli - Class in ubic.gemma.apps
RefreshExperimentCli() - Constructor for class ubic.gemma.apps.RefreshExperimentCli
refreshExpressionExperimentFromGemmaWeb(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Refresh a dataset for Gemma Web.
refreshExpressionExperimentFromGemmaWebSilently(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: A silent version of ExpressionExperimentManipulatingCLI.refreshExpressionExperimentFromGemmaWeb(ExpressionExperiment, boolean, boolean) that produces a warning via AbstractCLI.addWarningObject(Serializable, String, Throwable) instead of throwing an exception.
refreshGenesProbes() - Method in class ubic.gemma.rest.GeneWebService: Refresh gene-to-probe associations.
refreshHomeStats() - Method in class ubic.gemma.rest.StatsWebService
refreshOnStartup() - Method in class ubic.gemma.core.analysis.report.HomeStatsRefresher: Recompute the snapshot on context startup.
refreshOntology(String, boolean) - Method in class ubic.gemma.rest.AdminWebService: Refresh a single ontology in-process: re-run initialize(forceLoad=true) on a background thread so the source is re-fetched, the model is rebuilt, and the in-memory state is atomically swapped without a container restart.
REFSEQ - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType
REFUSED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionType: Do not make this change.
REFUTED - Enum constant in enum class ubic.gemma.model.common.description.AnnotationRelationStatus: The source states the relation does NOT hold — an explicit negative, not a missing positive.
regeneratePlatformReport(PlatformArg) - Method in class ubic.gemma.rest.AdminWebService: Regenerate the cached report for ONE platform, synchronously.
registerEntity(String, Class, int) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
registerEntity(String, Class, int, boolean) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer: Register an entity available at a given prefix.
registerObjectAlias(String, String, Class, String, int) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
registerObjectAlias(String, String, Class, String, int, boolean) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer: Register an alias for a property.
registerProperties(String...) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer: Register all the given properties.
registerProperty(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
registerProperty(String, boolean) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer: Register a given property.
regressed - Enum constant in enum class ubic.gemma.rest.DatasetsWebService.CorrelationMatrixChoice
ReindexAcceptedResponse(List) - Constructor for class ubic.gemma.rest.AdminWebService.ReindexAcceptedResponse
reindexAllOntologies() - Method in interface ubic.gemma.core.ontology.OntologyService: Recreate the search indices, for ontologies that are loaded.
reindexAllOntologies() - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
reindexSearchIndices(String) - Method in class ubic.gemma.rest.AdminWebService: Trigger a Hibernate Search 7 mass-reindex for one entity (or all of them).
reindexStale() - Method in class ubic.gemma.core.search.indexer.ScheduledSearchReindexer: Daily MassIndexer pass.
reinitializeAndReindexAllOntologies() - Method in interface ubic.gemma.core.ontology.OntologyService: Reinitialize (and reindex) all the ontologies "from scratch".
reinitializeAndReindexAllOntologies() - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
REJECT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.ScreeningResult: Do not admit / reject / this target needs no further action.
REJECTED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions.Disposition: The proposal had the key but the draft dropped it.
REJECTED - Enum constant in enum class ubic.gemma.model.common.description.PublicationAssociationStatus: This publication was considered for this experiment and ruled out.
relabelCellTypes(ExpressionExperiment, QuantitationType, SingleCellDimension, List, Protocol, String, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Relabel the cell types of an existing set of single-cell vectors.
relabelCellTypes(ExpressionExperiment, QuantitationType, SingleCellDimension, List, Protocol, String, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
RELATED - Enum constant in enum class ubic.gemma.core.ontology.model.OntologyXref.Strength: Associated, with no claim that either subsumes the other.
RELATED_PLATFORMS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
RELATED_SERIES - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
RELATED_SYNONYM - Enum constant in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia
RelationInferenceDirection - Enum Class in ubic.gemma.model.common.description: Which end of a relation implies the other.
RelationQuery() - Constructor for class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
RelationshipPersister - Class in ubic.gemma.persistence.persister: Persist objects like Gene2GOAssociation.
RelationshipPersister() - Constructor for class ubic.gemma.persistence.persister.RelationshipPersister
RelationSummary(String, String, String, String, String, String, String, String, String, String, Long, String, Integer, AnnotationRelationBasis, AnnotationRelationStatus, String, String, long, long, long, long, Long, long, long, long, String) - Constructor for class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary: 🛑 Build one with AnnotationRelationDao.RelationSummary.builder(), not with this. Twenty-six positional arguments, a dozen of them long and most of the rest String, is a constructor where a transposition compiles and passes — and adding a field to it broke a stale test class three times in one day, because Maven does not recompile a test whose source has not changed and the mismatch therefore arrives at runtime as NoSuchMethodError rather than at compile time.
RelationTopicality - Enum Class in ubic.gemma.model.common.description: Whether a relation says something about the TERM, or records a parameter of an EXPERIMENT.
release(Investigation, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService: Release the lock if heldBy holds it.
release(Investigation, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl
releaseCurationLock(DatasetArg, String) - Method in class ubic.gemma.rest.DatasetsWebService
releaseCurationLocks(String, DatasetsWebService.CurationLockBulkRequest) - Method in class ubic.gemma.rest.DatasetsWebService
releaseDate - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
ReleaseDetailsUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event triggered when the release details of a Versioned entity are updated.
ReleaseDetailsUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ReleaseDetailsUpdateEvent
ReleaseDetailsUpdatePayload - Record Class in ubic.gemma.core.security.audit.payload: Structured payload for ReleaseDetailsUpdateEvent writes against ExternalDatabase.
ReleaseDetailsUpdatePayload(String, String, Date, String) - Constructor for record class ubic.gemma.core.security.audit.payload.ReleaseDetailsUpdatePayload: Creates an instance of a ReleaseDetailsUpdatePayload record class.
releaseUrl() - Method in record class ubic.gemma.core.security.audit.payload.ReleaseDetailsUpdatePayload: Returns the value of the releaseUrl record component.
releaseVersion() - Method in record class ubic.gemma.core.security.audit.payload.ReleaseDetailsUpdatePayload: Returns the value of the releaseVersion record component.
reload(Collection) - Method in class ubic.gemma.persistence.service.AbstractDao
reload(Collection) - Method in interface ubic.gemma.persistence.service.BaseDao: Reload an entity from the persistent storage.
reload(T) - Method in class ubic.gemma.persistence.service.AbstractDao
reload(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Reload an entity from the persistent storage.
reload(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
reload(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl
reload(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
reload(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
reload(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
reload(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
reload(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
reload(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
reloadSingleCellDimension(ExpressionExperiment, SingleCellDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Reload a single-cell dimension.
reloadSingleCellDimension(ExpressionExperiment, SingleCellDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
remappedUriCount() - Static method in class ubic.gemma.model.common.description.CharacteristicUtils
remoteBaseDir - Variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
removals - Variable in class ubic.gemma.rest.AdminWebService.CacheStatRow
remove(int) - Method in class ubic.gemma.model.util.UninitializedList
remove(C) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService
remove(Object) - Method in class ubic.gemma.model.util.UninitializedCollection
remove(Object) - Method in class ubic.gemma.persistence.util.Slice: Deprecated.
remove(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService
remove(Collection) - Method in class ubic.gemma.persistence.service.AbstractService
remove(Collection) - Method in interface ubic.gemma.persistence.service.BaseImmutableService
remove(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseImmutableService
remove(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService
remove(Collection) - Method in class ubic.gemma.persistence.service.AbstractDao
remove(Collection) - Method in interface ubic.gemma.persistence.service.BaseDao: Remove all given persistent entities.
remove(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
remove(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
remove(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
remove(Collection) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
remove(Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
remove(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
remove(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl
remove(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
remove(Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService
remove(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl
remove(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
remove(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
remove(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
remove(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
remove(O) - Method in class ubic.gemma.persistence.service.AbstractService
remove(O) - Method in interface ubic.gemma.persistence.service.BaseImmutableService
remove(O) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseImmutableService
remove(O) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService
remove(T) - Method in class ubic.gemma.persistence.service.AbstractDao
remove(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Remove a persistent entity.
remove(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
remove(DifferentialExpressionAnalysisResult) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
remove(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
remove(PrincipalComponentAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImpl
remove(User) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
remove(UserGroup) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
remove(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
remove(Characteristic) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
remove(ExternalDatabase) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
remove(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
remove(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
remove(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
remove(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
remove(Compound) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.CompoundService
remove(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
remove(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl
remove(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService: Delete the factor, its associated factor values and all differential expression analyses in which it is used.
remove(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl
remove(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
remove(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Deletes an experiment and all of its associated objects, including coexpression links.
remove(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService: Deletes an experiment and all of its associated objects, including coexpression links.
remove(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl: Deletes an experiment and all of its associated objects, including coexpression links.
remove(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl
remove(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService: Deletes an experiment subset and all of its associated DifferentialExpressionAnalysis objects.
remove(ExpressionExperimentSubSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl: doesn't include removal of sample coexpression matrices, PCA, probe2probe coexpression links, or adjusting experiment set members
remove(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
remove(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
remove(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
remove(GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
remove(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
removeAggregatedVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateService: Remove aggregated vectors for the given quantitation type.
removeAggregatedVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl
removeAggregatedVectors(ExpressionExperiment, QuantitationType, boolean) - Method in interface ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateService: Remove aggregated vectors for the given quantitation type.
removeAggregatedVectors(ExpressionExperiment, QuantitationType, boolean) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl
removeAll() - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
removeAll() - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
removeAll() - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService: Remove all Gene2GO associations in batch.
removeAll() - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
removeAll() - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
removeAll() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
removeAll() - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService: Remove all blacklisted platforms and experiments.
removeAll() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
removeAll() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
removeAll() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
removeAll() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
removeAll() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
removeAll() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
removeAll() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
removeAll() - Method in interface ubic.gemma.persistence.service.genome.GeneDao
removeAll() - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
removeAll(Collection) - Method in class ubic.gemma.model.util.UninitializedCollection
removeAllByName(Collection, Collection) - Static method in class ubic.gemma.model.common.DescribableUtils: Remove all Describable objects from the collection that have the same name as any of those in the toRemove collection.
removeAllCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
removeAllCellLevelCharacteristics(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeAllCellTypeAssignments(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
removeAllCellTypeAssignments(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeAllRawDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Remove all raw data vectors.
removeAllRawDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
removeAllRawDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
removeAllRawDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
removeAllRawDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
removeAllRawDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
removeAllSingleCellDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Remove all single-cell data vectors and their quantitation types.
removeAllSingleCellDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
removeAnnotation(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Remove a single experiment-level tag from ee by characteristic id.
removeAnnotation(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Per-tag REST-write counterpart to ExpressionExperimentServiceImpl.removeCharacteristics(ExpressionExperiment, Collection).
removeAnnotation(ExpressionExperiment, Long, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: As ExpressionExperimentService.removeAnnotation(ExpressionExperiment, Long), with a caller-supplied reason appended to the audit note.
removeAnnotation(ExpressionExperiment, Long, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Reason-carrying overload; see ExpressionExperimentServiceImpl.addAnnotation(ExpressionExperiment, Characteristic, String).
removeAnnotation(ExpressionExperiment, BioMaterial, Long) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Per-tag remove of a characteristic from a biomaterial by id, the sample-level counterpart of ExpressionExperimentService.removeAnnotation(ExpressionExperiment, Long).
removeAnnotation(ExpressionExperiment, BioMaterial, Long) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
removeAnnotation(ExpressionExperiment, BioMaterial, Long, String) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: As BioMaterialService.removeAnnotation(ExpressionExperiment, BioMaterial, Long), with a caller-supplied reason appended to the audit note.
removeAnnotation(ExpressionExperiment, BioMaterial, Long, String) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl: Reason-carrying overload; see BioMaterialServiceImpl.addAnnotation(ExpressionExperiment, BioMaterial, Characteristic, String).
removeBiologicalCharacteristics(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
removeBiologicalCharacteristics(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
removeBiologicalCharacteristics(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Remove all associations that this array design has with BioSequences.
removeBiologicalCharacteristics(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
removeBioMaterialAssociation(BioAssay, BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService: Removes the association between a specific bioMaterial and a bioAssay.
removeBioMaterialAssociation(BioAssay, BioMaterial) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
removeByBasis(AnnotationRelationBasis, Long) - Method in interface ubic.gemma.persistence.service.common.description.AnnotationRelationDao: Remove every derived row for a basis, optionally for one experiment.
removeByBasis(AnnotationRelationBasis, Long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoImpl
removeByBasis(AnnotationRelationBasis, Long, String) - Method in interface ubic.gemma.persistence.service.common.description.AnnotationRelationDao: The same rebuild delete, narrowed to one source.
removeByBasis(AnnotationRelationBasis, Long, String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDaoImpl
removeByCompositeSequence(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDao: Remove all raw and processed vectors for a given probe.
removeByCompositeSequence(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
removeByCompositeSequence(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorService
removeByCompositeSequence(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl
removeByEE(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao: Remove every link row attached to the given EE.
removeByEE(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl
removeByEEAndQt(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao: Remove the link row for (ee, qt), if any.
removeByEEAndQt(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl
removeByIds(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDao: Remove the given audit trails by IDs.
removeByIds(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDaoImpl
removeByName(Collection, String) - Static method in class ubic.gemma.model.common.DescribableUtils: Remove one (or more if any duplicates) Describable from the collection by name.
removeByName(Collection, S) - Static method in class ubic.gemma.model.common.DescribableUtils: Remove one (or more if any duplicates) Describable from the collection by name.
removeBySingleCellDimension(SingleCellDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao: Remove every link row that references the given dimension.
removeBySingleCellDimension(SingleCellDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl
removeCellLevelCharacteristics(ExpressionExperiment, QuantitationType, CellLevelCharacteristics) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Remove existing cell-level characteristics by QT.
removeCellLevelCharacteristics(ExpressionExperiment, QuantitationType, CellLevelCharacteristics) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCellLevelCharacteristics(ExpressionExperiment, SingleCellDimension, CellLevelCharacteristics) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Remove existing cell-level characteristics.
removeCellLevelCharacteristics(ExpressionExperiment, SingleCellDimension, CellLevelCharacteristics) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCellLevelCharacteristicsById(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
removeCellLevelCharacteristicsById(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCellLevelCharacteristicsById(ExpressionExperiment, SingleCellDimension, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
removeCellLevelCharacteristicsById(ExpressionExperiment, SingleCellDimension, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCellLevelCharacteristicsByName(ExpressionExperiment, SingleCellDimension, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
removeCellLevelCharacteristicsByName(ExpressionExperiment, SingleCellDimension, String) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCellTypeAssignment(ExpressionExperiment, QuantitationType, CellTypeAssignment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Remove the given cell type assignment by QT.
removeCellTypeAssignment(ExpressionExperiment, QuantitationType, CellTypeAssignment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCellTypeAssignment(ExpressionExperiment, SingleCellDimension, CellTypeAssignment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Remove the given cell type assignment.
removeCellTypeAssignment(ExpressionExperiment, SingleCellDimension, CellTypeAssignment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCellTypeAssignmentById(ExpressionExperiment, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
removeCellTypeAssignmentById(ExpressionExperiment, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCellTypeAssignmentById(ExpressionExperiment, SingleCellDimension, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
removeCellTypeAssignmentById(ExpressionExperiment, SingleCellDimension, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCellTypeAssignmentByName(ExpressionExperiment, SingleCellDimension, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
removeCellTypeAssignmentByName(ExpressionExperiment, SingleCellDimension, String) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeCharacteristics(BioMaterial, Collection) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Remove the given characteristic from the given biomaterial
removeCharacteristics(BioMaterial, Collection) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
removeCharacteristics(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
removeCharacteristics(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
removeCharacteristics(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService
removeCharacteristics(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl
removeDatasetAnnotation(DatasetArg, Long) - Method in class ubic.gemma.rest.AnnotationsWebService
removeDatasetAnnotationTag(DatasetArg, Long) - Method in class ubic.gemma.rest.DatasetsWebService
removeDatasetDifferentialAnalysis(DatasetArg, Long) - Method in class ubic.gemma.rest.DatasetsWebService
removeDatasetDifferentialAnalysisAlias(DatasetArg, Long) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI compatibility alias for DatasetsWebService.removeDatasetDifferentialAnalysis(DatasetArg, Long): UI calls DELETE /datasets/{id}/analyses/differential/{aid}.
RemovedTargetResult(TicketTargetType, Long, TicketTargetStatus, TicketValueObject) - Constructor for class ubic.gemma.rest.TicketsWebService.RemovedTargetResult
removeDuplicates(Collection) - Static method in class ubic.gemma.core.analysis.sequence.ProbeMapUtils: Prune a set of results that have the same coordinates and query.
removeForExperiment(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
removeForExperiment(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
removeForExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDao
removeForExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImpl
removeForExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
removeForExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl
removeForExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService: Removes all coexpression matrices for the given experiment.
removeForExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
removeForExperiment(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService: Removes all analyses for the given experiment
removeForExperiment(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
removeForExperimentalFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService: Remove analyses using the given factor.
removeForExperimentalFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
removeForExperimentalFactors(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
removeForExperimentalFactors(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
removeForExperimentAnalyzed(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService: Remove all analysis for the given experiment or subset.
removeForExperimentAnalyzed(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
removeFromSets(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: Remove an experiment from all sets it is in.
removeFromSets(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
removeGeneProducts(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneWriteService: Remove gene products and their associated BLAT + AnnotationAssociation rows.
removeGeneProducts(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl
removeGroupAuthority(String, GrantedAuthority) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
removeGroupAuthority(UserGroup, String) - Method in interface ubic.gemma.core.security.authentication.BaseUserService: Remove an authority from a group.
removeGroupAuthority(UserGroup, String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
removeHighestComponents(int) - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD: Provide a reconstructed matrix removing the first N components (the most significant ones).
removeMember(Long, Long) - Method in class ubic.gemma.rest.GroupsWebService: Remove a member from a group.
removeMissing(DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
removeMissingOrInfinite(DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
removeMissingOrInfinite(DoubleMatrix1D, DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil: Remove values from data corresponding to missing values in reference.
removeOrphanQuantitationTypes(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Remove quantitation types attached to ee that are not referenced by any data vector.
removeOrphanQuantitationTypes(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
removeProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Remove the processed vectors of an EE.
removeProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
removeProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Remove processed data vectors.
removeProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
removeProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
removeProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
removeProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Remove the processed data vectors for the given experiment.
removeProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
removeRawDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService: Equivalent to removeRawDataVectors(ee, qt, false).
removeRawDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
removeRawDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
removeRawDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Remove raw data vectors for a given quantitation type.
removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
removeRootTerms(Collection) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
removeRootTerms(Collection) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationServiceImpl: Remove root terms, like "molecular_function", "biological_process" and "cellular_component" Also removes any null objects.
removeSample(String) - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence: Remove a sample from the maps
removeSampleCharacteristic(DatasetArg, Long, Long) - Method in class ubic.gemma.rest.DatasetsWebService
removeSamples(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries: Clean up samples we have decided are ineligible (i.e., non transcriptomic)
removeSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Remove single-cell data vectors for the given quantitation type.
removeSingleCellDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
removeSingleCellDataVectors(ExpressionExperiment, QuantitationType, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Remove the given single-cell data vectors.
removeSingleCellDataVectors(ExpressionExperiment, QuantitationType, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
removeStatement(FactorValue, Statement) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Remove a statement from a factor value.
removeStatement(FactorValue, Statement) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
removeTarget(Ticket, TicketTargetType, Long, Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Remove a target from a ticket.
removeTarget(Ticket, TicketTargetType, Long, Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
removeTicketTarget(Long, TicketTargetType, Long) - Method in class ubic.gemma.rest.TicketsWebService: Remove a target from a ticket.
removeUserFromGroup(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
removeUserFromGroup(String, String) - Method in interface ubic.gemma.core.security.SecurityService: Remove a user from a group.
removeUserFromGroup(String, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
removeUserFromGroup(User, UserGroup) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
removeUserFromGroup(User, UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
RenameDatasetRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.RenameDatasetRequest
RenameDatasetResponse(Long, String) - Constructor for class ubic.gemma.rest.DatasetsWebService.RenameDatasetResponse
renameDatasetShortName(DatasetArg, DatasetsWebService.RenameDatasetRequest) - Method in class ubic.gemma.rest.DatasetsWebService
renameGroup(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
RenamingBioAssayMapper - Class in ubic.gemma.core.loader.util.mapper: A BioAssay-to-sample-name matcher that renames samples before matching them.
RenamingBioAssayMapper(BioAssayMapper, String[], String[]) - Constructor for class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper
RenamingBioAssayMapperParser - Class in ubic.gemma.core.loader.util.mapper: Parses a file that contains a mapping between old and new bioassay names.
RenamingBioAssayMapperParser(BioAssayMapper) - Constructor for class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapperParser
renamingFile(Path) - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder: A file containing a mapping of sample names to bioassay names.
reopenAnnotationSet(Long) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Clear finalized status on an annotation set.
REOPENED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType
reopenSet(Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: Clear finalizedAt + finalizedBy + finalizedNotes on the row, reopening a finalized DRAFT or unblessing a polished SNAPSHOT.
reopenSet(Long) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
reorder(List) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
reorderByDesign(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.
reorderByDesign(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
repair(String) - Static method in class ubic.gemma.core.util.SymbolFontPua: Replace every mapped Symbol-font PUA codepoint with the character it was meant to be.
REPEAT_FRACTION_MAXIMUM - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig: Sequences which have more than this fraction accounted for by repeats (via repeatmasker) will not be examined if they produce multiple alignments to the genome, regardless of the alignment quality.
repeatScan(Collection) - Method in class ubic.gemma.core.analysis.sequence.RepeatScan: Run RepeatMasker on the sequences.
RepeatScan - Class in ubic.gemma.core.analysis.sequence: Scan sequences for repeats using RepeatMasker.
RepeatScan(String) - Constructor for class ubic.gemma.core.analysis.sequence.RepeatScan
RepetitiveValuesFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Filter design elements with repetitive values across samples.
RepetitiveValuesFilter() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter
RepetitiveValuesFilter.Mode - Enum Class in ubic.gemma.core.analysis.preprocess.filter
replace(Object, Object, Object) - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
replace(List, List, Object) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
replaceAllRawDataVectors(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService: Replace all raw vectors on an experiment, grouping the input by QT and routing each group to either ExpressionExperimentDataVectorService.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) or ExpressionExperimentDataVectorService.addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) depending on whether the QT already exists; any QT in the experiment that is no longer represented in the input is removed.
replaceAllRawDataVectors(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
replaceAllRawDataVectors(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Used when we are replacing data, such as when converting an experiment from one platform to another.
replaceAllRawDataVectors(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
replaceData(ExpressionExperiment, ArrayDesign, ExpressionDataDoubleMatrix) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
replaceData(ExpressionExperiment, ArrayDesign, ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.loader.expression.DataUpdaterImpl: Replace the data associated with the experiment (or add it if there is none).
replaceData(ExpressionExperiment, ArrayDesign, QuantitationType, DoubleMatrix) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
replaceData(ExpressionExperiment, ArrayDesign, QuantitationType, DoubleMatrix) - Method in class ubic.gemma.core.loader.expression.DataUpdaterImpl: Replace the data associated with the experiment (or add it if there is none).
ReplaceDataCli - Class in ubic.gemma.apps: Replace data in an existing data set.
ReplaceDataCli() - Constructor for class ubic.gemma.apps.ReplaceDataCli
replaceDatasetAnnotations(DatasetArg, AnnotationsWebService.AnnotationsReplaceRequest) - Method in class ubic.gemma.rest.AnnotationsWebService
replaceDatasetDesign(DatasetArg, Boolean, Long, ExperimentalDesignValueObject) - Method in class ubic.gemma.rest.DatasetsWebService: Apply a proposed ExperimentalDesignValueObject as the experiment's new design.
replaceExistingCellTypeAssignment(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: If there is already a cell type assignment with the same name, replace it with the new one.
replaceExistingOtherCellLevelCharacteristics(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: If there are already other CLCs with the same names, replace them with the new ones.
replaceExistingQuantitationType(boolean) - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder: Replace the vectors of an existing QT.
replaceProcessedDataVectors(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Replace processed data vectors.
replaceProcessedDataVectors(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
replaceProcessedDataVectors(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
replaceProcessedDataVectors(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
replaceProcessedDataVectors(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Replace the processed data vectors for the given experiment.
replaceProcessedDataVectors(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
replaceProcessedDataVectors(ExpressionExperiment, Collection, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Replace the processed vectors of a EE with the given vectors.
replaceProcessedDataVectors(ExpressionExperiment, Collection, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Replace raw data vectors for a given quantitation type.
replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl
replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
replaceSingleCellDataVectors(ExpressionExperiment, QuantitationType, Collection, String, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Replace existing single-cell data vectors for the given quantitation type.
replaceSingleCellDataVectors(ExpressionExperiment, QuantitationType, Collection, String, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
replaceValues(DoubleMatrix1D, BooleanArrayList, DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil: Perform the awkward operation of substituting certain values in a vector from values in another vector.
REPORT_BATCH_SIZE - Static variable in class ubic.gemma.persistence.persister.CommonPersister: Size if batch to report when persisting multiple entities with CommonPersister.doPersist(Collection, Map).
REPORT_BATCH_SIZE - Static variable in class ubic.gemma.persistence.persister.GenomePersister: Mirror of CommonPersister.REPORT_BATCH_SIZE; kept here so the still-extant ArrayDesignPersister subclass keeps inheriting the constant during S2b/c.
REPORT_SLOW_QUERY_AFTER_MS - Static variable in class ubic.gemma.persistence.service.AbstractVoEnabledDao: Amount of time in milliseconds after which a query (including post-processing) should be reported.
Reporter - Class in ubic.gemma.core.loader.expression.arrayDesign: A "probe" (Affymetrix); for other types of arrays, there is no practical distinction between compositesequences and reporters, and all analysis would take place at the level of CompositeSequences.
Reporter() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.Reporter: No-arg constructor added to satisfy javabean contract
REPORTER_IDENTIFIER - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
Reporter.Factory - Class in ubic.gemma.core.loader.expression.arrayDesign
reportInitializationTime(BeanInitializationTimeMonitor) - Method in class ubic.gemma.core.profiling.ProfilingConfig
reportProgress() - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter
reportProgress(long, long) - Method in class ubic.gemma.core.util.AbstractProgressReporter
reportProgress(long, long) - Method in interface ubic.gemma.core.util.ProgressReporter: Report progress.
reportProgress(long, long, boolean) - Method in class ubic.gemma.core.util.AbstractProgressReporter
reportProgress(long, long, boolean) - Method in interface ubic.gemma.core.util.ProgressReporter: Report progress.
reportProgressUpdate(String) - Method in interface ubic.gemma.core.job.progress.ProgressUpdateContext
reportProgressUpdate(String) - Method in class ubic.gemma.core.logging.log4j.ProgressUpdateAppender.ProgressUpdateContextImpl: Report a progress update.
RepresentationConversionUtils - Class in ubic.gemma.core.analysis.preprocess.convert: Convert DataVector to different PrimitiveType.
RepresentationConversionUtils() - Constructor for class ubic.gemma.core.analysis.preprocess.convert.RepresentationConversionUtils
reprocessAffyDataFromCel(ExpressionExperiment) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
reprocessAffyDataFromCel(ExpressionExperiment) - Method in class ubic.gemma.core.loader.expression.DataUpdaterImpl: Affymetrix only: Provide or replace data for an Affymetrix-based experiment, using CEL files.
reps - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode
REQUEST_ID_HEADER - Static variable in class ubic.gemma.rest.servlet.RequestIdMdcFilter
REQUEST_ID_MDC_KEY - Static variable in class ubic.gemma.rest.servlet.RequestIdMdcFilter
RequestAttributesBasedClientIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Strategy that retrieves and store client IDs in the RequestAttributes.
RequestAttributesBasedClientIdRetrievalStrategy() - Constructor for class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy
requestCancellation() - Method in interface ubic.gemma.core.job.SubmittedTask: Send cancellation request.
requestedCount - Variable in class ubic.gemma.rest.AdminWebService.GeoGrabResponse: Number of accessions in the request after trimming blanks.
RequestExceptionLogger - Class in ubic.gemma.rest.providers
RequestExceptionLogger() - Constructor for class ubic.gemma.rest.providers.RequestExceptionLogger
RequestHeaderBasedClientIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Strategy that retrieves the client ID in a request header.
RequestHeaderBasedClientIdRetrievalStrategy() - Constructor for class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy
RequestIdMdcFilter - Class in ubic.gemma.rest.servlet: Per-request filter that populates two MDC keys for the duration of a REST request: requestId — the inbound X-Request-Id header if present, otherwise a freshly generated UUID.
RequestIdMdcFilter() - Constructor for class ubic.gemma.rest.servlet.RequestIdMdcFilter
REQUIREMENTS_FILE - Static variable in interface ubic.gemma.core.loader.expression.singleCell.transform.PythonBasedSingleCellDataTransformation
requires(Predicate) - Static method in class ubic.gemma.cli.util.OptionsUtils: Make sure that the given predicate is satisfied.
REQUIRES_FORCE - Enum constant in enum class ubic.gemma.rest.util.CurationCommitConflictException.Reason: The change would delete differential-expression analyses or strand a subset.
requireSequences() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns the value of the requireSequences record component.
requiresForce() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport: Whether applying this change needs explicit consent (?force=true, admin) rather than proceeding silently.
requiresPostCommitHandling(EntityPersister) - Method in class ubic.gemma.core.security.acl.AclEventListener
requiresPostCommitHandling(EntityPersister) - Method in class ubic.gemma.persistence.audit.AuditTrailEventListener: Run inside the flushing transaction, not deferred to post-commit.
requiresStringPrior() - Method in interface ubic.gemma.rest.ranking.AnnotationSearchRankingStrategy: Whether this strategy reads the stringPriorByUri map during AnnotationSearchRankingStrategy.rank(String, List, Map).
requiresStringPrior() - Method in class ubic.gemma.rest.ranking.CommonalityRankingStrategy
requiresUsageCounts() - Method in interface ubic.gemma.rest.ranking.AnnotationSearchRankingStrategy: Whether this strategy reads the usageCountsByUri map during AnnotationSearchRankingStrategy.rank(String, List, Map).
requiresUsageCounts() - Method in class ubic.gemma.rest.ranking.CompositeRankingStrategy
requiresUsageCounts() - Method in class ubic.gemma.rest.ranking.UsageWeightedRankingStrategy
reset() - Static method in class ubic.gemma.core.config.Configuration: Reset all configurations set at runtime.
reset() - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor: Reset recorded times.
reset(String) - Static method in class ubic.gemma.core.config.Configuration: Reset a specific configuration by key.
resetForTesting() - Static method in class ubic.gemma.persistence.initialization.TestBootstrapState: Reset all flags.
resetHibernateStats() - Method in class ubic.gemma.rest.AdminWebService: Resets the Hibernate statistics counters to zero.
resetMexFileSuffixes() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
ResetPasswordResponse() - Constructor for class ubic.gemma.rest.AdminWebService.ResetPasswordResponse
resetRowKeys() - Method in class ubic.gemma.core.util.graphics.ColorMatrix
resetRowKeys() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
ResetSuitabilityForDifferentialExpressionAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Used to indicate that the suitability status of an experiment is the default.
ResetSuitabilityForDifferentialExpressionAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ResetSuitabilityForDifferentialExpressionAnalysisEvent
resetUserPassword(String) - Method in class ubic.gemma.rest.AdminWebService: Administrative password reset — set a user's password to a fresh server-generated one-time temporary password.
resnik - Enum constant in enum class ubic.gemma.core.ontology.GoMetric.Metric
resolve(AnnotatedType, ModelConverterContext, Iterator) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver
resolve(String) - Method in interface ubic.gemma.core.ontology.ols.OlsTermResolver: Resolve a term IRI against OLS.
resolve(String) - Method in class ubic.gemma.core.ontology.ols.OlsTermResolverImpl
resolve(String) - Method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex: The terms that may stand in for a foreign identifier.
resolve(String, boolean) - Method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex
resolve(Collection, String) - Static method in class ubic.gemma.core.ontology.providers.OntologyServiceResolver: Resolve a user-supplied token to one of the given ontologies.
resolveActingIdentity(String) - Static method in class ubic.gemma.core.security.util.SecurityUtil: Resolve the identity an action should be recorded against, given an optional onBehalfOf claim from the caller.
resolveAllowableValues(Annotated, Annotation[], Schema) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver: Resolves allowed values for the SearchWebService.search(QueryArg, DatasetArg, TaxonArg, PlatformArg, List, LimitArg, ExcludeArg, boolean, boolean) resultTypes argument.
resolveCorpusSeeds() - Method in class ubic.gemma.core.ontology.providers.chebi.ChebiSeedResolver: Read the set of distinct CHEBI URIs the corpus uses, across every slot a term can occupy.
resolveCorpusSeeds() - Method in class ubic.gemma.core.ontology.providers.mondo.MondoSeedResolver: Read the set of distinct MONDO URIs the corpus uses, across every slot a term can occupy.
RESOLVED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType
RESOLVED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketState
resolveDescription(Annotated, Annotation[], Schema) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver
resolvedWithinDays - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueResponse
resolveEntity(String, String) - Method in class ubic.gemma.persistence.hibernate.XSDEntityResolver
resolveEnvVar(String) - Static method in class ubic.gemma.core.config.ConfigUtils: Resolve an environment variable, honouring the *_FILE indirection pattern.
resolveEnvVar(String, Function) - Static method in class ubic.gemma.core.config.ConfigUtils: Test-friendly form: resolve against an arbitrary env source instead of System.getenv().
resolveExtensions(Annotated, Annotation[], Schema) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver
resolveFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao: Obtain various meta-information used to infer what to use in a Filter or Sort.
resolveFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: Obtain various meta-information used to infer what to use in a Filter or Sort.
resolveFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
resolveFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl: Checks for special properties that are allowed to be referenced on certain objects.
resolveFilterablePropertyMeta(String, Class, String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
resolvePath(Root, String) - Static method in class ubic.gemma.persistence.util.FilterJpaUtils: Walk a dot-separated property path from the root (e.g.
resolvePathWithAlias(Root, String, String, Map) - Static method in class ubic.gemma.persistence.util.FilterJpaUtils: Walk a dot-separated property path from the root, prepending the dotted prefix that the given objectAlias was registered with (if any).
resolveScopeMetadata(BeanDefinition) - Method in class ubic.gemma.cli.util.PrototypeScopeResolver
resourceToPath(String) - Static method in class ubic.gemma.core.util.FileTools: Resolve a classpath resource to an absolute filesystem path.
ResourceUtils - Class in ubic.gemma.core.util
ResourceUtils() - Constructor for class ubic.gemma.core.util.ResourceUtils
respond(T) - Static method in class ubic.gemma.rest.util.Responders: Produce a ResponseDataObject that wraps the given argument.
Responders - Class in ubic.gemma.rest.util: Handles setting of the response status code and composing a proper payload structure.
Responders() - Constructor for class ubic.gemma.rest.util.Responders
Responders.FilterMethod<T> - Interface in ubic.gemma.rest.util: A functional interface matching the signature of a paginating service method.
ResponseDataObject<T> - Class in ubic.gemma.rest.util: Wrapper for a non-error response payload compliant with the Google JSON style-guide
ResponseDataObject(T) - Constructor for class ubic.gemma.rest.util.ResponseDataObject
ResponseDataObjectBlacklistedValueObject(BlacklistedValueObject) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectBlacklistedValueObject
ResponseDataObjectCellTypeAssignmentValueObject(CellTypeAssignmentValueObject) - Constructor for class ubic.gemma.rest.DatasetsWebService.ResponseDataObjectCellTypeAssignmentValueObject
ResponseDataObjectCreateUserResponse(AdminWebService.CreateUserResponse) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectCreateUserResponse
ResponseDataObjectDbPoolResponse(AdminWebService.DbPoolResponse) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectDbPoolResponse
ResponseDataObjectExpressionExperimentValueObject(ExpressionExperimentValueObject) - Constructor for class ubic.gemma.rest.DatasetsWebService.ResponseDataObjectExpressionExperimentValueObject
ResponseDataObjectGeoScrapeSubmitResponse(AdminWebService.GeoScrapeSubmitResponse) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectGeoScrapeSubmitResponse
ResponseDataObjectImportGeoBatchResponse(AdminWebService.ImportGeoBatchResponse) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectImportGeoBatchResponse
ResponseDataObjectListAuditEventValueObject(List) - Constructor for class ubic.gemma.rest.DatasetsWebService.ResponseDataObjectListAuditEventValueObject
ResponseDataObjectListBioAssayValueObject(List) - Constructor for class ubic.gemma.rest.DatasetsWebService.ResponseDataObjectListBioAssayValueObject
ResponseDataObjectListCellLevelCharacteristicsValueObject(List) - Constructor for class ubic.gemma.rest.DatasetsWebService.ResponseDataObjectListCellLevelCharacteristicsValueObject
ResponseDataObjectListCompactAuditEventValueObject(List) - Constructor for class ubic.gemma.rest.DatasetsWebService.ResponseDataObjectListCompactAuditEventValueObject
ResponseDataObjectListTicketValueObject(List) - Constructor for class ubic.gemma.rest.DatasetsWebService.ResponseDataObjectListTicketValueObject
ResponseDataObjectMultifunctionalityRecomputeResponse(AdminWebService.MultifunctionalityRecomputeResponse) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectMultifunctionalityRecomputeResponse
ResponseDataObjectObsoleteTermCorrectionSubmission(AdminWebService.ObsoleteTermCorrectionSubmission) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectObsoleteTermCorrectionSubmission
ResponseDataObjectOntologyRefreshResponse(AdminWebService.OntologyRefreshResponse) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectOntologyRefreshResponse
ResponseDataObjectReindexAcceptedResponse(AdminWebService.ReindexAcceptedResponse) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectReindexAcceptedResponse
ResponseDataObjectSingleCellDimensionValueObject(SingleCellDimensionValueObject) - Constructor for class ubic.gemma.rest.DatasetsWebService.ResponseDataObjectSingleCellDimensionValueObject
ResponseDataObjectSubmittedJobResponse(AdminWebService.SubmittedJobResponse) - Constructor for class ubic.gemma.rest.AdminWebService.ResponseDataObjectSubmittedJobResponse
ResponseDataObjectTicketValueObject(TicketValueObject) - Constructor for class ubic.gemma.rest.TicketsWebService.ResponseDataObjectTicketValueObject
ResponseErrorObject - Class in ubic.gemma.rest.util: Wrapper for an error response payload compliant with the Google JSON style-guide.
ResponseErrorObject.ResponseErrorObjectBuilder - Class in ubic.gemma.rest.util
rest() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.AllEntitiesUrl
rest() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl: Generate a URL for the REST API.
rest() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.SomeEntitiesUrl
RestapidocsIndexRewriteFilter - Class in ubic.gemma.rest.servlet: Rewrites the path to the index file.
RestapidocsIndexRewriteFilter() - Constructor for class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilter
RestAuthEntryPoint - Class in ubic.gemma.rest.security: Implementation of AuthenticationEntryPoint for the RESTful API to handle authentication.
RestAuthEntryPoint(ObjectMapper, Future, BuildInfo) - Constructor for class ubic.gemma.rest.security.RestAuthEntryPoint
RestCacheEviction - Class in ubic.gemma.cli.util: Tells the running gemma-rest to drop what a CLI rebuild has just made stale.
RestComponentScanConfig - Class in ubic.gemma.rest.util: Component-scan configuration for the gemma-rest module, replacing the XML <context:component-scan> block previously declared in applicationContext-component-scan.xml.
RestComponentScanConfig() - Constructor for class ubic.gemma.rest.util.RestComponentScanConfig
RestInitializeContext - Class in ubic.gemma.rest.context: Standalone gemma-rest counterpart to ubic.gemma.web.context.InitializeContext (which lives in gemma-web and pulls in JSP / theme / servlet-context configuration that the REST WAR has no use for).
RestInitializeContext() - Constructor for class ubic.gemma.rest.context.RestInitializeContext
restoreDatasetCurationFromSnapshot(DatasetArg, Long, Boolean, Boolean, String) - Method in class ubic.gemma.rest.DatasetsWebService
RestSecurityConfig - Class in ubic.gemma.rest.security: Spring Security 6 configuration for the Gemma RESTful API (/rest/v2/**).
RestSecurityConfig() - Constructor for class ubic.gemma.rest.security.RestSecurityConfig
restSecurityFilterChain(HttpSecurity, AuthenticationEntryPoint, AuthenticationManager, TokenStore) - Method in class ubic.gemma.rest.security.RestSecurityConfig: Registered with @Order(1) so this chain is consulted BEFORE the gemma-web XML <s:http pattern="/**"> chain.
Result(Resource, String, double) - Constructor for class ubic.gemma.core.ontology.search.OntologySearchService.Result
RESULT_TYPES_SCHEMA_NAME - Static variable in class ubic.gemma.rest.SearchWebService: Name used in the OpenAPI schema to identify result types as per SearchWebService.search(QueryArg, DatasetArg, TaxonArg, PlatformArg, List, LimitArg, ExcludeArg, boolean, boolean)'s fourth argument.
ResultSetCountsValueObject - Class in ubic.gemma.model.analysis.expression.diff: Cacheable, immutable snapshot of the per-result-set hit-list counts displayed by DiffExResultSetSummaryValueObject.
ResultSetCountsValueObject(Integer, Integer, Double, Integer, Integer, Integer) - Constructor for class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
resultType(Class) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder
resultTypes(Collection) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder
Resync() - Constructor for class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync
retainAll(Collection) - Method in class ubic.gemma.model.util.UninitializedCollection
RETAINED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions.Disposition: Draft still carries the proposal's element verbatim.
retainHavingEvent(Collection, Class) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
retainHavingEvent(Collection, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
retainLackingEvent(Collection, Class) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
retainLackingEvent(Collection, Class) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
retrieve(String) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch: Retrieve a single PubMed record by ID.
retrieve(Collection) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch: Retrieve multiple PubMed records by ID.
retrieveAllGeoRecords(GeoQuery, GeoRetrieveConfig) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser
retrieveAllGeoRecords(GeoQuery, GeoRetrieveConfig) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl
retrieveByDoi(String) - Method in class ubic.gemma.core.loader.crossref.CrossRefFetcher: Retrieve a BibliographicReference for the given DOI from CrossRef.
retrieveExisting(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService
retrieveExisting(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
retrieveGeoRecords(GeoQuery, int, int) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser
retrieveGeoRecords(GeoQuery, int, int, GeoRetrieveConfig) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Retrieve records from a GEO query.
retrieveGeoRecords(GeoQuery, int, int, GeoRetrieveConfig) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl
retrieveSummaryObjects(Collection) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: retrieves a collection of cached value objects containing summary information
retrieveSummaryObjects(Collection) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
retry(SimpleRetryCallable, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector: Retry the given callable a certain number of times before giving up.
Retryable - Annotation Interface in ubic.gemma.persistence.retry: Indicate that the method should be retried on failure.
retryableMethod() - Method in class ubic.gemma.persistence.util.Pointcuts: A method that can be retried, public and annotated with Retryable.
retryableOrTransactionalServiceMethod() - Method in class ubic.gemma.persistence.util.Pointcuts: A retryable or transactional service method.
retryAdvice(SimpleRetryPolicy, RetryLogger) - Method in class ubic.gemma.persistence.hibernate.HibernateConfig: Retry advice that wraps service methods matching the Pointcuts.retryableOrTransactionalServiceMethod() pointcut.
retryAdvisor(RetryOperationsInterceptor) - Method in class ubic.gemma.persistence.hibernate.HibernateConfig: Bind the retry advice to the pointcut ubic.gemma.persistence.util.Pointcuts.retryableOrTransactionalServiceMethod() with order=2 — outside the @EnableTransactionManagement advisor (order=3) — so a stale-state failure rolls back the inner transaction before the retry advisor restarts the call in a fresh tx.
RetryLogger - Class in ubic.gemma.persistence.retry: Provide logging when an operation has failed and is being retried.
RetryLogger() - Constructor for class ubic.gemma.persistence.retry.RetryLogger
retryNicely(SimpleRetryCallable, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Wrap a SimpleRetryCallable such that it will respect the recommended usage of the Entrez API.
retryPolicy() - Method in class ubic.gemma.persistence.hibernate.HibernateConfig: Retry policy: max-attempts + a fixed map of retryable Hibernate exceptions (stale state).
returnedClass() - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
returnedClass() - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
returnedCount - Variable in class ubic.gemma.rest.AdminWebService.GeoGrabResponse: Number of GEO records actually returned by NCBI (may be less than requestedCount).
reverseComplement(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
reviewedByHuman(Collection) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
reviewedByHuman(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService: Whether a person — not only a machine — has ruled on this set.
reviewedByHuman(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
revoke(String) - Method in class ubic.gemma.rest.security.TokenStore: Revoke a token.
RIBO_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
RIGHT - Enum constant in enum class ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod: Signifies that the distance to the 3' end was measured from the right edge of the query.
rightHandOverlap(BioSequence, BioSequence) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Compute just any overlap the compare sequence has with the target on the right side.
RIP_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
RNA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType
RNA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
RNA - Enum constant in enum class ubic.gemma.model.genome.biosequence.PolymerType
RNA_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
RNASEQ_OF_CODING_RNA_FROM_SINGLE_CELLS - Static variable in class ubic.gemma.model.common.description.Values: TODO: find a replacement for this from OBI
RNASEQ_PIPELINE_REPORT - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
RNASEQ_PIPELINE_REPORT_DATA - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
RNASEQ_PIPELINE_REPORT_LOG - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
RNASeqDataAddCli - Class in ubic.gemma.apps: Designed to add count and/or RPKM data to a data set that has only meta-data.
RNASeqDataAddCli() - Constructor for class ubic.gemma.apps.RNASeqDataAddCli
RO - Class in ubic.gemma.core.ontology.jena
RO() - Constructor for class ubic.gemma.core.ontology.jena.RO
role - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
role - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
role - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
role - Variable in class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
role - Variable in class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest: Annotation set role; default "proposal" matches the original /proposals endpoint semantics.
ROLE_PREFIX - Static variable in class ubic.gemma.core.security.AuthorityConstants: Prefix used for roles.
roleHierarchy() - Method in class ubic.gemma.core.security.acl.GemmaAclConfiguration: Role hierarchy used by ACL authorization (and any other consumer that injects RoleHierarchy).
root - Variable in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao.CriteriaContext
RootWebService - Class in ubic.gemma.rest: Handles calls to the root API url and user info api
RootWebService() - Constructor for class ubic.gemma.rest.RootWebService
RootWebService.ApiInfoValueObject - Class in ubic.gemma.rest
RootWebService.ChangePasswordRequest - Class in ubic.gemma.rest: Request body for RootWebService.changeMyPassword(RootWebService.ChangePasswordRequest).
RootWebService.UserValueObject - Class in ubic.gemma.rest
round(double) - Static method in class ubic.gemma.core.util.RoundingUtils: Round to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits.
round(Double) - Static method in class ubic.gemma.core.util.RoundingUtils: Null-tolerant RoundingUtils.round(double), for boxed value-object fields.
roundedCopy(double[]) - Static method in class ubic.gemma.core.util.RoundingUtils: Round every element into a new array.
roundedCopy(double[][]) - Static method in class ubic.gemma.core.util.RoundingUtils: Row-by-row RoundingUtils.roundedCopy(double[]); see it for why this copies.
RoundingUtils - Class in ubic.gemma.core.util: Rounding of floating-point payloads on their way into JSON.
RoundingUtils.SignificantDigitsSerializer - Class in ubic.gemma.core.util: Applies RoundingUtils.round(double) at serialization time, leaving the in-memory value exact.
roundValuesForJson() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject: Round every expression value and per-gene statistic in this response to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits.
Row(Long, String, List, double) - Constructor for class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject.Row: Creates a new Row instance.
rowMeans(DoubleMatrix) - Static method in class ubic.gemma.core.util.MatrixStats: Return the mean of each row in the matrix.
RowMeta() - Constructor for class ubic.gemma.rest.HeatmapDataValueObject.RowMeta
RowMissingFilter<M,R,C,V> - Class in ubic.gemma.core.util.matrix.datafilter: Remove rows from a matrix that are missing too many points.
RowMissingFilter() - Constructor for class ubic.gemma.core.util.matrix.datafilter.RowMissingFilter
RowMissingValueFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Filter out rows that have "too many" missing values.
RowMissingValueFilter() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter
rowNameMap - Variable in class ubic.gemma.core.util.matrix.MatrixWriter
rows() - Method in class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
rows() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
rows() - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
rows() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
rows() - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
rows() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
rows() - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
rows() - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
rows() - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
rows() - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
rows() - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
rows() - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Get the number of rows the matrix has
rows() - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
rows() - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
rows() - Method in class ubic.gemma.core.util.matrix.StringMatrix
rowsAfter() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage: Returns the value of the rowsAfter record component.
RowsWithSequencesFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Only retain design elements that have a BioSequence associated.
RowsWithSequencesFilter() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.RowsWithSequencesFilter
RRNA - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
RTPCR - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
rule(AnnotationSet, String, String, FindingDisposition, String, TriageJudgeKind, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionService: Record a ruling on one finding.
rule(AnnotationSet, String, String, FindingDisposition, String, TriageJudgeKind, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionServiceImpl
RULE_clause - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_collection - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_collectionOperator - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_disjunction - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_filter - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_operator - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_predicate - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_quantifier - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_scalar - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_subClause - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RuledOutTermValueObject(String, String, String, String) - Constructor for class ubic.gemma.rest.AnnotationsWebService.RuledOutTermValueObject
ruleNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
ruleNames - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
ruleOnFinding(Long, String, AnnotationSetsWebService.DispositionRequest) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Record a curator's ruling on ONE finding inside an audit set.
run() - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextRunnable
run(DoubleArrayList, DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis: Following CH section 2.2.
run(DoubleArrayList, DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
run(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
run(ExpressionExperiment, Map, ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer: Analyze a dataset with a pre-existing subset structure.
run(ExpressionExperiment, Map, ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
run(ExpressionExperiment, ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer: Analyze a dataset.
run(ExpressionExperiment, ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer: I apologize for this being so complicated.
run(ExpressionExperimentSubSet, ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer: Analyze a subset.
run(ExpressionExperimentSubSet, ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer: Check if a factor value should be excluded from the analysis.
RUN_AS_ADMIN_AUTHORITY - Static variable in class ubic.gemma.core.security.AuthorityConstants: Used when we are running at elevated permissions.
RUN_AS_USER_AUTHORITY - Static variable in class ubic.gemma.core.security.AuthorityConstants: Used when we are running at elevated permissions.
runAsAuthenticationProvider(String) - Method in class ubic.gemma.core.security.SecurityConfig: Provider that validates the temporary RunAsUserToken produced by SecurityConfig.runAsManager(String).
runAsManager() - Method in class ubic.gemma.core.security.MethodSecurityConfig: Return the existing runAsManager bean (RunAsManagerImpl with the GROUP_ role prefix and the configured run-as key).
runAsManager(String) - Method in class ubic.gemma.core.security.SecurityConfig: RunAsManagerImpl keyed by ${gemma.runas.password} with role prefix GROUP_.
runDatasetBatchInformationFetch(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
runDatasetBatchInformationFetchAlias(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI compatibility alias for DatasetsWebService.runDatasetBatchInformationFetch(DatasetArg): UI calls POST /datasets/{id}/batchInformation/fetch.
runDatasetDiagnostics(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
runDatasetDiagnosticsAlias(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI compatibility alias for DatasetsWebService.runDatasetDiagnostics(DatasetArg): UI calls POST /datasets/{id}/preprocess/diagnostics.
runDatasetDifferentialAnalysis(DatasetArg, DatasetsWebService.DifferentialAnalysisRunRequest) - Method in class ubic.gemma.rest.DatasetsWebService
runDatasetDifferentialAnalysisAlias(DatasetArg, DatasetsWebService.DifferentialAnalysisRunRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Alias for DatasetsWebService.runDatasetDifferentialAnalysis(DatasetArg, DifferentialAnalysisRunRequest) that exposes the DEA dispatch under /datasets/{id}/analyses/differential.
runDatasetGeeq(DatasetArg, GeeqService.ScoreMode) - Method in class ubic.gemma.rest.DatasetsWebService
runDatasetPreprocess(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
runDatasetPreprocessAlias(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService: Curation-UI compatibility alias for DatasetsWebService.runDatasetPreprocess(DatasetArg): UI calls POST /datasets/{id}/preprocess.
runDatasetSvd(DatasetArg) - Method in class ubic.gemma.rest.DatasetsWebService
runDatasetSwitchPlatform(DatasetArg, DatasetsWebService.PlatformSwitchRequest) - Method in class ubic.gemma.rest.DatasetsWebService
runDifferentialExpressionAnalyses(ExpressionExperiment, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService
runDifferentialExpressionAnalyses(ExpressionExperiment, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
runId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
runId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
runId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
runId - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockResponse: What is holding it, when that is a job rather than a person; null for a person.
runId - Variable in class ubic.gemma.rest.PreboardedWebService.AnnotationSetSnapshotResponse
runId - Variable in class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest
RunMetrics(String, Map) - Constructor for class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.RunMetrics: Creates a new RunMetrics instance.
running - Variable in class ubic.gemma.rest.AdminWebService.JobsListResponse
RUNNING - Enum constant in enum class ubic.gemma.core.job.SubmittedTask.Status
RUNNING - Enum constant in enum class ubic.gemma.model.pipeline.JobState
RunProvenance(String, String, String, String, Date) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.RunProvenance
RunQcMetricsValueObject(SequencingQcMetrics.RunMetrics) - Constructor for class ubic.gemma.rest.DatasetsWebService.RunQcMetricsValueObject
runSha - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest: The producing repository's git head sha.
runSha - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse: Round-tripped so a trace does not stop at Gemma's boundary; see the request DTO for why it matters.
runSha - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse: Present on the thin shape too: the cross-experiment role=commit listing is the "which agent applied this, from which build" query, and answering it must not require an N+1 into the full endpoint for the two fields that carry the answer.
runSha - Variable in class ubic.gemma.rest.AnnotationSetsWebService.ProvenanceRequest

S

SAGE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType
SAGE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SAGE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
SAGENlaIII - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SAGERsaI - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SAGESau3A - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
sameTag(Characteristic, Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Statement-aware equality for the "is this the same tag?" question driving the idempotent set-replace annotation writes (experiment- and biomaterial-level).
SAMPLE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoRecordType
SAMPLE_SOURCE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
SAMPLE_TYPE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
SAMPLE_VALUE_TYPE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
SampleCharacteristicAdd(String, Long, Characteristic) - Constructor for class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.SampleCharacteristicAdd
SampleCharacteristicCommit() - Constructor for class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit
sampleCharacteristics(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig.GeoUpdateConfigBuilder
SampleCoexpressionAnalysis - Class in ubic.gemma.model.analysis.expression.coexpression: The 'analysis' in the name is a bit of a stretch here, as this object servers purely as an aggregator of all the sample coexpression matrices.
SampleCoexpressionAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis
SampleCoexpressionAnalysis.Factory - Class in ubic.gemma.model.analysis.expression.coexpression
SampleCoexpressionAnalysisService - Interface in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression
SampleCoexpressionAnalysisServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression: Manage the "sample correlation/coexpression" matrices.
SampleCoexpressionAnalysisServiceImpl() - Constructor for class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
SampleCoexpressionAuditService - Interface in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression: Co-bean facade for the SampleCorrelationAnalysisEvent success-path audit emission carried out by SampleCoexpressionAnalysisServiceImpl.compute(ExpressionExperiment, PreparedCoexMatrices).
SampleCoexpressionAuditServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression: Implementation of SampleCoexpressionAuditService: a thin co-bean whose only purpose is to expose an Audited-annotated method through a Spring proxy, so AuditedAspect fires, picks up the SampleCorrelationAnalysisPayload argument, serialises it to JSON and writes it to AUDIT_EVENT.PAYLOAD.
SampleCoexpressionAuditServiceImpl() - Constructor for class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAuditServiceImpl
SampleCoexpressionMatrix - Class in ubic.gemma.model.analysis.expression.coexpression: Holds the data of the sample coexpression matrix
SampleCoexpressionMatrix() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
SampleCoexpressionMatrix.Factory - Class in ubic.gemma.model.analysis.expression.coexpression
SampleCoexpressionRelatedPreprocessingException - Exception Class in ubic.gemma.core.analysis.preprocess: Exception raised in preprocessing when there is a problem with sample coexpression analysis.
SampleCoexpressionRelatedPreprocessingException(ExpressionExperiment, Throwable) - Constructor for exception class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException
SampleCorrelationAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
SampleCorrelationAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SampleCorrelationAnalysisEvent
SampleCorrelationAnalysisPayload - Record Class in ubic.gemma.core.security.audit.payload: Structured payload for SampleCorrelationAnalysisEvent writes: the row-and-column attrition of the expression matrix as each filter was applied, plus the filter configuration that produced it.
SampleCorrelationAnalysisPayload(SampleCorrelationAnalysisPayload.FilterConfig, List, int, int, int, int) - Constructor for record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Creates an instance of a SampleCorrelationAnalysisPayload record class.
SampleCorrelationAnalysisPayload.FilterConfig - Record Class in ubic.gemma.core.security.audit.payload: The settings the filter ran under.
SampleCorrelationAnalysisPayload.FilterStage - Record Class in ubic.gemma.core.security.audit.payload: One rung of the attrition funnel, in the order the filters ran.
SampleCorrelationMatrixValueObject(DoubleMatrix, String, Set, Set) - Constructor for class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject
sampleDetails - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
sampleDetails(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig.GeoRetrieveConfigBuilder: Fill sample details.
sampleFactorName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
sampleKurtosis(DoubleArrayList, double, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the sample kurtosis (aka excess) of a data sequence.
SampleMetrics(Long, String, String, boolean, Map, List, Long, String) - Constructor for class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics: Creates a new SampleMetrics instance.
SampleOutlierRequest() - Constructor for class ubic.gemma.rest.DatasetsWebService.SampleOutlierRequest
SampleQcMetricsValueObject(SequencingQcMetrics.SampleMetrics) - Constructor for class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject
SampleRemovalEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Event used when a sample is removed from an experiment (typically due to QC concerns or when marked as an outlier).
SampleRemovalEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalEvent
SampleRemovalPayload - Record Class in ubic.gemma.core.security.audit.payload: Structured payload for SampleRemovalEvent and SampleRemovalReversionEvent.
SampleRemovalPayload(List) - Constructor for record class ubic.gemma.core.security.audit.payload.SampleRemovalPayload: Creates an instance of a SampleRemovalPayload record class.
SampleRemovalReversionEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that samples that were previously removed have been "put back", e.g.
SampleRemovalReversionEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalReversionEvent
SAMPLES - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoScope
sampleSkew(DoubleArrayList, double, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the sample skew of a data sequence.
sampleStandardDeviation(double[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleStandardDeviation(float[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleStandardDeviation(int[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleStandardDeviation(long[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleStandardDeviation(DataVector) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleStandardDeviation(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
sampleStandardDeviation(SingleCellExpressionDataVector, BioAssay) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
sampleStandardDeviations(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixRowStats: Calculates the sample standard deviation of each row of a matrix
sampleTypeSet(String, String) - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParser
sampleVariance(double[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleVariance(float[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleVariance(int[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleVariance(long[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleVariance(DoubleArrayList, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the sample variance of a data sequence.
sampleVariance(DataVector) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sampleVariance(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
sampleVariance(SingleCellExpressionDataVector, BioAssay) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive: Calculate the variance of a given assay.
samplingVariance(double, double) - Static method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis: Equation 18-10 from CH.
samplingVariance(double, double, double) - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis: CH eqn 18-7
samplingVariances(DoubleArrayList, DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis: Run equation CH 18-10 on a list of sample sizes and effects.
samplingVariances(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis: Run eqn 18-7 on a set of effect sizes.
SARST - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SARST - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
save(C) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService
save(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService
save(Collection) - Method in class ubic.gemma.persistence.service.AbstractService
save(Collection) - Method in interface ubic.gemma.persistence.service.BaseService
save(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService
save(Collection) - Method in class ubic.gemma.persistence.service.AbstractDao
save(Collection) - Method in interface ubic.gemma.persistence.service.BaseDao: Create (if transient) or update all the given entities in the persistent storage.
save(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
save(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
save(Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
save(O) - Method in class ubic.gemma.persistence.service.AbstractService
save(O) - Method in interface ubic.gemma.persistence.service.BaseService
save(O) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService
save(T) - Method in class ubic.gemma.persistence.service.AbstractDao
save(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Create (if transient) or update an entity.
save(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
save(Characteristic) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
save(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
save(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
save(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
saveImage(String) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay: Saves the image to a png file.
saveImage(String, boolean, boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
saveImage(ColorMatrix, String, boolean, boolean, boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
saveImageToPng(ColorMatrix, OutputStream, boolean, boolean, boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
saveStatement(FactorValue, Statement) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Create a given statement as per FactorValueService.createStatement(FactorValue, Statement) if it is transient, otherwise update an existing statement.
saveStatement(FactorValue, Statement) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
saveStatementIgnoreAcl(FactorValue, Statement) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Deprecated.
do not use this, it is meant for FactorValue migration only
saveStatementIgnoreAcl(FactorValue, Statement) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
SC_MATRIX_VECTOR_COUNT_LIMIT - Static variable in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl: Vector-count ceiling above which SingleCellExpressionExperimentServiceImpl.getSingleCellExpressionDataMatrix(ExpressionExperiment, List, QuantitationType) refuses to materialize.
scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser
scalar(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
ScalarContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
scalarDivideMatrix(ExpressionDataDoubleMatrix, double) - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder: Divide all values by the dividend
SCALE_TYPE_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
scaleType - Variable in class ubic.gemma.cli.options.ExpressionDataFileOptionValue
ScaleType - Enum Class in ubic.gemma.model.common.quantitationtype
ScaleTypeConversionUtils - Class in ubic.gemma.core.analysis.preprocess.convert: Convert DataVector to different ScaleType.
ScaleTypeConversionUtils() - Constructor for class ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils
ScanDateExtractor - Interface in ubic.gemma.core.analysis.preprocess.batcheffects: Generic interface for classes that extract scan dates from raw data files.
scanFrom - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
scannedAt - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
scanTo - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
schedule(Runnable, long, TimeUnit) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextScheduledExecutorService
schedule(Callable, long, TimeUnit) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextScheduledExecutorService
scheduleAtFixedRate(Runnable, long, long, TimeUnit) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextScheduledExecutorService
ScheduledSearchReindexer - Class in ubic.gemma.core.search.indexer: Nightly @Scheduled task that runs Hibernate Search's MassIndexer for any @Indexed entity class whose underlying rows have been touched since the last successful reindex, or whose index no longer holds one document per row.
ScheduledSearchReindexer() - Constructor for class ubic.gemma.core.search.indexer.ScheduledSearchReindexer
SCHEDULER - Static variable in class ubic.gemma.core.context.EnvironmentProfiles: Independent feature toggles.
SchedulerConfig - Class in ubic.gemma.core.config: Quartz scheduler configuration for Gemma, replacing the deprecated XML applicationContext-schedule.xml.
SchedulerConfig() - Constructor for class ubic.gemma.core.config.SchedulerConfig
schedulerFactoryBean(Trigger, Trigger, Trigger, Trigger, Trigger, Trigger, Trigger, Trigger, Trigger) - Method in class ubic.gemma.core.config.SchedulerConfig: Main Quartz entry point.
SchedulerHandle - Class in ubic.gemma.core.pipeline: Opaque pointer to a scheduler-side job.
SchedulerHandle(SchedulerKind, String) - Constructor for class ubic.gemma.core.pipeline.SchedulerHandle
SchedulerKind - Enum Class in ubic.gemma.model.pipeline: External scheduler that owns the runtime of a PipelineJob.
scheduleWithFixedDelay(Runnable, long, long, TimeUnit) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextScheduledExecutorService
SCHEMA_VERSION - Static variable in class ubic.gemma.core.loader.expression.geo.GeoSourceMetadataBuilder: Schema version written into the document and into Investigation.sourceMetadataSchemaVersion.
SCHEMA_VERSION - Static variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta: Bumped when the meaning of a field changes or the slim is built a materially different way.
schemaVersion - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta
scope - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionRequest
scope - Variable in class ubic.gemma.rest.DatasetsWebService.CurationDecisionResponse
scope(String) - Static method in class ubic.gemma.core.security.util.ActingIdentity: Bind onBehalfOf for the current thread until the returned scope is closed.
score() - Method in record class ubic.gemma.core.ontology.lexical.LexicalOntologyIndex.Hit: Returns the value of the score record component.
score(BlatResult) - Static method in class ubic.gemma.core.analysis.sequence.BlatAssociationScorer: Based on the JKSrc method in psl.c, but without double-penalizing for mismatches.
scoreResults(Collection) - Static method in class ubic.gemma.core.analysis.sequence.BlatAssociationScorer: From a collection of BlatAssociations from a single BioSequence, reduce redundancy, fill in the specificity and score and pick the one with the best scoring statistics.
scrape(String) - Method in class ubic.gemma.rest.monitoring.MetricsWebService
scrape(GeoScrapeService.ScrapeRequest) - Method in interface ubic.gemma.core.geoscrape.GeoScrapeService: Deprecated.

Run a scrape.
scrape(GeoScrapeService.ScrapeRequest) - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImpl
scrapeDryRun(GeoScrapeService.ScrapeRequest) - Method in interface ubic.gemma.core.geoscrape.GeoScrapeService: Deprecated.

Evaluate matchers against the same window GeoScrapeService.scrape(ScrapeRequest) would inspect, but persist nothing — no watermark row, no PreboardedExperiment row, no ticket.
scrapeDryRun(GeoScrapeService.ScrapeRequest) - Method in class ubic.gemma.core.geoscrape.GeoScrapeServiceImpl
ScrapeRequest() - Constructor for class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
SCRATCHPAD - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: A curator's personal scratchpad: a ticket kept open indefinitely, holding whatever they are currently looking at.
scratchpadOpen - Variable in class ubic.gemma.rest.TicketsWebService.OpenTicketSummaryResponse: Open scratchpads, held out of TicketsWebService.OpenTicketSummaryResponse.totalOpen so the exclusion is a number a caller can see and add back rather than a filter it has to know about.
SCREENING - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: Pre-import triage: a curator decides include / exclude on a candidate GEO accession before it is loaded into Gemma at all.
SCREENING_RESULT_CHANGED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType: One per screening decision recorded on a target (see ScreeningResult).
ScreeningResult - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: The outcome a curator or agent recorded for one TicketTarget when screening it.
SCRNA - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
SCRNA_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy: GEO's own, not SRA's.
SDRFFetcher - Class in ubic.gemma.core.loader.expression.arrayExpress: Fetch the SRDF file
SDRFFetcher() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher
search(String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
search(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
search(String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
search(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
search(String, boolean, boolean) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
search(String, boolean, boolean) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
search(String, boolean, boolean) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
search(String, boolean, boolean) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
search(String, int) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch: Gets all the pubmed ID's that would be returned from a pubmed search string, using two eUtil calls.
search(String, int) - Method in class ubic.gemma.core.ontology.lexical.LexicalOntologyIndex: Run a full-text query, returning up to maxResults URI hits ordered by descending score.
search(String, int) - Method in class ubic.gemma.core.ontology.search.JenaTextOntologySearchService
search(String, int) - Method in interface ubic.gemma.core.ontology.search.OntologySearchService: Search the backing dataset for resources whose indexed properties (label, synonyms, OBO ids, etc.) match the given Lucene query.
search(String, String, EntrezRetmode, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Perform a search on an Entrez database.
search(String, EntrezQuery, EntrezRetmode, int, int, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Replay a previous EntrezUtils.search(String, String, EntrezRetmode, String) query.
search(Collection, int) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch: Gets all the pubmed ID's that would be returned given a list of input terms, using two eUtil calls.
search(SearchSettings) - Method in interface ubic.gemma.core.search.SearchService
search(SearchSettings) - Method in class ubic.gemma.core.search.SearchServiceImpl
search(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchService: The results are sorted in order of decreasing score, organized by class.
search(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.SearchServiceImpl
search(QueryArg, DatasetArg, TaxonArg, PlatformArg, List, LimitArg, ExcludeArg, boolean, boolean) - Method in class ubic.gemma.rest.SearchWebService: Search everything subject to taxon and platform constraints.
searchAndRetrieve(String, int) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch: Search based on terms and retrieve the PubMed records.
searchAndRetrieveByDoi(String) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch: Retrieve PubMed records by DOI.
searchAndRetrieveGeoRecords(GeoRecordType, String, GeoSearchField, Collection, Collection, Collection, int, int, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Search and retrieve GEO records.
searchAnnotations(StringArrayArg, String, int, String, boolean, boolean, boolean, String, boolean, boolean, TaxonArg, boolean, int, boolean, boolean, String, boolean) - Method in class ubic.gemma.rest.AnnotationsWebService: Does a search for annotation tags based on the given string.
searchAnnotationsBatch(AnnotationsWebService.AnnotationSearchBatchRequest) - Method in class ubic.gemma.rest.AnnotationsWebService
searchAnnotationsByPathQuery(StringArrayArg) - Method in class ubic.gemma.rest.AnnotationsWebService
searchArrayDesign(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource
searchArrayDesign(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchArrayDesign(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchArrayDesign(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchBibliographicReference(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource
searchBibliographicReference(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchBibliographicReference(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchBioSequence(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource
searchBioSequence(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchBioSequence(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchBioSequence(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchBioSequenceAndGene(SearchSettings, SearchContext, Collection) - Method in interface ubic.gemma.core.search.SearchSource: Deprecated.
use SearchSource.searchBioSequence(SearchSettings, SearchContext) instead
searchBioSequenceAndGene(SearchSettings, SearchContext, Collection) - Method in class ubic.gemma.core.search.source.CompositeSearchSource: Deprecated.
searchBioSequenceAndGene(SearchSettings, SearchContext, Collection) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchBlacklistedEntities(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource
searchBlacklistedEntities(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchBlacklistedEntities(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchCompositeSequence(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource
searchCompositeSequence(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchCompositeSequence(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchCompositeSequence(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchCompositeSequenceAndGene(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource: Deprecated.
use SearchSource.searchCompositeSequence(SearchSettings, SearchContext) instead
searchCompositeSequenceAndGene(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource: Deprecated.
searchCompositeSequenceAndGene(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
SearchContext - Class in ubic.gemma.core.search
SearchContext(Highlighter, Consumer) - Constructor for class ubic.gemma.core.search.SearchContext
searchDatasets(QueryArg, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService: Deprecated.
redundant with GET /datasets?query=... (the paginated catalogue runs the same search), which every known client uses instead — no caller of this endpoint was found across gemma-ui, gemma-curation-agents, or gemma.R. Scheduled for removal in the 2.10 release.
searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) - Method in class ubic.gemma.rest.AnnotationsWebService: Does a search for datasets containing characteristics matching the given string.
searchDatasetsByQueryInPath(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) - Method in class ubic.gemma.rest.AnnotationsWebService
searchEnabled - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject
SearchException - Exception Class in ubic.gemma.core.search: Exception raised by the SearchService when the search could not be performed.
SearchException(String, Throwable) - Constructor for exception class ubic.gemma.core.search.SearchException
SearchException(Throwable) - Constructor for exception class ubic.gemma.core.search.SearchException
searchExperimentsAndExperimentGroups(String, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService: does not include session bound sets
searchExperimentsAndExperimentGroups(String, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl
searchExperimentSet(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource
searchExperimentSet(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchExperimentSet(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchExperimentSet(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchExpressionExperiment(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource
searchExpressionExperiment(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchExpressionExperiment(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchExpressionExperiment(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchExpressionExperiment(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.OntologySearchSource: Search via characteristics i.e.
searchExpressionExperiments(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService
searchExpressionExperiments(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl
searchExpressionExperiments(String, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService
searchExpressionExperiments(String, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl
searchExpressionExperiments(List) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService
searchExpressionExperiments(List) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl
searchGene(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource
searchGene(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchGene(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchGene(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.GeneOntologySearchSource
searchGene(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchGenes(String, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
searchGenes(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl: Search for genes (by name or symbol)
searchGenes(String, TaxonArg, int) - Method in class ubic.gemma.rest.GeneWebService: Free-text typeahead for genes.
searchGenesAndGeneGroups(String, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSearchService
searchGenesAndGeneGroups(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
searchGeneSet(SearchSettings, SearchContext) - Method in interface ubic.gemma.core.search.SearchSource
searchGeneSet(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchGeneSet(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchGeneSet(SearchSettings, SearchContext) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchGeoRecords(GeoRecordType, String) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Search GEO records.
searchGeoRecords(GeoRecordType, String) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl
searchGeoRecords(GeoRecordType, String, GeoSearchField, Collection, Collection, Collection) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Search GEO records.
searchGeoRecords(GeoRecordType, String, GeoSearchField, Collection, Collection, Collection, Date, Date) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Search GEO records, restricted to a publication-date window.
searchGeoRecords(GeoRecordType, String, GeoSearchField, Collection, Collection, Collection, Date, Date) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl
SearchIndexBootstrapper - Class in ubic.gemma.rest.startup: Boot-time check: enumerate every @Indexed entity Hibernate Search 7 knows about and trigger a one-shot mass-reindex for any that come back with zero documents.
SearchIndexBootstrapper() - Constructor for class ubic.gemma.rest.startup.SearchIndexBootstrapper
SearchIndicesResponse() - Constructor for class ubic.gemma.rest.AdminWebService.SearchIndicesResponse
SearchMatchType - Enum Class in ubic.gemma.model.common.search: How a SearchResult matched the query — the structured discriminant that a double score cannot carry on its own.
searchMultipleGenes(String, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSearchService: Search for multiple genes at once.
searchMultipleGenes(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
searchMultipleGenesGetMap(Collection, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSearchService: Search for multiple genes at once.
searchMultipleGenesGetMap(Collection, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
SearchResult<T> - Class in ubic.gemma.model.common.search: Represents an individual search result.
SearchResult(Class, long, double, Map, Object) - Constructor for class ubic.gemma.model.common.search.SearchResult: Creates a new SearchResult instance.
SearchResultDisplayObject - Class in ubic.gemma.core.search: Object to store search results of different classes in a similar way for displaying to user (ex: enables genes and gene sets to be entries in the same combo box) object types handled are: Gene, GeneSet, GeneSetValueObject, ExpressionExperiment and ExpressionExperimentSet SearchObject is also handled if the object it holds is of any of those types for a gene or experiment, the memberIds field is a collection just containing the object's id.
SearchResultDisplayObject() - Constructor for class ubic.gemma.core.search.SearchResultDisplayObject: satisfy javaBean contract
SearchResultDisplayObject(Object) - Constructor for class ubic.gemma.core.search.SearchResultDisplayObject
SearchResultDisplayObject(SessionBoundGeneSetValueObject) - Constructor for class ubic.gemma.core.search.SearchResultDisplayObject
SearchResultSet<T> - Class in ubic.gemma.model.common.search: This is a special kind of set designed for holding SearchResult.
SearchResultSet(SearchSettings) - Constructor for class ubic.gemma.model.common.search.SearchResultSet
SearchResultsResponseDataObject(List, SearchWebService.SearchSettingsValueObject) - Constructor for class ubic.gemma.rest.SearchWebService.SearchResultsResponseDataObject
SearchResultValueObject<T> - Class in ubic.gemma.model.common.search
SearchResultValueObject(SearchResult) - Constructor for class ubic.gemma.model.common.search.SearchResultValueObject
SearchResultValueObject(SearchResult, String, boolean) - Constructor for class ubic.gemma.model.common.search.SearchResultValueObject
SearchResultValueObject(SearchResult, String, boolean) - Constructor for class ubic.gemma.rest.SearchWebService.SearchResultValueObject
SearchService - Interface in ubic.gemma.core.search
SearchService.SearchResultMap - Interface in ubic.gemma.core.search
SearchServiceImpl - Class in ubic.gemma.core.search: Free-text search service: delegates per-result-type lookups to a CompositeSearchSource composed of all registered SearchSource beans (e.g.
SearchServiceImpl() - Constructor for class ubic.gemma.core.search.SearchServiceImpl
SearchSettings - Class in ubic.gemma.model.common.search: Configuration options for searching.
SearchSettings.SearchMode - Enum Class in ubic.gemma.model.common.search
SearchSettings.SearchSettingsBuilder - Class in ubic.gemma.model.common.search
SearchSettingsValueObject - Class in ubic.gemma.model.common.search: author: anton date: 18/03/13
SearchSettingsValueObject() - Constructor for class ubic.gemma.model.common.search.SearchSettingsValueObject
SearchSettingsValueObject(SearchSettings) - Constructor for class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
SearchSource - Interface in ubic.gemma.core.search: Search source that provides SearchResult from a search engine.
searchTaxonDatasets(TaxonArg, StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) - Method in class ubic.gemma.rest.AnnotationsWebService: Same as AnnotationsWebService.searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
searchTaxonDatasetsByQueryInPath(TaxonArg, StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) - Method in class ubic.gemma.rest.AnnotationsWebService
searchTickets(String, boolean, Long, int) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Find tickets a curator could be meaning when they type into a ticket picker — backs GET /tickets/search.
searchTickets(String, boolean, Long, int) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
searchTickets(String, boolean, LimitArg) - Method in class ubic.gemma.rest.TicketsWebService: Ticket picker: "choose a ticket by typing".
SearchTimeoutException - Exception Class in ubic.gemma.core.search: Indicate that the search failed due to a TimeoutException.
SearchTimeoutException(String, TimeoutException) - Constructor for exception class ubic.gemma.core.search.SearchTimeoutException
SearchWebService - Class in ubic.gemma.rest: Provides search capabilities to the RESTful API.
SearchWebService() - Constructor for class ubic.gemma.rest.SearchWebService
SearchWebService.SearchResultsResponseDataObject - Class in ubic.gemma.rest
SearchWebService.SearchResultValueObject<T> - Class in ubic.gemma.rest: Representation of SearchResult for the RESTful API.
SearchWebService.SearchSettingsValueObject - Class in ubic.gemma.rest: Represents search settings for the RESTful API.
secondLevelCacheHitCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
secondLevelCacheMissCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
secondLevelCachePutCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
secondObject - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
secondObjectUri - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
secondPredicate - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
secondPredicateUri - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
Section() - Constructor for class ubic.gemma.rest.DatasetsWebService.Section
Securable - Interface in ubic.gemma.core.security.model: Interface that indicates an entity can be secured.
Securable - Interface in ubic.gemma.model.common.auditAndSecurity
SecurableBaseImmutableService<C> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
SecurableBaseReadOnlyService<C> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
SecurableBaseService<C> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity: A base service for securable entities.
SecurableBaseVoEnabledService<C,VO> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
SecurableFilteringVoEnabledService<C,VO> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity: A base service for securable entities with filtering and VO capabilities.
SecuredChild - Interface in ubic.gemma.core.security.model: Indicates a securable that must have a parent that holds the permissons.
SecuredChild<OT> - Interface in ubic.gemma.model.common.auditAndSecurity
SecuredNotChild - Interface in ubic.gemma.core.security.model: Interface to mark entities which are secured, and which should not have 'parent's, and therefore do not inherit permissions from other objects.
SecuredNotChild - Interface in ubic.gemma.model.common.auditAndSecurity
SecureMethodInvokingJobDetailFactoryBean - Class in ubic.gemma.core.scheduler: Specialization of Spring task-running support so task threads have secure context (without using MODE_GLOBAL!).
SecureMethodInvokingJobDetailFactoryBean(SecurityContext) - Constructor for class ubic.gemma.core.scheduler.SecureMethodInvokingJobDetailFactoryBean
SecureQuartzJobBean - Class in ubic.gemma.core.scheduler: A secure Quartz job bean that executes with a given security context.
SecureQuartzJobBean() - Constructor for class ubic.gemma.core.scheduler.SecureQuartzJobBean
SecureValueObject - Interface in ubic.gemma.core.security.model: Indicates that a value object represents a Securable so security filtering can be provided during reading.
securityCheck(Acl, int) - Method in class ubic.gemma.core.security.acl.AclAuthorizationStrategyImpl
SecurityConfig - Class in ubic.gemma.core.security: Core Spring Security wiring for Gemma, replacing the legacy applicationContext-security.xml.
SecurityConfig() - Constructor for class ubic.gemma.core.security.SecurityConfig
SecurityService - Interface in ubic.gemma.core.security: High-level methods for security-related manipulations.
SecurityServiceImpl - Class in ubic.gemma.core.security: Methods for changing security on objects, creating and modifying groups, checking security on objects.
SecurityServiceImpl(AclService, SessionRegistry, ObjectIdentityRetrievalStrategy, SidRetrievalStrategy, UserDetailsManager, GroupManager, BaseUserService) - Constructor for class ubic.gemma.core.security.SecurityServiceImpl
SecurityUtil - Class in ubic.gemma.core.security.util: Database-independent methods for ACLs
SecurityUtil() - Constructor for class ubic.gemma.core.security.util.SecurityUtil
SecurityUtils - Class in ubic.gemma.persistence.util
SecurityUtils() - Constructor for class ubic.gemma.persistence.util.SecurityUtils
SEED_POLICY_CORPUS - Static variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta: Seeded only from CHEBI URIs already used in the corpus.
seedCount - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta
seedDirection(AnnotationRelationDao.Direction) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery: Which side of the relation an experiment seed is matched against.
seedFromExperimentId(Long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery: Seed from every annotation an experiment carries, instead of from a list of terms.
seedHash - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta: SHA-256 of the sorted seed URIs joined by \n.
seedPolicy - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta: Which seeding rule produced this slim, e.g.
seedPolicyWithRoles(Collection) - Static method in class ubic.gemma.core.ontology.providers.OntologySlimMeta: Seeded from corpus usage PLUS every bearer of the given role(s); see the extractor.
select(DoubleMatrix1D, Collection) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
selectColumns(DoubleMatrix2D, Collection) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
selectColumns(CompRowMatrix, int[]) - Static method in class ubic.gemma.core.datastructure.sparse.CompRowMatrixUtils: Select the specified columns from a compressed row matrix.
selectColumnsAndRows(DoubleMatrix2D, Collection) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
selectRows(DoubleMatrix2D, Collection) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
selectRows(CompRowMatrix, int[]) - Static method in class ubic.gemma.core.datastructure.sparse.CompRowMatrixUtils: Select the specified rows from a compressed row matrix.
selectVectors(Collection) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix: Selects all the vectors passed in (uses them to initialize the data)
selectVectors(Collection, Collection) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
selectVectors(Collection, List) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
selectVectors(Collection, QuantitationType) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
SELEX - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
self() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder
self() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder
self() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder
self() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
self() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder
self() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder
SELF - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoScope
selfSquaredMatrix(double[][]) - Static method in class ubic.gemma.core.util.math.MatrixStats
send(SimpleMailMessage) - Method in class ubic.gemma.core.util.DummyMailSender
send(SimpleMailMessage[]) - Method in class ubic.gemma.core.util.DummyMailSender
sendAddUserToGroupEmail(User, String, User) - Method in interface ubic.gemma.core.mail.MailService
sendAddUserToGroupEmail(User, String, User) - Method in class ubic.gemma.core.mail.MailServiceImpl: Send an email when a user is added to a group.
sendEvent(String, String...) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider: Publish an event without specifying a date.
sendEvent(String, Date, String...) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider: Publish an event with additional parameters expressed as a sequence of keys and values.
sendEvent(String, Date, Map) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider: Publish an event.
sendEvent(String, Date, Map) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
sendfile(Path) - Static method in class ubic.gemma.rest.util.Responders
Sendfile - Class in ubic.gemma.rest.util: Indicate that a file should be sent using Tomcat sendfile.
SendfileProvider - Class in ubic.gemma.rest.providers
SendfileProvider() - Constructor for class ubic.gemma.rest.providers.SendfileProvider
sendMessage(String, String, String, Map) - Method in interface ubic.gemma.core.mail.MailEngine: Send a templated email message.
sendMessage(String, String, String, Map) - Method in class ubic.gemma.core.mail.MailEngineImpl
sendMessageToAdmin(String, String) - Method in interface ubic.gemma.core.mail.MailEngine: Send an email message to the administrator.
sendMessageToAdmin(String, String) - Method in class ubic.gemma.core.mail.MailEngineImpl
sendRemoveUserFromGroupEmail(User, String, User) - Method in interface ubic.gemma.core.mail.MailService
sendRemoveUserFromGroupEmail(User, String, User) - Method in class ubic.gemma.core.mail.MailServiceImpl: Send an email when a user is removed from a group.
sendResetConfirmationEmail(String, String, String, String, Locale) - Method in interface ubic.gemma.core.mail.MailService
sendResetConfirmationEmail(String, String, String, String, Locale) - Method in class ubic.gemma.core.mail.MailServiceImpl: Send an email to request signup confirmation.
sendSignupConfirmationEmail(String, String, String, Locale) - Method in interface ubic.gemma.core.mail.MailService
sendSignupConfirmationEmail(String, String, String, Locale) - Method in class ubic.gemma.core.mail.MailServiceImpl: Send an email to request signup confirmation.
sendTaskCompletedEmail(User, String, String, String, String) - Method in interface ubic.gemma.core.mail.MailService
sendTaskCompletedEmail(User, String, String, String, String) - Method in class ubic.gemma.core.mail.MailServiceImpl
sendTaskCompletedNotificationEmail(EmailNotificationContext, TaskResult) - Method in interface ubic.gemma.core.job.notification.TaskMailUtils
sendTaskCompletedNotificationEmail(EmailNotificationContext, TaskResult) - Method in class ubic.gemma.core.job.notification.TaskMailUtilsImpl
SentinelPropertyValidator - Class in ubic.gemma.core.config: Fail-fast startup hook for unresolved sentinel (XXXXXX) placeholder values shipped by default.properties.
SentinelPropertyValidator(PropertySources) - Constructor for class ubic.gemma.core.config.SentinelPropertyValidator
sep - Variable in class ubic.gemma.core.util.matrix.MatrixWriter
SEPARATE_SAMPLE_FROM_ASSAYS_IDENTIFIERS_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
sequence() - Method in record class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao.BioSequenceLite: Returns the value of the sequence record component.
SEQUENCE - Enum constant in enum class ubic.gemma.model.common.description.DatabaseType
SEQUENCE_PAIRED_READS - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssayCategories
SEQUENCE_READ_COUNT - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssayCategories
SEQUENCE_READ_LENGTH - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssayCategories
SequenceBinUtils - Class in ubic.gemma.core.analysis.sequence: Used to assign a bin to a chromosome location, identify bins for a range, or to generate SQL to add to a query on a GoldenPath database.
SequenceBinUtils() - Constructor for class ubic.gemma.core.analysis.sequence.SequenceBinUtils
SequenceManipulation - Class in ubic.gemma.core.analysis.sequence: Convenient methods for manipulating BioSequences and PhysicalLocations
SequenceManipulation() - Constructor for class ubic.gemma.core.analysis.sequence.SequenceManipulation
sequenceOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
SequenceOntologyService - Class in ubic.gemma.core.ontology.providers: Sequence types and features ontology
SequenceOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.SequenceOntologyService
SequenceSimilaritySearchResult - Class in ubic.gemma.model.genome.sequenceAnalysis
SequenceSimilaritySearchResult() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
SequenceType - Enum Class in ubic.gemma.model.genome.biosequence
SequenceTypeValueObject - Class in ubic.gemma.model.genome.sequenceAnalysis
SequenceTypeValueObject() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject
SequenceTypeValueObject(SequenceType) - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject
SequenceWriter - Class in ubic.gemma.core.analysis.sequence: Tools for writing biosequences to files so they can be analyzed by external tools, and then read back into Gemma.
SequenceWriter() - Constructor for class ubic.gemma.core.analysis.sequence.SequenceWriter
SEQUENCING - Enum constant in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType: Indicate the platform is based on sequencing (e.g.
SequencingDataLoader - Interface in ubic.gemma.core.loader.expression.sequencing: An interface for data loaders that can load sequencing data.
SequencingDataLoaderConfig - Class in ubic.gemma.core.loader.expression.sequencing: Configuration for loading sequencing data.
SequencingDataLoaderConfig(SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder) - Constructor for class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig
SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C,B> - Class in ubic.gemma.core.loader.expression.sequencing
SequencingDataLoaderConfigBuilder() - Constructor for class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder
SequencingMetadata - Class in ubic.gemma.core.loader.expression.sequencing: Represents sequencing metadata for a BioAssay.
SequencingMetadata.SequencingMetadataBuilder - Class in ubic.gemma.core.loader.expression.sequencing
sequencingMetadataFile(Path) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder: File containing per-assay sequencing metadata.
SequencingMetadataFileDataLoader - Class in ubic.gemma.core.loader.expression.sequencing: Load sequencing metadata from a TSV file.
SequencingMetadataFileDataLoader(SequencingDataLoader, Path, SequencingMetadata, BioAssayMapper) - Constructor for class ubic.gemma.core.loader.expression.sequencing.SequencingMetadataFileDataLoader
SequencingMetadataFileSingleCellDataLoader - Class in ubic.gemma.core.loader.expression.singleCell: Adapt a SequencingMetadataFileDataLoader so that it can be used as a SingleCellDataLoader.
SequencingMetadataFileSingleCellDataLoader(SingleCellDataLoader, Path, SequencingMetadata, BioAssayMapper) - Constructor for class ubic.gemma.core.loader.expression.singleCell.SequencingMetadataFileSingleCellDataLoader
SequencingMetadataFileSingleCellDataLoaderConfigurer - Class in ubic.gemma.core.loader.expression.singleCell
SequencingMetadataFileSingleCellDataLoaderConfigurer(SingleCellDataLoaderConfigurer, BioAssayMapper) - Constructor for class ubic.gemma.core.loader.expression.singleCell.SequencingMetadataFileSingleCellDataLoaderConfigurer
SequencingQcMetrics - Class in ubic.gemma.core.analysis.preprocess.qc: Per-sample sequencing QC metrics for one experiment, read out of the RNA-Seq pipeline's MultiQC report and joined to the experiment's BioAssays.
SequencingQcMetrics(boolean, List, List, List) - Constructor for class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics: Creates a new SequencingQcMetrics instance.
SequencingQcMetrics.MetricDefinition - Class in ubic.gemma.core.analysis.preprocess.qc: A metric column as MultiQC describes it.
SequencingQcMetrics.RunMetrics - Class in ubic.gemma.core.analysis.preprocess.qc: One report row below the sample level — a sequencing run, or one mate of a paired run.
SequencingQcMetrics.SampleMetrics - Class in ubic.gemma.core.analysis.preprocess.qc: The metrics resolved for a single bioAssay.
SequencingQcMetricsService - Interface in ubic.gemma.core.analysis.preprocess.qc: Reads the per-sample sequencing QC metrics the RNA-Seq pipeline's MultiQC report carries, and joins them to the experiment's bioAssays.
SequencingQcMetricsServiceImpl - Class in ubic.gemma.core.analysis.preprocess.qc: Streams report_general_stats_data out of the MultiQC report and resolves its row keys to bioAssays.
SequencingQcMetricsServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetricsServiceImpl
SequencingQcMetricsValueObject(SequencingQcMetrics) - Constructor for class ubic.gemma.rest.DatasetsWebService.SequencingQcMetricsValueObject
serialize(Double, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.core.util.RoundingUtils.SignificantDigitsSerializer
serialize(T, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer
serializeInternal(T, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer
serializeInternal(FactorValueBasicValueObject, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer
serializeInternal(FactorValueValueObject, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer: Deprecated.
serializeSupportingEvidence(JsonNode) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Inverse of CharacteristicUtils.parseSupportingEvidence(String): flatten a supporting-evidence tree back to the string the SUPPORTING_EVIDENCE column stores.
SERIES - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoRecordType
SERIES - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoScope
SeriesAwareSingleCellDetector - Interface in ubic.gemma.core.loader.expression.geo.singleCell: Interface implemented by single-cell detector that can contextualize a sample within a series.
SeriesFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher
SeriesFetcher() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.SeriesFetcher
seriesType - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
service - Variable in class ubic.gemma.rest.util.args.AbstractEntityArgService
ServiceBasedEntityConverter<O> - Class in ubic.gemma.persistence.util: Performs conversion by identifier and collection of identifier for a BaseReadOnlyService.
ServiceBasedEntityConverter(BaseReadOnlyService, Class) - Constructor for class ubic.gemma.persistence.util.ServiceBasedEntityConverter
ServiceBasedValueObjectConverter<O,VO> - Class in ubic.gemma.persistence.util: Perform conversion to value object by entity, ID and collections of entities and IDs and also to entity by ID and collection of IDs.
ServiceBasedValueObjectConverter(BaseVoEnabledService, Class, Class) - Constructor for class ubic.gemma.persistence.util.ServiceBasedValueObjectConverter
ServiceBeansConfig - Class in ubic.gemma.core.config: Phase 3 XML->Java migration: replaces the default-profile beans from applicationContext-serviceBeans.xml — entityUrlBuilder, taskExecutor, and expressionDataFileTaskExecutor.
ServiceBeansConfig() - Constructor for class ubic.gemma.core.config.ServiceBeansConfig
serviceMethod() - Method in class ubic.gemma.persistence.util.Pointcuts: A public method defined in a service.
SessionBoundExpressionExperimentSetValueObject - Class in ubic.gemma.model.expression.experiment
SessionBoundExpressionExperimentSetValueObject() - Constructor for class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject: Required when using the class as a spring bean.
SessionBoundExpressionExperimentSetValueObject(Long) - Constructor for class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject: default constructor to satisfy java bean contract
SessionBoundGeneSetValueObject - Class in ubic.gemma.model.genome.gene
SessionBoundGeneSetValueObject() - Constructor for class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject: default constructor to satisfy java bean contract
sessionCloseCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
sessionCount - Variable in class ubic.gemma.rest.AdminWebService.SessionPrincipalValueObject
sessionFactory(DataSource) - Method in class ubic.gemma.persistence.hibernate.HibernateConfig: Native Hibernate SessionFactory built from hibernate.cfg.xml.
sessionOpenCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
SessionPrincipalValueObject() - Constructor for class ubic.gemma.rest.AdminWebService.SessionPrincipalValueObject
sessionRegistry() - Method in class ubic.gemma.core.security.SecurityConfig: Session registry consumed by the <s:concurrency-control> element in gemma-web's applicationContext-security.xml.
SessionsResponse() - Constructor for class ubic.gemma.rest.AdminWebService.SessionsResponse
sessionVariables - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
set(int, int, double) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix: Primitive overload of DenseDoubleMatrix.set(int, int, Double) that avoids autoboxing on hot paths.
set(int, int, Double) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Deprecated.
modifying the matrix directly is not recommended, make a copy instead.
set(int, int, Double) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
set(int, int, Double) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
set(int, int, Double) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
set(int, int, Double) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
set(int, int, Integer) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
set(int, int, String) - Method in class ubic.gemma.core.util.matrix.StringMatrix
set(int, int, V) - Method in interface ubic.gemma.core.util.matrix.Matrix2D
set(int, int, V) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
set(int, T) - Method in class ubic.gemma.model.util.UninitializedList
set(CompositeSequence, BioAssay, Double) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Deprecated.
setAbortOnError() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Set this to stop processing experiments if an error occurs.
setAbsentPresentCalls(ExpressionDataBooleanMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter: Supply a separate matrix of booleans.
setAbstract_(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
setAbstractText(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setAbstractText(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setAcceptsTargets(boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setAcceptsTargets(boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: Whether experiments may be added to this ticket after it was opened.
setAcceptsTargets(Boolean) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setAcceptsTargets(Boolean) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setAccessDenied(boolean) - Method in class ubic.gemma.model.common.BaseValueObject
setAccession(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
setAccession(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
setAccession(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
setAccession(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setAccession(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
setAccession(String) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setAccession(String) - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
setAccession(String) - Method in class ubic.gemma.model.common.description.DatabaseEntry
setAccession(String) - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
setAccession(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setAccession(String) - Method in class ubic.gemma.model.expression.experiment.PreboardedExperiment
setAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
setAccession(String) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setAccession(String) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
setAccession(SimpleDatabaseEntry) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
setAccession(SimpleDatabaseEntry) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
setAccession(DatabaseEntry) - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
setAccession(DatabaseEntry) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setAccession(DatabaseEntry) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setAccession(DatabaseEntryValueObject) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setAccessions(Collection) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
setAccessions(Set) - Method in class ubic.gemma.model.genome.gene.GeneProduct
setAccessions(Set) - Method in class ubic.gemma.model.genome.Gene
setAccessions(Set) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setAccessionVersion(String) - Method in class ubic.gemma.model.common.description.DatabaseEntry
setAccToDatasetOrPlatformMap(Map) - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
setAccToTitleMap(Map) - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
setAceOrder(int) - Method in class ubic.gemma.core.security.acl.domain.AclEntry
setAclIsAuthenticatedAnonymouslyMask(int) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setAction(String) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setActiveExperiments(Collection) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setActor(Contact) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
setActorId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
setActorName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
setAdditionalPropertyUris(Set) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
setAdditionalPropertyUris(Set) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
setAdditionalPropertyUris(Set) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
setAdditionalPropertyUris(Set) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Set the URIs to be used as additional properties when inferring parents and children.
setAdditionalPropertyUris(Set) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Set the URIs used for inferring additional properties.
setAddress(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setAdvanceLinkedTickets(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setAdvertisedNumberOfDesignElements(Integer) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setAffyControlsFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setAfterAffyControlsFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setAfterLowExpressionFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setAfterLowVarianceFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setAfterMinPresentFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setAfterNoSequencesFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setAfterOutliersFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setAfterZeroVarianceFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setAgentName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setAgentName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setAgentName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
setAgentName(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
setAgentVersion(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setAgentVersion(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setAgentVersion(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
setAggressiveQtRemoval(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setAggressiveQtRemoval(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setAlias(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
setAlias(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setAlias(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
setAlias(String) - Method in class ubic.gemma.model.genome.gene.GeneAlias
setAliases(Set) - Method in class ubic.gemma.model.genome.Gene
setAliases(SortedSet) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Gene aliases, sorted alphabetically.
setAll(Boolean) - Method in class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskCommand
setAll(Boolean) - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
setAllCharacteristics(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setAllIsLazy() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Enable the "all is lazy" mode.
setAllowArrayExpressDesign(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setAllowArrayExpressDesign(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setAllowCredentials(boolean) - Method in class ubic.gemma.rest.servlet.CorsFilter: Indicate if the credentials (i.e.
setAllowedHeaders(String) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the allowed headers by a CORS request.
setAllowedMethods(String) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the allowed methods by a CORS request.
setAllowedOrigins(String) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the allowed origins of a CORS request.
setAllowedUriPrefixes(String...) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
setAllowedUriPrefixes(String...) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
setAllowedUriPrefixes(String...) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
setAllowedUriPrefixes(String...) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: List of URI prefixes to load from the ontology.
setAllowedUriPrefixes(String[]) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Set the URI prefixes that can be returned from the ontology.
setAllowMappingDesignElementsToGeneSymbols(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader: Allow mapping probe to gene symbols.
setAllowPositionalArguments() - Method in class ubic.gemma.cli.util.AbstractCLI: Allow positional arguments to be specified.
setAllowPredictedGenes(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setAllowSlicingColumns(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter: Sets whether to slice columns instead of masking them.
setAllowSubSeriesLoad(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setAllowSuperSeriesLoad(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setAllowSuperSeriesLoad(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setAllowUseExisting(boolean) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
setAllTracksOff() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig: Set to use no tracks.
setAllTracksOn() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig: Set to use all tracks, including ESTs
setAlreadyPresentInDatabase(boolean) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
setAlreadyPresentOnGene(boolean) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
setAlternateNames(Set) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setAlternativeTo(ArrayDesign) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setAnalysis(DifferentialExpressionAnalysis) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setAnalysis(DifferentialExpressionAnalysisValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
setAnalysisId(Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setAnalysisId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
setAnalysisId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
setAnalysisNotRun(boolean) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setAnalysisType(AnalysisType) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Type of analysis to perform.
setAnalysisType(AnalysisType) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: Proposed analysis type.
setAnchor(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setAnnotatedAbstract(String) - Method in class ubic.gemma.model.common.description.BibliographicReference: Deprecated.
setAnnotatedClasses(Class...) - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean: Register @Entity-annotated classes (typically test fixtures defined inline in a JUnit class).
setAnnotation(String) - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
setAnnotationRelationRowsWritten(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync
setAnnotations(List) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationsReplaceRequest
setAnnotations(List) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationsUpdateRequest
setAnnotations(Map) - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta: Free-form, gene-shaped annotation bag.
setAnnotations(Set) - Method in class ubic.gemma.model.common.description.BibliographicReference: Deprecated.
setAnnotations(Set) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor: Deprecated.
setAnnotationSet(AnnotationSet) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
setAnnotationSet(AnnotationSet) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
setAnnotationSet(AnnotationSet) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
setAnnotationSetId(Long) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationsReplaceRequest
setAnnotationSetStatus(Long, AnnotationSetsWebService.StatusRequest) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Set where a proposal stands with its reviewer.
setAnnotationValueObjects(Collection) - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
setApplicationContext(ApplicationContext) - Method in class ubic.gemma.cli.util.AbstractCLI
setApplicationContext(ApplicationContext) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceImpl
setApplied(boolean) - Method in class ubic.gemma.model.expression.experiment.DesignApplyOutcome
setArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
setArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
setArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskCommand
setArrayDesign(ArrayDesign) - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
setArrayDesign(ArrayDesignValueObject) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: The platform this assay was run on, serialized as ArrayDesignReferenceValueObject — id, shortName, name, technologyType.
setArrayDesign(ArrayDesignValueObject) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
setArrayDesignCount(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setArrayDesignId(Long) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setArrayDesignName(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setArrayDesignName(String) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setArrayDesignName(String) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setArrayDesigns(Collection) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: Platforms associated to the experiments.
setArrayDesigns(Collection) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: As a side effect, sets the technology type and taxon of this based on the first arrayDesign.
setArrayDesignShortName(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setArrayDesignsUsed(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
setArrayDesignsUsed(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
setArrayDesignUsed(ArrayDesign) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setArrayExpress(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setArrType(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
setAsNonSignficant(Long, Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject: Mark data as available, but not significant (so details will be missing).
setAssay(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setAssayDescription(String) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
setAssayName(String) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
setAssayProcessingDate(Date) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
setAssemblyDatabase(ExternalDatabase) - Method in class ubic.gemma.model.genome.Chromosome
setAssertedAt(Date) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setAssertedAt(Date) - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
setAssertedBy(String) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setAssertedBy(String) - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
setAssertedBy(String) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
setAssignee(Contact) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setAssigneeId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setAssigneeId(Long) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
setAssigneeId(Long) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setAssigneeId(Long) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setAssigneeName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setAssociatedExperimentCount(Integer) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: How many experiments "involve" (manipulate, etc.) this gene
setAssociation(PublicationAssociationValueObject) - Method in class ubic.gemma.model.common.description.DatasetPublicationValueObject
setAttribute(String) - Method in class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy: Set the attribute to retrieve to obtain the client ID.
setAuditEventService(AuditEventService) - Method in class ubic.gemma.core.scheduler.BatchInfoRepopulationJob
setAuditTrail(AuditTrail) - Method in class ubic.gemma.model.common.auditAndSecurity.AbstractAuditable
setAuditTrail(AuditTrail) - Method in interface ubic.gemma.model.common.auditAndSecurity.Auditable
setAuditTrail(AuditTrail) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setAuthenticateAnonymously() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI: Indicate that the command should authenticate anonymously, i.e.
setAuthentication(Authentication) - Method in interface ubic.gemma.cli.authentication.CLIAuthenticationAware
setAuthentication(Authentication) - Method in class ubic.gemma.cli.authentication.GemmaRestApiClientAuthenticator
setAuthentication(Authentication) - Method in class ubic.gemma.cli.logging.log4j.UserDetailsThreadContextPopulator
setAuthentication(Authentication) - Method in class ubic.gemma.cli.metrics.MeterRegistryCliConfigurer
setAuthentication(Authentication) - Method in interface ubic.gemma.core.util.GemmaRestApiClient: Set credentials used for authenticating API requests.
setAuthentication(Authentication) - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
setAuthenticator(FTPClientAuthenticator) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl: Set the authenticator to use to authenticate against FTP servers.
setAuthorities(Set) - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup
setAuthority(String) - Method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority
setAuthorList(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setAuthorList(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setAutoCorrectable(boolean) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setAutoFlush(boolean) - Method in interface ubic.gemma.core.datastructure.matrix.io.ExpressionDataMatrixWriter: Flush every time a complete line is written.
setAutoFlush(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.JsonMatrixWriter
setAutoFlush(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.MatrixWriter
setAutoFlush(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter
setAutoFlush(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
setAutoFlush(boolean) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter
setAutoFlush(boolean) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter
setAutoLoad(boolean) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Enable loading of ontologies on startup.
setAuxiliaryDatabaseObjects(AuxiliaryDatabaseObject...) - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean: DDL that the mapping cannot express, replayed against an hbm2ddl-built schema.
setAverage(double) - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
setAvoidDownload(boolean) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
setBackgroundSubtracted(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setBarcodeMetadataFileSuffix(String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
setBarcodesFileSuffix(String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
setBaseline(Boolean) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: Whether this factor value is a "forced" baseline condition.
setBaseline(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: null = leave the baseline flag unchanged.
setBaseline(String, String) - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
setBaseline(FactorValueBasicValueObject) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
setBaseline(DatasetsWebService.CurationBaseline) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setBaselineFactorValue(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setBaselineFactorValueId(Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setBaselineGroup(FactorValue) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setBaselineGroup(FactorValueBasicValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
setBaselineGroup(FactorValueValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
setBaselineRelevance(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Curator/agent hint about whether this factor warrants picking a baseline factor value.
setBaselineRelevance(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setBaselineRelevance(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject: Curator/agent hint about baseline relevance.
setBaselineRelevance(String) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Curator/agent hint about whether this factor warrants picking a baseline factor value — the write side of ExperimentalFactorValueObject.baselineRelevance, which was readable and unsettable until now (cab, 2026-09-04: the curation UI offers "Tick to override: no baseline" with a reason box and had nowhere to put the answer).
setBaselineRelevanceReason(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Free-text rationale paired with ExperimentalDesignValueObject.ExperimentalFactorEntry.baselineRelevance.
setBaselineRelevanceReason(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setBaselineRelevanceReason(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject: Free-text rationale paired with ExperimentalFactorValueObject.baselineRelevance.
setBaselineRelevanceReason(String) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Free-text rationale paired with DatasetsWebService.FactorCommit.baselineRelevance — what the curator typed in the reason box.
setBases(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
setBases(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
setBases(List) - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
setBases(SraBases) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setBasicFVs(boolean) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Indicate if this is using the BioMaterialValueObject.fVBasicVOs or BioMaterialValueObject.factorValueObjects for representing factor values.
setBasics(DatasetsWebService.CurationBasics) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setBasicsChanged(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setBasicsPresent(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setBasis(AnnotationRelationBasis) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setBatch(PipelineJobBatch) - Method in class ubic.gemma.model.pipeline.PipelineJob
setBatchConfound(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setBatchConfound(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setBatchCorrected(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setBatchCorrected(boolean) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setBatchEffect(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Batch effect type.
setBatchEffect(BatchEffectType) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setBatchEffectStatistics(double, int, double) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails: Set the batch effect statistics.
setBatchEffectStatistics(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setBatchEffectStatistics(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Summary statistics of a batch effect is present.
setBatchFetchEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setBeanFactory(BeanFactory) - Method in class ubic.gemma.rest.util.OpenApiFactory
setBin(Integer) - Method in class ubic.gemma.model.genome.PhysicalLocation
setBin(Integer) - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
setBinCounts(double[]) - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
setBioAssayDimension(BioAssayDimension) - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
setBioAssayDimension(BioAssayDimension) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setBioAssayDimension(BioAssayDimension) - Method in class ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector: A dimension of BioAssay the elements of this vector apply to.
setBioAssayDimension(BioAssayDimensionValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject: Represents the order of the bioassays for this.
setBioAssayId(Long) - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta
setBioAssayIds(Collection) - Method in class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
setBioAssayIds(Collection) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Related BioAssay IDs.
setBioAssayIds(List) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: A list of BioAssay IDs that are applicable to the cells.
setBioAssays(Collection) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setBioAssays(List) - Method in class ubic.gemma.core.visualization.SingleCellDataBoxplot
setBioAssays(List) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
setBioAssays(List) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: List of BioAssays applicable to the cells.
setBioAssays(Set) - Method in class ubic.gemma.model.expression.experiment.BioAssaySet
setBioAssays(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setBioAssays(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
setBioAssaysAnalyzed(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject: The BioAssays analyzed in this differential expression analysis.
setBioAssaysAnalyzed(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: List of BioAssays analyzed
setBioAssaySetAnalyzedId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Analyzed BioAssaySet ID.
setBioassayShortName(String) - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit: Deprecated.
use DatasetsWebService.SampleCharacteristicCommit.bioMaterialId, for the reasons on DatasetsWebService.FactorValueCommit.getBiomaterialShortNames().
setBioAssaysOffset(int[]) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Offsets of the BioAssay in SingleCellDimension.cellIds.
setBioAssaysUsedIn(Set) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setBioAssayToSampleNameMapper(BioAssayMapper) - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
setBioAssayToSampleNameMapper(BioAssayMapper) - Method in interface ubic.gemma.core.loader.expression.DataLoader: Set the strategy used for mapping BioAssay to sample names from the data.
setBioAssayToSampleNameMapper(BioAssayMapper) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
setBioAssayToSampleNameMapper(BioAssayMapper) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
setBioAssayToSampleNameMapper(BioAssayMapper) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
setBioAssayToSampleNameMapper(BioAssayMapper) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
setBiologicalCharacteristic(BioSequence) - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
setBioMartEnsemblNcbiFetcher(BiomartEnsemblNcbiFetcher) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
setBioMartFields(String[]) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
setBioMartFileName(File) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator: Set a biomart file name can be null if retrieving all taxons
setBioMaterialAssignments(List) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject: Many-to-many assignment of BioMaterials to FactorValues, materialized as a flat list.
setBioMaterialCount(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setBioMaterialId(Long) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
setBioMaterialId(Long) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.BioMaterialFactorValueAssignment
setBioMaterialId(Long) - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit: The sample this characteristic belongs to, by BioMaterial id.
setBioMaterialId(Long) - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta
setBiomaterialIds(List) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: Samples this value applies to, by BioMaterial id — the identifier GET /datasets/{id}/design already reports as bioMaterialAssignments[].bioMaterialId.
setBioMaterialName(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.BioMaterialFactorValueAssignment
setBioMaterialProvider(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setBiomaterialShortNames(List) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: Deprecated.
use DatasetsWebService.FactorValueCommit.biomaterialIds. Scheduled for removal — Paul, 2026-09-05: "as a choice of way to parameterize, we should not allow it, by removing that as an option for the endpoints. Deprecation is the right step now." Kept working meanwhile so no existing caller breaks.
A name is not an addressing form. It is not guaranteed to EXIST — a single-cell sub-bioassay has no accession of its own — and not guaranteed to be UNIQUE: on GEO-sourced single-cell data every sub-bioassay descends from one GSM, so that accession names fifteen samples rather than one. Such a name is now a 400 rather than an arbitrary pick.
An id, by contrast, always exists here: these endpoints never add or remove a dataset's samples, so every sample a commit can refer to was already persisted and already has one. That is what makes removal safe rather than merely desirable — there is no new-entity case for samples, and clientRef covers the entities a commit genuinely does create.
setBiomaterialsWithChangedAssignments(int) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
setBioSequence(BioSequence) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setBioSequence2GeneProduct(Set) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setBioSequenceId(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setBioSequenceName(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setBioSequenceNcbiId(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setBlackListed(Boolean) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setBlastHome(Path) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd: Override the BLASTDB environment variable.
setBlatResult(BlatResult) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
setBlatResult(BlatResultValueObject) - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
setBlatResult(BlatResultValueObject) - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummaryValueObject: The alignment this mapping rests on, carrying the scores (identity, score), the genomic coordinates, and the probe's biological sequence under querySequence.
setBlatResults(Collection) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
setBlatScoreThreshold(double) - Method in interface ubic.gemma.core.analysis.sequence.Blat: Set the blat score threshold to use.
setBlatScoreThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setBlatScoreThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
setBlockCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setBlockCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setBlockedReason(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setBlockers(List) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport: Hard validation errors.
setBlockSizes(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setBlockSizes(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setBody(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setBody(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: Curator-facing instructions text.
setBody(String) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
setBody(String) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setBody(String) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setBodyParts(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setBodyParts(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
setBrokerName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
setBuckets(List) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig: Ordered list of explicit buckets.
setByAnnotationCategory(Map) - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-category distinct-term counts.
setByKeys(R, C, Double) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
setByKeys(R, C, Integer) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
setByKeys(R, C, String) - Method in class ubic.gemma.core.util.matrix.StringMatrix
setByKeys(R, C, V) - Method in interface ubic.gemma.core.util.matrix.Matrix2D
setByKeys(R, C, V) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
setByPlatformType(Map) - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-platform-technology-type dataset counts.
setByTaxon(List) - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-taxon dataset counts, sorted descending by count.
setBytes(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
setCatalogNumbers(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setCategory(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Gemma's canonical category label (e.g.
setCategory(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat: Gemma's canonical category label carried on ExperimentalFactor.category (e.g.
setCategory(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Category label.
setCategory(String) - Method in class ubic.gemma.model.common.description.Characteristic
setCategory(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
setCategory(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
setCategory(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setCategory(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setCategory(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setCategory(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest.Item
setCategory(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setCategory(Characteristic) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setCategory(CharacteristicValueObject) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
setCategory(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
setCategory(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit
setCategory(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
setCategory(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
setCategoryDistribution(List) - Method in class ubic.gemma.core.analysis.report.HomeStats: Distribution of annotation categories observed across public datasets — the top-N categories Gemma actually uses, with the number of experiments each appears on.
setCategoryUri(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Ontology URI of the category, if any.
setCategoryUri(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat: Ontology URI of the category, if any.
setCategoryUri(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Category URI.
setCategoryUri(String) - Method in class ubic.gemma.model.common.description.Characteristic
setCategoryUri(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
setCategoryUri(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
setCategoryUri(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setCategoryUri(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setCategoryUri(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setCategoryUri(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setCellBrowserDatasetName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setCellBrowserUrl(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: URL for the Cell Browser, if available.
setCellCount(int) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setCellIds(List) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Cell identifiers.
setCellIds(List) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: Cell identifiers.
setCellLevelCharacteristics(Set) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Set of cell-level characteristics.
setCellLevelCharacteristics(Set) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: All the other cell-level characteristics.
setCellLevelCharacteristics(CellLevelCharacteristics) - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
setCellLevelCharacteristics(CellLevelCharacteristics) - Method in class ubic.gemma.core.visualization.SingleCellDataBoxplot
setCellRangerPrefix(Path) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation: Installation prefix of Cell Ranger.
setCellRangerPrefix(Path) - Method in interface ubic.gemma.core.loader.expression.singleCell.transform.CellRangerBasedTransformation: Set the installation prefix of Cell Ranger.
setCellSize(int) - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
setCellSize(int) - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
setCellSize(Dimension) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
setCellType(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setCellTypeAssignmentDescription(String) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
setCellTypeAssignmentName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
setCellTypeAssignmentProtocol(Protocol) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
setCellTypeAssignments(Set) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: All the cell type assignments.
setCellTypeAssignments(Set) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Set of cell types assignment to individual cells.
setCellTypeFactorName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: The name of the cell type factor under /var.
setCellTypeIds(List) - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: A list of IDs, one-per-cell, that refers to one of the cell type labels in CellTypeAssignmentValueObject.cellTypes.
setCellTypeIndices(int[]) - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Cell types assignment to individual cells from the CellTypeAssignment.cellTypes collections.
setCellTypes(List) - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: List of cell types.
setCellTypes(Set) - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: A set of cell types that are assigned to individual cells.
setCellTypeUriFactorName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: The name of the cell type URI factor under /var.
setCellXGeneAssays(Set) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Set the list of "supported" CELLxGENE gene expression assays.
setCellXGeneFetcher(CellXGeneFetcher) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
setCenterName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
setChannel(String) - Method in class ubic.gemma.core.logging.log4j.SlackAppender.Builder
setChannelNumber(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setCharacteristicIds(List) - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
setCharacteristicOriginalValues(Map) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Map of categories to original text values (for this biomaterial).
setCharacteristics(Collection) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
setCharacteristics(Collection) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
setCharacteristics(Collection) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setCharacteristics(List) - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
setCharacteristics(List) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The characteristics associated with this factor value.
setCharacteristics(Set) - Method in class ubic.gemma.model.analysis.Investigation
setCharacteristics(Set) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setCharacteristics(Set) - Method in class ubic.gemma.model.genome.gene.GeneSet
setCharacteristics(Set) - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
setCharacteristics(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setCharacteristics(Set) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setCharacteristicsRewritten(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
setCharacteristicsRewritten(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setCharacteristicValues(Map) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
setCharId(Long) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.

It could be the id of the measurement if there is no characteristic.
setCheckArchiveIntegrity(boolean) - Method in class ubic.gemma.core.util.SimpleDownloader: Set whether to check the integrity of gzipped files after downloading.
setChecked(boolean) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
setChemicals(Set) - Method in class ubic.gemma.model.common.description.BibliographicReference
setChemistry(String) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter: Chemistry to use for filtering data.
setChild(boolean) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: child term from a root
setChromosome(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setChromosome(String) - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
setChromosome(String) - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
setChromosome(Chromosome) - Method in class ubic.gemma.model.genome.ChromosomeLocation
setCitation(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setCitation(String) - Method in class ubic.gemma.model.common.description.CitationValueObject
setCitation(CitationValueObject) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setCity(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setCity(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
setClientIdRetrievalStrategy(ClientIdRetrievalStrategy) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Set the strategy used to retrieve client IDs.
setClientRef(String) - Method in class ubic.gemma.rest.DatasetsWebService.EntityRef
setClosedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
setCluster(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setClusterField(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setClusterName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setCoating(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setCode(String) - Method in class ubic.gemma.rest.TaskStatusValueObject.TaskError: Stable, machine-readable code.
setCoefficient(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setCoefficient(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
setCoexpressionMatrix(byte[]) - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
setCol(Integer) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
setCollapsedCount(int) - Method in class ubic.gemma.rest.CompactAuditEventValueObject
setCollection(boolean) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
setCollectionId(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setColNameMap(Map) - Method in class ubic.gemma.core.util.matrix.MatrixWriter: Use to customize the labels instead of relying on the toString method of the column object
setColor(int, int, Color) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
setColor(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Deprecated.
setColorMap(Color[]) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
setColorMap(Color[]) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
setColsCount(int) - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection
setColumnName(C, int) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
setColumnName(C, int) - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Add a column name associated with an index.
setColumnNames(List) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
setColumnNames(List) - Method in interface ubic.gemma.core.util.matrix.Matrix2D
setColumns(List) - Method in class ubic.gemma.rest.HeatmapDataValueObject: Optional.
setColumnsAfterOutliersFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setComment(String) - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
setComment(String) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setCommitAnnotationSetId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setCommonName(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
setCommonName(String) - Method in class ubic.gemma.model.genome.Taxon
setCommonName(String) - Method in class ubic.gemma.model.genome.TaxonValueObject
setCompletedAt(Date) - Method in class ubic.gemma.rest.TaskStatusValueObject
setCompleteness(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setComponentNumber(Integer) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
setComponentNumber(Integer) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
setComponentNumber(Integer) - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
setCompositeSequence(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
setCompositeSequence(CompositeSequenceValueObject) - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
setCompositeSequenceCount(Integer) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Number of probes (composite sequences) across all platforms that map to this gene.
setCompositeSequenceDescription(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setCompositeSequenceId(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setCompositeSequenceName(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setCompositeSequences(Set) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setConfidence(Double) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setConfidence(Double) - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
setConfidence(Double) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
setConfigLocation(Resource) - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
setConnectTimeout(Duration) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
setConsiderUris(List) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setConstructionProtocol(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
setContact(GeoContact) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
setContact(SraContact) - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
setContactName(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setContrasts(List) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
setContrasts(Set) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setContrasts(ContrastsValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setContrastsFactorValues(Map) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setContributer(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setContributors(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setControlTimeout(Duration) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
setCoordFiles(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
setCoords(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setCorrectedPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setCorrectedPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject: Rounded on the way out, as pValue is.
setCorrectedPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setCorrectedPValueBin(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setCorrespondingExperiments(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setCorrMatIssues(byte) - Method in class ubic.gemma.model.expression.experiment.Geeq
setCorrMatIssues(byte) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setCorrP(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setCount(int) - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
setCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat: Number of public expression experiments with this accession source.
setCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow: Public experiments whose creation event falls on or after HomeStats.AddedInWindow.since.
setCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
setCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat: Number of expression experiments carrying this term as a treatment annotation.
setCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Annotation-burden metric: Σ numberOfExpressionExperiments over each matched term — a popular drug used in 40 datasets contributes 40, not 1.
setCount(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraBase
setCount(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
setCountry(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setCountry(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
setCreatedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setCreatedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setCreatedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setCreatedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setCreateDate(Date) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setCreatedBy(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setCreatedBy(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setCriteria(Collection) - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
setCriteria(Collection) - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
setCriteriaApplied(String) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
setCsNative(boolean) - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
setCtx(OpenApiContext) - Method in class ubic.gemma.rest.util.OpenApiFactory
setCurationDetails(CurationDetails) - Method in interface ubic.gemma.model.common.auditAndSecurity.curation.Curatable
setCurationDetails(CurationDetails) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setCurationDetails(CurationDetails) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setCurationDetails(DatasetsWebService.CurationDetailsCommit) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setCurationDetailsNote(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setCurationDetailsPresent(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setCurationNote(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setCurationNote(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setCurationNote(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
setCurationNote(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
setCurationNote(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsUpdateRequest
setCurationNote(String) - Method in class ubic.gemma.rest.PipelineStatusValueObject: Admin-only; remains null for non-administrators.
setCurationNoteChanged(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setCurationPending(Boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject: Whether curation of the dataset is under way right now.
setCurrentAssignee(String) - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
setCurrentPassword(String) - Method in class ubic.gemma.rest.RootWebService.ChangePasswordRequest
setData(boolean[]) - Method in class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
setData(byte[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setData(double[]) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: The data of this vector.
setDataAsBooleans(boolean[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setDataAsChars(char[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setDataAsDoubles(double[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setDataAsFloats(float[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setDataAsInts(int[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setDataAsLongs(long[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setDataAsObjects(Object[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setDataAsStrings(String[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setDataAsTabbedStrings(String[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setDatabaseSupplier(Contact) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setDataIndices(int[]) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector: Positions of the non-zero data in the DataVector.getData() vector.
setDataProcessing(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setDataSet(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
setDatasetAssets(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setDatasetConstraint(String) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setDatasetConstraint(ExpressionExperiment) - Method in class ubic.gemma.model.common.search.SearchSettings: Constraint results to be related to the given dataset.
setDatasetCount(int) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
setDatasetCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Total public expression experiments.
setDatasetId(Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setDatasetId(Long) - Method in class ubic.gemma.rest.HeatmapDataValueObject
setDatasetId(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
setDatasetIds(List) - Method in class ubic.gemma.rest.DatasetsWebService.CurationLockBulkRequest
setDatasetIds(List) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetTicketsBulkRequest
setDatasetIds(List) - Method in class ubic.gemma.rest.DatasetsWebService.PipelineStatusBulkRequest
setDatasetLink(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setDatasetName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setDatasetQuantitationTypePreferred(DatasetArg, Long, DatasetsWebService.QuantitationTypePreferredRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Mark a QuantitationType as the preferred one (within its vector-type bucket) for the given dataset.
setDatasets(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
setDataSets(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setDatasetsAdded(List) - Method in class ubic.gemma.core.analysis.report.HomeStats: How many public experiments were added to Gemma over each of several trailing windows, newest window first.
setDatasetsByAccessionSource(List) - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-external-database dataset counts — GEO, ArrayExpress, CELLxGENE, etc., plus a "none" bucket for datasets without an external accession (direct lab submissions / Gemma-native).
setDatasetShortName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setDatasetShortName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: The dataset's short name (GSE6966), so a list row can name its experiment.
setDatasetShortName(String) - Method in class ubic.gemma.rest.HeatmapDataValueObject
setDatasetType(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setDataSource(DataSource) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterServiceImpl
setDataSource(DataSource) - Method in class ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategyImpl
setDataSource(DataSource) - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
setDataTimeout(Duration) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl
setDate(Date) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setDate(Date) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setDate(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setDate(Date) - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject
setDateArrayDesignLastUpdated(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: The date the platform associated with the experiment was last updated.
setDateBatchFetch(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDateCached(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setDateCached(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: The date this object was generated.
setDateCreated(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: When the dataset was created in Gemma — loaded, not published.
setDateDifferentialAnalysis(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDateLinkAnalysis(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDateMissingValueAnalysis(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDatePcaAnalysis(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDateProcessedDataVectorComputation(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDays(int) - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow: Width of the window in days (7, 30, 90, 365).
setDeaResultSetCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Total distinct differential-expression analysis result sets across public datasets.
setDebug(boolean) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Enable the debug mode.
setDecidedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
setDecidedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
setDecidedBy(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
setDecidedBy(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
setDecision(CurationDecisionType) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
setDecisionKey(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
setDefaultSymbol(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setDefaultToAll() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Default to all datasets if no options are provided.
setDefaultToPreferredQuantitationType() - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli: Use the preferred QT if no identifier is provided, otherwise process all the QTs.
setDefaultUnknownCellTypeIndicator(String) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: Declare an indicator that a subclass applies by convention to every dataset it reads.
setDeleteAfterUnpack(boolean) - Method in interface ubic.gemma.core.loader.util.fetcher.ArchiveFetcher: Should the downloaded archive be deleted after unpacking?
setDeleteAfterUnpack(boolean) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
setDeletedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setDeletedBy(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setDeletedIds(List) - Method in class ubic.gemma.rest.DatasetsWebService.Section
setDepartment(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setDescription(String) - Method in class ubic.gemma.core.job.progress.ProgressData
setDescription(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
setDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
setDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
setDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
setDescription(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
setDescription(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
setDescription(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
setDescription(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
setDescription(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
setDescription(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setDescription(String) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
setDescription(String) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setDescription(String) - Method in class ubic.gemma.model.analysis.ProtocolValueObject
setDescription(String) - Method in class ubic.gemma.model.common.AbstractDescribable
setDescription(String) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setDescription(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setDescription(String) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
setDescription(String) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject: Deprecated.
setDescription(String) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
setDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setDescription(String) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setDescription(String) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setDescription(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setDescription(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setDescription(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationBasics
setDescription(String) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetBasicsUpdateRequest
setDescription(String) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
setDescription(String) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setDescription(String) - Method in class ubic.gemma.rest.GroupsWebService.GroupCreateRequest
setDescription(String) - Method in class ubic.gemma.rest.GroupsWebService.GroupUpdateRequest
setDesign(SraExperimentDesign) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
setDesign(ExperimentalDesignValueObject) - Method in class ubic.gemma.model.expression.experiment.DesignApplyOutcome
setDesign(DatasetsWebService.DesignCommit) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setDesignAuditEventIds(List) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setDesignCreated(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setDesignDeleted(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setDesignElement(CompositeSequence) - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
setDesignElement(CompositeSequenceValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
setDesignElementCount(Integer) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setDesignElementId(Long) - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta
setDesignElementName(String) - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta
setDesignElementsAfterLowVariance(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Number of design elements left after filtering for low variance.
setDesignElementsAfterMinimumCells(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Number of design elements left after filtering for minimum number of cells.
setDesignElementsAfterOutliers(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
setDesignElementsAfterRepetitiveValues(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Number of design elements left after filtering for repetitive values.
setDesignElementToGeneMapper(DesignElementMapper) - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
setDesignElementToGeneMapper(DesignElementMapper) - Method in interface ubic.gemma.core.loader.expression.DataLoader: Set the strategy used for mapping CompositeSequence to gene identifiers from the data.
setDesignElementToGeneMapper(DesignElementMapper) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
setDesignElementToGeneMapper(DesignElementMapper) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
setDesignElementToGeneMapper(DesignElementMapper) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
setDesignIdMap(Map) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setDesignPlan(DesignCommitPlan) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setDesignPresent(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setDesignProvider(Contact) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setDesignUnchanged(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setDesignUpdated(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setDetail(String) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setDetailsIncomplete(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord: True when the detailed MINiML fetch for this record failed and was tolerated (GeoRetrieveConfig.isIgnoreErrors()), so the record is returned with whatever the eutils summary gave and without sample details.
setDetectedQualityScore(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setDetectedQualityScore(double) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setDevelopmentStage(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setDiagnosticsOnly(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand: If true, we'll try to just update the diagnostics (M-V, PCA and sample correlation)
setDifferentialAnalysisEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDifferentialExpressionAnalyses(Collection) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDifferentialExpressionAnalysesToDelete(int) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
setDifferentialExpressionAnalysesToDelete(List) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport
setDiffValCount(int) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
setDirection(Direction) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setDirection(Direction) - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
setDiscardEmptyCells(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader: Discard empty cells by removing columns from MTX file that have no gene-associated counts.
setDiscontinuedId(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setDisease(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setDiseases(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setDiseases(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
setDisplayLabel(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject: Short display label for the target (e.g.
setDisplayName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject: Human-readable name for the target (e.g.
setDisplayRange(double, double) - Method in class ubic.gemma.core.util.graphics.ColorMatrix: Standardized display range
setDisplayRange(double, double) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
setDisposition(FindingDisposition) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
setDistinctAccessionCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Distinct external accessions across all public EEs.
setDistribution(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setDoDownload(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
setDoDownload(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
setDoi(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: DOI of the primary publication, when it is a preprint or otherwise identified by a DOI rather than a PubMed ID.
setDoi(String) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
setDone(boolean) - Method in class ubic.gemma.core.job.progress.ProgressData
setDonorId(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setDoSampleMatching(boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
setDownloadDirectory(Path) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector: Set the download directory to use for storing single-cell data.
setDownloadDirectory(Path) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Directory where single-cell data is downloaded.
setDownloadDirectory(Path) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Set the download directory single-cell data.
setDownloads(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
setDownregulatedCount(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Number of diffex probes in the Direction.DOWN hit list if available.
setDropIfExists(boolean) - Method in class ubic.gemma.persistence.initialization.CreateDatabasePopulator
setDrugCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Distinct CHEBI-anchored drug / chemical annotations in use (characteristics whose valueUri starts with http://purl.obolibrary.org/obo/CHEBI_).
setDryRun(boolean) - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
setDryRun(boolean) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
setDryRun(boolean) - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
setDueDate(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setDueDate(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setDueDate(Date) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setDueDate(Date) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setDummy(boolean) - Method in class ubic.gemma.model.genome.gene.GeneProduct
setEditable(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
setEditor(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setEe2cRowsWritten(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync
setEeId(Long) - Method in class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
setEfId(Long) - Method in class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
setEigenValues(Set) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setEigenVectors(Set) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setElementLimitForStrictness(int) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
setElementLimitForStrictness(int) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
setEmail(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setEmail(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
setEmail(String) - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
setEmail(String) - Method in class ubic.gemma.model.common.auditAndSecurity.Contact
setEmailAlert(boolean) - Method in class ubic.gemma.core.job.TaskCommand: Should an email be sent to the user when the job is done?
setEnableAuthorities(boolean) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
setEnabled(boolean) - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
setEnabled(boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setEnabled(Boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
setEnabled(Boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
setEnableGroups(boolean) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
setEnableSearch(boolean) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Enable full-text search for the ontology.
setEncoding(String) - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection
setEndPosition(Long) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setEndTime(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setEnsemblGeneId(String) - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
setEnsemblId(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setEnsemblId(String) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setEnsemblId(String) - Method in class ubic.gemma.model.genome.Gene
setEnsemblPeptideId(String) - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
setEnsemblTranscriptId(String) - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
setEntityId(Long) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
setEntityId(Long) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
setEntries(Set) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
setEntriesInheriting(boolean) - Method in class ubic.gemma.core.security.acl.domain.AclImpl
setEntriesInheriting(boolean) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
setEnvironment(Environment) - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI
setError(Exception) - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
setError(TaskStatusValueObject.TaskError) - Method in class ubic.gemma.rest.TaskStatusValueObject: Structured failure detail.
setErrorFound(boolean) - Method in class ubic.gemma.model.common.BaseValueObject
setErrorMessage(String) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
setErrorMessage(String) - Method in class ubic.gemma.model.pipeline.PipelineJob
setEstimatedMaxTasks(int) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter: Set the maximum number of tasks that are expected to be run.
setEstimatedMaxTasks(int) - Method in class ubic.gemma.cli.util.AbstractCLI: Set the estimated maximum number of batch tasks to be processed.
setEvents(List) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
setEvents(List) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setEvents(List) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setEvents(Set) - Method in class ubic.gemma.model.pipeline.PipelineJob
setEventType(Class) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setEventType(String) - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject: Simple class name of the audit event type (ExpressionExperimentUpdateFromGEOEvent, DifferentialExpressionAnalysisEvent, …).
setEventType(String) - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: Simple class name of the latest audit event (BatchInformationFetchingEvent, FailedPCAAnalysisEvent, etc.).
setEvidence(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setEvidence(String) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setEvidence(String) - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
setEvidence(String) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
setEvidenceCode(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setEvidenceCode(String) - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
setEvidenceCode(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: How this statement was arrived at, as a GOEvidenceCode name (IC, IEA, IIA, TAS, …).
setEvidenceCode(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setEvidenceCode(String) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
setEvidenceCode(String) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit: How this statement was arrived at, as a GOEvidenceCode name.
setEvidenceCode(String) - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit: How this tag was arrived at, as a GOEvidenceCode name.
setEvidenceCode(GOEvidenceCode) - Method in class ubic.gemma.model.association.Gene2GOAssociation
setEvidenceCode(GOEvidenceCode) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setEvidenceCode(GOEvidenceCode) - Method in class ubic.gemma.model.common.description.Characteristic
setEvidenceCode(GOEvidenceCode) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setExactIdentifierMatch(boolean) - Method in class ubic.gemma.model.common.search.SearchResult: Whether this result was produced by an exact-identifier lookup (numeric id, short name, accession, NCBI id).
setExactLabel(Boolean) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setExceptionType(String) - Method in class ubic.gemma.rest.TaskStatusValueObject.TaskError: Simple class name of the underlying exception, for diagnostics.
setExcludedWordsFromStemming(Set) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
setExcludedWordsFromStemming(Set) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
setExcludedWordsFromStemming(Set) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
setExcludedWordsFromStemming(Set) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Set words that should be excluded from stemming when searching.
setExcludedWordsFromStemming(Set) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Set the list of words that should be excluded from stemming.
setExcludePattern(String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
setExcludeSampleIdentifiers(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.MatrixWriter: Only include bioassays in the formed column name instead of prepending it with the sample name.
setExcludeSampleIdentifiers(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
setExecutableName(String) - Method in class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator: Suffix to append to each page name.
setExecutorService(Executor) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter: Executor to use to write MEX files in parallel.
setExistingExperimentId(Long) - Method in class ubic.gemma.rest.TaskStatusValueObject.TaskError: For ALREADY_EXISTS, the id of the experiment that already holds the accession, when resolvable.
setExitStatus(int, Exception) - Method in interface ubic.gemma.cli.util.CLIContext
setExitStatus(int, Exception) - Method in class ubic.gemma.cli.util.SystemCLIContext
setExons(Set) - Method in class ubic.gemma.model.genome.gene.GeneProduct: Only used for transient instances, we do not store exon locations in the database.
setExpectedLastUpdated(Date) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setExperiment(SraExperiment) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
setExperiment(ExpressionExperiment) - Method in class ubic.gemma.model.pipeline.PipelineJob
setExperimentalDesign(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setExperimentalDesign(ExperimentalDesign) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setExperimentalDesign(ExperimentalDesign) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setExperimentalDesignDescription(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
setExperimentalDesignName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
setExperimentalFactor(ExperimentalFactor) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setExperimentalFactorCategory(CharacteristicValueObject) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The experiment factor category.
setExperimentalFactorId(Long) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The ID of the experimental factor this factor value belongs to.
setExperimentalFactors(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
setExperimentalFactors(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setExperimentalFactors(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
setExperimentalFactors(List) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
setExperimentalFactors(Set) - Method in class ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet
setExperimentalFactors(Set) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setExperimentalFactorType(String) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The experimental factor type.
setExperimentAnalyzed(T) - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis
setExperimentAnalyzedId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
setExperimentAnalyzedId(Long) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject: The ID of the experiment analyzed which is either an ExpressionExperiment or an ExpressionExperimentSubSet.
setExperimentCount(long) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setExperimentId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
setExperimentId(Long) - Method in class ubic.gemma.rest.PipelineStatusValueObject
setExperimentId(Long) - Method in class ubic.gemma.rest.TaskStatusValueObject: Identifier of the experiment the task is operating on, when derivable from the task command.
setExperimentPackages(List) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackageSet
setExperiments(Collection) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setExperiments(Set) - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
setExperimentsAffected(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
setExperimentsAffected(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setExperimentsResynced(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync
setExperimentType(GeoDataset.ExperimentType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setExpiresAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
setExpressionExperiment(BioAssaySetValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setExpressionExperiment(BioAssaySetValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.expression.GeeqTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
setExpressionExperimentCount(Long) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setExpressionExperimentId(Long) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject: Associated expression experiment ID.
setExpressionExperimentIds(Collection) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setExpressionExperimentReportService(ExpressionExperimentReportService) - Method in class ubic.gemma.core.scheduler.BatchInfoRepopulationJob
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.core.scheduler.BatchInfoRepopulationJob
setExpressionExperimentSets(Collection) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: EE sets this experiment is part of.
setExternalAccession(DatabaseEntry) - Method in class ubic.gemma.model.blacklist.BlacklistedEntity
setExternalAccession(DatabaseEntry) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setExternalDatabase(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setExternalDatabase(ExternalDatabase) - Method in class ubic.gemma.model.common.description.DatabaseEntry
setExternalDatabase(ExternalDatabase) - Method in class ubic.gemma.model.genome.Taxon
setExternalDatabase(ExternalDatabaseValueObject) - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
setExternalDatabase(ExternalDatabaseValueObject) - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
setExternalDatabase(ExternalDatabaseValueObject) - Method in class ubic.gemma.model.genome.TaxonValueObject
setExternalDatabaseId(Long) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
setExternalDatabaseName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
setExternalDatabases(Set) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setExternalDatabases(Set) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
setExternalDatabaseUri(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setExternalIds(List) - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
setExternalIssueSyncState(ExternalIssueSyncState) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setExternalIssueSyncState(ExternalIssueSyncState) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setExternalIssueUrl(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setExternalIssueUrl(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setExternalLabel(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setExternalReferences(Set) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setExternalReferences(Set) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Main external reference.
setExternalUri(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setExtractedMolecule(ExtractedMolecule) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setExtractedMolecule(ExtractedMolecule) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: What was extracted from the sample and assayed — GEO's molecule.
setExtractProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setExtraMissingValueIndicators(Collection) - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
setFactor(ExperimentalFactorValueObject) - Method in class ubic.gemma.rest.HeatmapDataValueObject.FactorEntry: Full factor VO: id, name, description, type, category(+Uri), values (with statements + is_baseline + measurement), baseline_relevance, baseline_relevance_reason.
setFactorCategory(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setFactorCount(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setFactorCount(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: Derived hint; null means unknown, never zero.
setFactorDescription(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setFactorId(Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setFactorId(Long) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
setFactorId(Long) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.

ID of the experimental factor this FV belongs to.
setFactorIds(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
setFactorIds(List) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialAnalysisRunRequest
setFactorIdToFactorValueId(Map) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Map of factor ids (factor232) to factor value (id or the actual value) for this biomaterial.
setFactorName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setFactors(Collection) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: The factors to actually use in the analysis.
setFactors(List) - Method in class ubic.gemma.rest.HeatmapDataValueObject: Optional.
setFactors(DatasetsWebService.Section) - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit
setFactorsToCreate(int) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
setFactorsToDelete(int) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
setFactorsToDelete(List) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport
setFactorsToUpdate(int) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
setFactorsToUpdate(List) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport: Kept factors whose name, description or category the proposal rewrites.
setFactorValue(FactorValue) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setFactorValue(FactorValueBasicValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
setFactorValueId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
setFactorValueId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
setFactorValueId(Long) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
setFactorValueIds(List) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.BioMaterialFactorValueAssignment
setFactorValueIds(Map) - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta: factorId -> factorValueId.
setFactorValueObjects(Collection) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
setFactorValues(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject: Deprecated.
setFactorValues(Map) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Map of ids (fv133) to a representation of the value (for this biomaterial.)
setFactorValues(Set) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setFactorValues(Set) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setFactorValues(DatasetsWebService.Section) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
setFactorValuesByCategory(List) - Method in class ubic.gemma.core.analysis.report.HomeStats: Distinct factor-value count per ExperimentalFactor category.
setFactorValuesToCreate(int) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
setFactorValuesToDelete(int) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
setFactorValuesToDelete(List) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport
setFactorValuesToUpdate(int) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
setFactorValuesToUpdate(List) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport: Kept factor values the proposal edits in place: a statement re-termed, evidence attached, the baseline flag flipped, a measurement retimed, the deprecated free-text value rewritten.
setFactorValuesUsed(Map) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
setFailed(boolean) - Method in class ubic.gemma.core.job.progress.ProgressData
setFailedMessage(String) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setFastqHeaders(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setFastqHeaders(String) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
setFastqHeadersDir(Path) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationService: Set the path to use to resolve FASTQ headers.
setFastqHeadersDir(Path) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl
setFastWarningThresholdMillis(int) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
setFax(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setFeatureCount(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setFeaturesFileSuffix(String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
setFileLockManager(FileLockManager) - Method in class ubic.gemma.core.loader.util.fetcher2.AbstractFetcher: Set the file lock manager to use for managing locks on downloaded files.
setFileLockManager(FileLockManager) - Method in class ubic.gemma.core.util.SimpleDownloader
setFilename(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setFiles(List) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFiles
setFiles(SraFiles) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setFileSize(long) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
setFiletype(FileType) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
setFillResults(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Indicate if result objects (i.e.
setFilter(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
setFilterAttrition(SampleCorrelationAnalysisPayload) - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: How many design elements and samples each filter removed while the step ran, and the filter settings that produced those numbers.
setFinalColumns(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setFinalDesignElements(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Final number of design elements.
setFinalizedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setFinalizedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setFinalizedBy(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setFinalizedBy(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setFinalizedNotes(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setFinalRows(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setFinalSamples(Set) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Final set of samples.
setFindingId(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
setFinishedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJob
setFirstBuildTipe(Date) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setFirstName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
setFirstQuartile(double) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
setFisherContribution(Boolean) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setFisherPValue(Double) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setFixed(boolean) - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
setFocusedCellLevelCharacteristic(Characteristic) - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
setFocusedCharacteristic(Characteristic) - Method in class ubic.gemma.core.visualization.SingleCellDataBoxplot
setFont(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Font to use when rendering diagnostic plots, etc.
setForce() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Enable the forcing mode.
setForce(boolean) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher: Set to true if downloads should proceed even if the file already exists.
setForce(boolean) - Method in interface ubic.gemma.core.loader.util.fetcher.Fetcher: Set whether existing files should be overwritten.
setForce(boolean) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
setForceAnalysis(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setForceAnalysis(boolean) - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
setForceConvertElements(boolean) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
setForceConvertElements(boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
setForceIndexing(boolean) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Force indexing for full-text search.
setForceLoad(boolean) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Force loading, regardless of the load.{name}Ontology property value.
setForwardingURL(String) - Method in class ubic.gemma.core.job.progress.ProgressData
setFractionRepeats(Double) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setFractionRepeats(Double) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setFreeTextIntended(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit: Declares that this tag is meant to be free text — no value.uri — on purpose.
setFreeTextLabel(String) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: The value's human-readable label.
setFromLabel(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setFromUri(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setFtpClientFactory(FTPClientFactory) - Method in class ubic.gemma.core.loader.util.fetcher2.AbstractFetcher: Set the FTP client factory to use for downloading files over FTP.
setFtpClientFactory(FTPClientFactory) - Method in class ubic.gemma.core.util.SimpleDownloader: Set the factory for creating FTP clients.
setFTPClientFactory(FTPClientFactory) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector: Set the FTP client factory to use for downloading data over FTP.
setFTPClientFactory(FTPClientFactory) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Set the FTPClient factory used to create FTP connection to retrieve supplementary materials.
setFtpUri(String) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setFullCoexpressionMatrix(SampleCoexpressionMatrix) - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis
setFullName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
setFullTextUri(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setFVBasicVOs(Collection) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: 🛑 This field's JsonIgnore does not hide it: the payload carries an fvbasicVOs key regardless.
setGeeq(Geeq) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setGeeq(GeeqValueObject) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setGeeq(GeeqValueObject) - Method in class ubic.gemma.rest.PipelineStatusValueObject
setGemmaId(Long) - Method in class ubic.gemma.rest.DatasetsWebService.EntityRef
setGene(Gene) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setGene(Gene) - Method in class ubic.gemma.model.association.Gene2GOAssociation
setGene(Gene) - Method in class ubic.gemma.model.genome.gene.GeneProduct
setGene(Gene) - Method in class ubic.gemma.model.genome.gene.GeneSetMember
setGene(GeneValueObject) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setGene(GeneValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setGene2GOAssociationReadService(Gene2GOAssociationReadService) - Method in interface ubic.gemma.core.ontology.GoMetric
setGene2GOAssociationReadService(Gene2GOAssociationReadService) - Method in class ubic.gemma.core.ontology.GoMetricImpl
setGeneCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Number of distinct genes in the database.
setGeneCountMaxTerms(Integer) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setGeneCountsLastUpdated(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: When the report backing ArrayDesignValueObject.numberOfGenes / ArrayDesignValueObject.numberOfMappedElements was written, as yyyy.MM.dd HH:mm.
setGeneId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setGeneId(Long) - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
setGeneId(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setGeneId(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setGeneIds(Collection) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject: Gene IDs part of this gene set.
setGeneInfo(NCBIGeneInfo) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
setGeneManipulatedCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Distinct genes annotated as manipulation targets across the corpus — characteristics whose valueUri starts with Gene.NCBI_URI_PREFIX AND whose own categoryUri is genotype.
setGeneManipulatedExperimentCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Companion to HomeStats.geneManipulatedCount: number of distinct experiments carrying at least one genotype-category gene-URI annotation.
setGeneMappingSummaries(List) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Per-alignment gene mappings for this element, or null when the caller did not ask for them (only GET /platforms/{platform}/elements/{probe}/mappingSummary populates this).
setGeneName(String) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
setGeneOntologyService(GeneOntologyService) - Method in interface ubic.gemma.core.ontology.GoMetric
setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.core.ontology.GoMetricImpl
setGenePix(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setGeneProduct(GeneProduct) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setGeneProductMap(Map) - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary
setGeneProducts(Collection) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
setGeneProducts(Map) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setGeneralType(String) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setGeneralType(GeneralType) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
setGeneralType(GeneralType) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setGeneralType(GeneralType) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setGeneratedAt(Date) - Method in class ubic.gemma.core.analysis.report.HomeStats: When the snapshot was last refreshed (ISO-8601 in JSON via default Jackson).
setGeneratedAt(Date) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setGenes(Collection) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
setGenes(Collection) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
setGenes(List) - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummaryValueObject: Genes this alignment supports, deduplicated — a gene reached through several of its gene products appears once.
setGenes(List) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Compact identities of the genes this element maps to, via the denormalized GENE2CS table.
setGenes(List) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
setGenes(List) - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta: Genes mapped to this probe.
setGenes(Map) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setGeneService(GeneService) - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService
setGeneSets(Collection) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Gene sets this gene belongs to, in their light form (no members).
setGenesFileSuffix(String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
setGeneSymbol(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat: Canonical Gemma gene symbol (e.g.
setGeneSymbol(String) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
setGeneType(NCBIGeneInfo.GeneType) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setGeneWriteService(GeneWriteService) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
setGenome(String) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter: Genome identifier to use.
setGenomePersister(GenomePersister) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoader: Persister-shrink S3: was setPersisterHelper(Persister); now takes the typed GenomePersister bean directly.
setGenomicNucleotideAccession(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setGenomicNucleotideAccessionVersion(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setGenomicNucleotideGI(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setGeoAccession(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
setGeoDomainObjectGenerator(GeoDomainObjectGenerator) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService
setGeoDomainObjectGenerator(GeoDomainObjectGenerator) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
setGeoSeries(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
setGoId(String) - Method in class ubic.gemma.model.genome.gene.GOGroupValueObject
setGoId(String) - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
setGrantedAuthority(String) - Method in class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
setGranting(boolean) - Method in class ubic.gemma.core.security.acl.domain.AclEntry
setGrantOnTransient(boolean) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter: Set whether to grant access to transient objects or simply abstain.
setGrantOnTransient(boolean) - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoter: Set whether to grant access to transient objects or simply abstain.
setGroup(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Coarse UI grouping carried through from the bucket spec — control, pharmacology, biological, unclassified.
setGroup(String) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Coarse UI grouping.
setGroupDescription(String, String) - Method in interface ubic.gemma.core.security.authentication.GroupManager: Update the human-readable description of a group.
setGroupDescription(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
setGroupMembers(Set) - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup
setGroupName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
setGroups(Set) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setGrowthProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setHasBatchInformation(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: FIXME: rename this to hasUsableBatchInformation
setHasBatchInformation(boolean) - Method in class ubic.gemma.rest.PipelineStatusValueObject
setHasBlatAssociations(Boolean) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setHasBothIntensities(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasCellBrowser(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Indicate if this experiment has a Cell Browser associated with it.
setHasCoexpressionAnalysis(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasCoexpressionAnalysis(boolean) - Method in class ubic.gemma.rest.PipelineStatusValueObject
setHasDifferentialExpressionAnalysis(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasDifferentialExpressionAnalysis(boolean) - Method in class ubic.gemma.rest.PipelineStatusValueObject
setHasEitherIntensity(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Indicate if the experiment has any intensity information available.
setHasFile(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
setHasFiles(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setHasGeneAssociations(Boolean) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setHasMultiplePreferredQuantitationTypes(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasMultipleTechnologyTypes(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasSequenceAssociations(Boolean) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setHgnc_id(String) - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
setHibernateProperties(Properties) - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean
setHighExpressionCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: High cut for expression.
setHistory(NcbiGeneHistory) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setHitListSizes(Set) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setHomologues(Collection) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Homologues of this gene across taxa.
setHost(String) - Method in class ubic.gemma.core.util.NetDatasourceUtil
setHybProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setId(long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
setId(Long) - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
setId(Long) - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
setId(Long) - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
setId(Long) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
setId(Long) - Method in class ubic.gemma.core.security.acl.domain.AclEntry
setId(Long) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
setId(Long) - Method in class ubic.gemma.core.security.acl.domain.AclSid
setId(Long) - Method in class ubic.gemma.model.analysis.AnalysisResultSet
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setId(Long) - Method in class ubic.gemma.model.common.AbstractIdentifiable
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setId(Long) - Method in class ubic.gemma.model.common.description.CitationValueObject: The ID of the BibliographicReference being represented.
setId(Long) - Method in interface ubic.gemma.model.common.GemmaSessionBackedValueObject
setId(Long) - Method in class ubic.gemma.model.common.IdentifiableValueObject: Only used by the spring java-beans in jsp files.
setId(Long) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: Gemma-internal platform id, suitable for GET /platforms/{id}.
setId(Long) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
setId(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject: Gemma-internal dataset id, suitable for GET /datasets/{id}.
setId(Long) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
setId(Long) - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject: Gemma-internal gene id, suitable for GET /genes/{id}.
setId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
setId(Long) - Method in class ubic.gemma.rest.HeatmapDataValueObject.GeneRef
setId(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
setId(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
setId(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setId(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setId(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setId(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExternalId
setId(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
setId(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
setIdentifier(Long) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
setIdentifiers(SraIdentifiers) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
setIdentifiers(SraIdentifiers) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
setIdentifiers(SraIdentifiers) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setIdentifiers(SraIdentifiers) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
setIdentity(Double) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setIdentityThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setIgnoreCellTypeFactor(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: Ignore cell type assignment.
setIgnoreDataVectors(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: Explicitly ignore data vectors.
setIgnoreDataVectors(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader: Explicitly ignore data vectors.
setIgnoreFailingSubsets(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Keep processing other subsets when encountering an AnalysisException on a subset.
setIgnoreMinimumDesignElementsThreshold(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: If true, the ExpressionExperimentFilter.MINIMUM_DESIGN_ELEMENTS is ignored.
setIgnoreMinimumSamplesThreshold(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: If true, ExpressionExperimentFilter.MINIMUM_SAMPLES is ignored.
setIgnoreUnmatchedCellIds(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
setIgnoreUnmatchedCellIds(boolean) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixReader: Ignore cell identifiers in the header for which no assay can be found instead of throwing an exception.
setIgnoreUnmatchedDesignElements(boolean) - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
setIgnoreUnmatchedDesignElements(boolean) - Method in interface ubic.gemma.core.loader.expression.DataLoader: Ignore unmatched design elements from the data when creating vectors.
setIgnoreUnmatchedDesignElements(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
setIgnoreUnmatchedDesignElements(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
setIgnoreUnmatchedDesignElements(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
setIgnoreUnmatchedGenes(boolean) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixReader: Ignore gene identifiers in the "gene" column for which no design element can be found instead of throwing an exception.
setIgnoreUnmatchedSamples(boolean) - Method in class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
setIgnoreUnmatchedSamples(boolean) - Method in interface ubic.gemma.core.loader.expression.DataLoader: Ignore unmatched samples from the data.
setIgnoreUnmatchedSamples(boolean) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadataFileDataLoader
setIgnoreUnmatchedSamples(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader
setIgnoreUnmatchedSamples(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader: Ignore unmatched samples from the data.
setIgnoreUnmatchedSamples(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader
setIgnoreUnmatchedSamples(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
setImmobilizedCharacteristic(BioSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
setInCategory(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setIncludedResultSetsInfo(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
setIncludeGeneCount(Boolean) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setIncludeGenes(Boolean) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setIncludeInteractions(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: Whether interactions among the factors should be included.
setIncludeInteractions(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialAnalysisRunRequest
setIncludeTaxon(boolean) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setIndex(int) - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
setIndexBioSequences(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexDatasetGroups(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexDatasets(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexDesignElements(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexGeneGroups(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexGenes(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexPlatforms(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexPublications(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndices(int[]) - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
setInferenceMode(OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
setInferenceMode(OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
setInferenceMode(OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
setInferenceMode(OntologyService.InferenceMode) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Set the inference mode used for this ontology.
setInferenceMode(OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Set the inference mode for the ontology.
setInferSamplesFromCellIdsOverlap(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
setInfo(NCBIGeneInfo) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setInObject(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setInPredicate(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setInputFile(Path) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter
setInputFile(Path, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedAnnDataTransformation
setInputFile(Path, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter
setInputFile(Path, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationPipeline
setInputFile(Path, SingleCellDataType) - Method in interface ubic.gemma.core.loader.expression.singleCell.transform.SingleCellInputOutputFileTransformation
setInstitute(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setInstrumentModel(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: Verbatim !Sample_instrument_model, e.g.
setInstrumentModel(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPlatform
setInstrumentPlatform(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPlatform
setInValue(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setInvestigation(Investigation) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setInvestigation(Investigation) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
setInvestigation(Investigation) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
setInvestigation(Investigation) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setInvestigationId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setIsAffymetrixAltCdf(Boolean) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setIsAggregated(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsApproximateLength(Boolean) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setIsArrayExpress(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setIsBackground(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsBackground(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setIsBackgroundSubtracted(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsBackgroundSubtracted(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setIsBaseline(Boolean) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setIsBatchCorrected(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsBatchCorrected(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setIsBatchCorrected(Boolean) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
setIsCircular(Boolean) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setIsGenesUsable(boolean) - Method in class ubic.gemma.model.genome.Taxon
setIsGenesUsable(Boolean) - Method in class ubic.gemma.model.genome.TaxonValueObject: Whether Gemma has gene records loaded for this taxon — a loader-maintained capability bit, written false at creation and flipped by NcbiGeneLoader.updateTaxaWithGenesUsable once genes actually land.
setIsMajorTopic(Boolean) - Method in class ubic.gemma.model.common.description.BibRefAnnotation
setIsMaskedPreferred(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType: Deprecated.
setIsMaskedPreferred(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject: Deprecated.
setIsMerged(Boolean) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Indicates this array design is the merger of other array designs.
setIsMergee(Boolean) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Indicates that this array design has been merged into another.
setIsNormalized(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsNormalized(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setIsOutlier(boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setIsPaired(Boolean) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata: Whether the reads are paired.
setIsPreferred(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsPreferred(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setIsPreferred(boolean, Class) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType: Set the preferred status for a particular vector type.
setIsPreferred(Boolean) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
setIsProbeOmitted(boolean) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
setIsPublic(boolean) - Method in interface ubic.gemma.core.security.model.SecureValueObject
setIsPublic(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setIsPublic(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setIsPublic(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setIsPublic(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setIsPublic(boolean) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setIsPublic(boolean) - Method in class ubic.gemma.rest.PipelineStatusValueObject
setIsPublic(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.PermissionsUpdateRequest
setIsQuery(Boolean) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Was this gene directly used in a query? Or is it inferred somehow.
setIsRatio(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsRatio(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setIsRatio(Boolean) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
setIsRecomputedFromRawData(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsRecomputedFromRawData(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setIsRNASeq(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setIsShared(boolean) - Method in interface ubic.gemma.core.security.model.SecureValueObject
setIsShared(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setIsShared(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setIsShared(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setIsShared(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setIsShared(boolean) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setIsSingleCell(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setIsSingleCellPreferred(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsSingleCellPreferred(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setIsSpecies(Boolean) - Method in class ubic.gemma.model.genome.TaxonValueObject
setIsSubSeries(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setIsSubset(boolean) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
setIsSubsumed(Boolean) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Indicate if this array design is subsumed by some other array design.
setIsSubsumer(Boolean) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Indicates if this array design subsumes some other array design(s)
setIssue(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setIssue(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setIsSuperSeries(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setItems(List) - Method in class ubic.gemma.rest.DatasetsWebService.Section
setJob(PipelineJob) - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
setJobs(Set) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setJobs(Set) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
setJudgedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
setJudgedBy(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
setJudgeKind(TriageJudgeKind) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
setJudgeKind(TriageJudgeKind) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
setJudgeKind(TriageJudgeKind) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
setKey(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Stable lowercase-snake-case label used in byAnnotationCategory (e.g.
setKey(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Stable lowercase-snake-case identifier the frontend matches in code — e.g.
setKey(String) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Stable lowercase-snake-case identifier the frontend matches in code.
setKeywords(Set) - Method in class ubic.gemma.model.common.description.BibliographicReference
setKeyWords(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setKillRequestedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
setKind(String) - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
setKind(AgentCurationKind) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setKind(AgentCurationKind) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setKindCV(MeasurementKind) - Method in class ubic.gemma.model.common.measurement.Measurement
setLabel(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat: Curator-visible label (the Characteristic.value).
setLabel(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Visitor-facing label with the canonical phrasing.
setLabel(String) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Visitor-facing label (canonical phrasing).
setLabel(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
setLabel(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setLabel(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
setLabel(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setLabel(String) - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject: A label for display purposes.
setLabel(String) - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
setLabel(String) - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermRef
setLabel(String) - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject
setLabelField(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setLabelMd5(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setLabelProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setLabelsVisible(boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay: If this display component has already been added to the GUI, it will be resized to fit or exclude the row names
setLabName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
setLaboratory(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setLanguageLevel(OntologyService.LanguageLevel) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
setLanguageLevel(OntologyService.LanguageLevel) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
setLanguageLevel(OntologyService.LanguageLevel) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
setLanguageLevel(OntologyService.LanguageLevel) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Set the OWL language level supported by this ontology.
setLanguageLevel(OntologyService.LanguageLevel) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Set the supported OWL language level for the ontology.
setLastArrayDesignUpdateDate(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setLastBuildTime(Date) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setLastComputed(Date) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject: Timestamp of the last GeeqEvent for the experiment, populated by callers that have access to the audit log.
setLastEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
setLastEventAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJob
setLastEventKind(String) - Method in class ubic.gemma.model.pipeline.PipelineJob
setLastGeneMapping(Date) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setLastModified(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationBaseline
setLastName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
setLastName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.Person: Deprecated.
setLastNeedsAttentionEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setLastNeedsAttentionEvent(AuditEventValueObject) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setLastNeedsAttentionEvent(AuditEventValueObject) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
setLastNoteUpdateEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setLastNoteUpdateEvent(AuditEventValueObject) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setLastNoteUpdateEvent(AuditEventValueObject) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
setLastOccurrence(Date) - Method in class ubic.gemma.rest.CompactAuditEventValueObject
setLastProgressJson(String) - Method in class ubic.gemma.model.pipeline.PipelineJob
setLastRepeatMask(Date) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setLastRun(Date) - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject
setLastSequenceAnalysis(Date) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setLastSequenceUpdate(Date) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setLastTroubledEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setLastTroubledEvent(AuditEventValueObject) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setLastTroubledEvent(AuditEventValueObject) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
setLastUpdate(Date) - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
setLastUpdate(DatasetUpdateSummaryValueObject) - Method in class ubic.gemma.rest.PipelineStatusValueObject: What changed here most recently, as a short label plus its date and performer — the thing curationDetails.lastUpdated leaves out.
setLastUpdated(Date) - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
setLastUpdated(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setLastUpdated(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setLastUpdated(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
setLastUpdated(Date) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setLastUpdated(Date) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
setLastUpdateDate(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setLastUpdateDate(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setLastUpdateDate(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setLayout(SraLibraryLayout) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
setLength(Long) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setLength(Long) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setLevel(Class) - Method in class ubic.gemma.core.scheduler.Ee2cUpdateJob
setLevel(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setLibraryDescriptor(SraLibraryDescriptor) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
setLibrarySelection(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: Verbatim !Sample_library_selection, e.g.
setLibrarySelection(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setLibrarySelection(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: How the library was selected — GEO's library_selection (polyA, cDNA, RANDOM, …), verbatim.
setLibrarySource(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setLibraryStrategy(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setLibraryStrategy(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setLibraryStrategy(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: What kind of library — GEO's library_strategy (RNA-Seq, scRNA-seq, Ribo-Seq, ATAC-seq, …).
setLibSource(GeoLibrarySource) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setLibStrategy(GeoLibraryStrategy) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setLimit(Integer) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setLinkAnalysisEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setLinkName(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
setLinks(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
setLinkType(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
setLinkUrl(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
setLiteratureSources(Set) - Method in class ubic.gemma.model.genome.gene.GeneSet
setLoadDone(boolean) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setLoadInBackground(boolean) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Initialize the service using a background thread.
setLoading(Double) - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
setLoadingRank(Integer) - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
setLoadPlatformOnly(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setLoadPlatformOnly(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setLocalBasePath(String) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher: Set the local directory where fetched files will be written.
setLocalInstallDbName(String) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setLocalName(String) - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
setLockedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
setLockedBy(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
setLocusTag(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setLogFoldChange(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setLogFoldChange(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
setLogFoldChange(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
setLoggedIn(boolean) - Method in class ubic.gemma.core.security.authentication.LoginDetailsValueObject
setLogin(String) - Method in class ubic.gemma.core.util.NetDatasourceUtil
setLowDistinctValueCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Minimum fraction of distinct values for a design element to be retained.
setLowExpressionCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Low cut for expression.
setLowExpressionFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setLowVarianceCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: This threshold applies on the variance of the row.
setLowVarianceFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Indicate if the low variance filter was applied.
setLowVarianceFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setMakeArchiveFile(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Whether to create archive files.
setManualAuthenticationService(ManualAuthenticationService) - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceBasedSecurityContextFactory
setManualBatchConfoundActive(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualBatchConfoundActive(boolean) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setManualBatchEffectActive(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualBatchEffectActive(boolean) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setManualHasBatchConfound(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualHasBatchConfound(boolean) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setManualHasNoBatchEffect(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualHasNoBatchEffect(boolean) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setManualHasStrongBatchEffect(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualHasStrongBatchEffect(boolean) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setManualQualityOverride(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualQualityOverride(boolean) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setManualQualityScore(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualQualityScore(double) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setManufactureProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setManufacturer(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setMapLocation(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setMarkers(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setMask(int) - Method in class ubic.gemma.core.security.acl.domain.AclEntry
setMasked(boolean) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: Indicate if this vector is "masked", i.e.
setMaskOutliers(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Mask outliers in the data by replacing the affected columns with Double.NaN.
setMatchedCriteria(String) - Method in class ubic.gemma.model.expression.experiment.PreboardedExperiment
setMatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setMatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setMatchKind(SearchMatchType) - Method in class ubic.gemma.model.common.search.SearchResult: How this result matched the query (exact symbol, alias, prefix look-alike, …), or null when the producing source did not classify it.
setMatchType(String) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: How this gene matched the search query (e.g.
setMatrix(ColorMatrix) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
setMatrix(HeatmapDataValueObject.MatrixSection) - Method in class ubic.gemma.rest.HeatmapDataValueObject: The numeric matrix; row-major (one row per probe).
setMatrixFile(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
setMatrixFileSuffix(String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
setMatrixWasFiltered(boolean) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setMaxAge(int) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the maximum time in seconds that the results of a preflight request can be cached by the client.
setMaxAnalysisTimeMillis(long) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Maximum time to spend on the analysis, in milliseconds.
setMaxCharacteristics(int) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: Maximum number of characteristics to consider when loading a cell-level characteristic.
setMaxColumnLength(int) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
setMaxEntrySizeInArchiveToSkip(long) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.ArchiveBasedSingleCellDetector: Set the maximum size of an archive entry to skip the supplementary file altogether.
setMaxEntrySizeInArchiveToSkip(long) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
setMaxEntrySizeInArchiveToSkip(long) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
setMaxFractionRemoved(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter: Set the maximum fraction of rows which will be removed from the data set.
setMaxFractionRemoved(double) - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilter: Set the maximum fraction of rows which will be removed from the data set.
setMaxIdleConnections(int) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl: Set the maximum number of idle FTP connections to keep in the pool.
setMaximumRepeatFraction(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setMaxNumberOfEntriesToSkip(long) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.ArchiveBasedSingleCellDetector: Set the maximum number of archive entries to skip in order to ignore the supplementary file altogether.
setMaxNumberOfEntriesToSkip(long) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
setMaxNumberOfEntriesToSkip(long) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
setMaxNumProbesPerComponent(Integer) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setMaxQueueMillis(long) - Method in class ubic.gemma.core.job.TaskCommand: How long we will allow this task to be queued before giving up, or -1 for no limit.
setMaxRecords(Integer) - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
setMaxRecords(Integer) - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
setMaxResults(int) - Method in class ubic.gemma.model.common.search.SearchSettings: Limit for the number of results per result type.
setMaxResults(Integer) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setMaxResultsIfPositive(Query, int) - Static method in class ubic.gemma.persistence.util.QueryUtils: Apply Query.setMaxResults(int) only when maxResults is positive.
setMaxRuntimeMillis(long) - Method in class ubic.gemma.core.job.TaskCommand: How long we will allow this task to run before giving up, or -1 for no limit.
setMaxSize(int) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
setMaxTotalConnections(int) - Method in class ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl: Set the maximum number of FTP connections.
setMaxX(double) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setMaxY(double) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setMd5(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setMd5(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setMd5(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setMd5(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
setMd5(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
setMeanGenesPerCell(double) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setMeanLogFoldChange(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setMeans(double[]) - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
setMeanVarianceRelation(MeanVarianceRelation) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setMeasurement(Measurement) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setMeasurement(DatasetsWebService.MeasurementRef) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit
setMeasurementObject(MeasurementValueObject) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The measurement associated with this factor value.
setMeasurements(Map) - Method in class ubic.gemma.rest.HeatmapDataValueObject.FactorEntry: bioAssayId -> measurement value.
setMedianCorrelation(double) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
setMembers(List) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPool
setMembers(Set) - Method in class ubic.gemma.model.genome.gene.GeneSet
setMerged(Boolean) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
setMergedInto(ArrayDesign) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setMergedInto(ArrayDesignReferenceValueObject) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The platform this one was merged into, or null when it was not merged.
setMergees(List) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The platforms merged INTO this one — the inverse of ArrayDesignValueObject.mergedInto, empty when there are none.
setMergees(Set) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setMeshHeadings(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord: MeSh headings, collected from PubMed.
setMeshTerms(Set) - Method in class ubic.gemma.model.common.description.BibliographicReference
setMessage(String) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
setMessage(String) - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: Note attached to the latest audit event, when present.
setMessage(String) - Method in class ubic.gemma.rest.TaskStatusValueObject: Last progress update emitted by the task.
setMessage(String) - Method in class ubic.gemma.rest.TaskStatusValueObject.TaskError: Human-readable description of the failure.
setMessages(String) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setMetadata(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setMetadata(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setMetadata(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setMetadata(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setMetadataCacheDir(File) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator: Override where metadata-only records are cached; defaults to geo.local.datafile.basepath, the directory the family SOFT files already live in.
setMetadataOnly(boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParser: Parse records that carry no data and no platform, as GEO's view=brief series and sample records do.
setMetaFields(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setMetaPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setMetaPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
setMetaPvalueRank(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setMetaQvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setMetaQvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
setMethods(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
setMetThreshold(Boolean) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setMexFileSuffixes(String, String, String) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Set the suffixes to use to detect MEX metadata.
setMightNotHaveDataInFile(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: Indicate if the data might be separate, as for some RNA-seq studies.
setMigratedToStatement(boolean) - Method in class ubic.gemma.model.common.description.Characteristic: Deprecated.
setMinimumCellsFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Indicate if the minimum cells filter was applied.
setMinimumExonOverlapFraction(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setMinimumFractionOfUniqueValues(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter: This threshold is used to determine if a row has too many identical value; a value of N means that the number of distinct values in the expression vector of length M must be at least N * M.
setMinimumFractionOfUniqueValues(Double) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum number of unique values (as a fraction of the number of assays) for a particular design element to be included in the analysis.
setMinimumNumberOfCellsPerGene(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter: Sets the minimum number of cells required for a gene to be retained.
setMinimumNumberOfCellsPerGene(Integer) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum number of cells for a particular gene to be included in the analysis.
setMinimumNumberOfCellsPerSample(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter: Sets the minimum number of cells required for a sample to be retained.
setMinimumNumberOfCellsPerSample(Integer) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum number of cells for a particular sample to be included in the analysis.
setMinimumNumberOfSamplesToApplyFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter: Minimum number of samples (columns) in the matrix to apply the unique values filter.
setMinimumNumberOfSamplesToApplyRepetitiveValuesFilter(Integer) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum number of samples to apply the repetitive value filter.
setMinimumVariance(Double) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the minimum variance for a particular design element to be included in the analysis.
setMinPresentCount(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Minimum number of samples for keeping rows when min-present filtering.
setMinPresentCount(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter: Set the minimum number of values that must be present in each row.
setMinPresentCount(int) - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilter: Set the minimum number of values that must be present in each row.
setMinPresentFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setMinPresentFraction(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Minimum fraction of samples that must have a value (or a present call if a present/absent boolean matrix is provided) for the design element to be retained.
setMinPresentFraction(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter
setMinPresentFraction(double) - Method in class ubic.gemma.core.util.matrix.datafilter.RowMissingFilter
setMinPvalue(Double) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setMinPvalue(Double) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setMinX(double) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setMinY(double) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setMismatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setMismatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setMissingValueAnalysisEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setMode(RepetitiveValuesFilter.Mode) - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter: Set the mode of operation for detecting repetitive values.
setMode(TicketMode) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setMode(TicketMode) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: How the ticket advances between actions.
setMode(TicketMode) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
setMode(TicketMode) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setMode(TicketMode) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setMode(SearchSettings.SearchMode) - Method in class ubic.gemma.model.common.search.SearchSettings: Indicate the search mode to use.
setMode(GeeqService.ScoreMode) - Method in class ubic.gemma.core.tasks.analysis.expression.GeeqTaskCommand
setMode(GeeqService.ScoreMode) - Method in class ubic.gemma.rest.DatasetsWebService.GeeqRecomputeRequest
setModel(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setModel(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setModel(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
setModelConverters(List) - Method in class ubic.gemma.rest.util.OpenApiFactory: A list of model converters to register.
setModerateStatistics(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Whether moderated test statistics should be used.
setModerateStatistics(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: Whether to moderate test statistics via empirical Bayes
setModifiable(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject: If modifying the set is constrained by existing analyses.
setModified(boolean) - Method in interface ubic.gemma.model.common.GemmaSessionBackedValueObject
setModified(boolean) - Method in class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject
setModified(boolean) - Method in class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject
setMolecule(GeoChannel.ChannelMolecule) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setMultifunctionality(Multifunctionality) - Method in class ubic.gemma.model.genome.Gene
setMultifunctionalityRank(Double) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setName(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
setName(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
setName(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setName(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
setName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
setName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
setName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
setName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata: Taxon name, either common or scientific.
setName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
setName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
setName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
setName(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setName(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setName(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
setName(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
setName(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
setName(String) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
setName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
setName(String) - Method in class ubic.gemma.model.analysis.Analysis
setName(String) - Method in class ubic.gemma.model.analysis.AnalysisValueObject
setName(String) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setName(String) - Method in class ubic.gemma.model.analysis.ProtocolValueObject
setName(String) - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
setName(String) - Method in class ubic.gemma.model.common.AbstractDescribable
setName(String) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
setName(String) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setName(String) - Method in class ubic.gemma.model.expression.arrayDesign.AlternateName
setName(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: Full name, e.g.
setName(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setName(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setName(String) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject: Deprecated.
setName(String) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
setName(String) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
setName(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
setName(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
setName(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
setName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject: Full title.
setName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setName(String) - Method in class ubic.gemma.model.genome.Chromosome
setName(String) - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
setName(String) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setName(String) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setName(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
setName(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationBasics
setName(String) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetBasicsUpdateRequest
setName(String) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
setName(String) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setName(String) - Method in class ubic.gemma.rest.GroupsWebService.GroupCreateRequest
setName(String) - Method in class ubic.gemma.rest.GroupsWebService.GroupUpdateRequest
setName(String) - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta
setName(String) - Method in class ubic.gemma.rest.HeatmapDataValueObject.GeneRef: Full gene name, e.g.
setNameIsFromAuthority(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setNamespace(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExternalId
setNamespace(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
setNamespace(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
setNcbiApiKey(String) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator: Set the NCBI API key to use.
setNcbiGeneId(Integer) - Method in class ubic.gemma.model.genome.Gene
setNcbiGi(String) - Method in class ubic.gemma.model.genome.gene.GeneProduct
setNcbiId(Integer) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
setNcbiId(Integer) - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject: NCBI gene id.
setNcbiId(Integer) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setNcbiId(Integer) - Method in class ubic.gemma.model.genome.Taxon
setNcbiId(Integer) - Method in class ubic.gemma.model.genome.TaxonValueObject
setNcbiId(Integer) - Method in class ubic.gemma.rest.HeatmapDataValueObject.GeneRef: NCBI (Entrez) gene ID.
setNcbiId(String) - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
setNcbiTaxonId(Integer) - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
setNeedsAttention(boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setNeedsAttention(boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
setNeedsAttention(boolean) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setNeedsAttention(boolean) - Method in class ubic.gemma.rest.PipelineStatusValueObject: The curator flag that predates the agent workflow: a human marked this dataset as wanting a look.
setNeedsAttention(Boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setNeedsAttention(Boolean) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setNeedsAttention(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
setNeedsAttention(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsUpdateRequest
setNetDataSourceUtil() - Method in class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
setNetDataSourceUtil() - Method in class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher
setNetDataSourceUtil() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.GeoFetcher
setNetDataSourceUtil() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
setNetDataSourceUtil() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher
setNetDataSourceUtil() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
setNetDataSourceUtil() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonFetcher
setNetDataSourceUtil() - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
setNewBioMaterialCount(long) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setNewEEIdsPerTaxon(Map) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setNewFactorClientRefs(List) - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
setNewFactorValueClientRefsByParentKey(Map) - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
setNewLastUpdated(Date) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setNewObjects(Collection) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setNewPassword(String) - Method in class ubic.gemma.rest.RootWebService.ChangePasswordRequest
setNodeDegreeNegRanks(double[]) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setNodeDegreePosRanks(double[]) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setNodeDegreesNeg(int[]) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Array containing number of links supported by 0,1,2, ....
setNodeDegreesPos(int[]) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Array containing number of links supported by 0,1,2, ....
setNomenclatureStatus(NCBIGeneInfo.NomenclatureStatus) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setNonRepeatNonSpecificSiteCountThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setNonSpecificSiteCountThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setNormalizationDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setNormalizationDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
setNormalized(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setNoSequencesFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setNote(String) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setNote(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
setNote(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsUpdateRequest
setNote(String) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueNeedsAttentionRequest
setNoVectors(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setNoVectors(boolean) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setNs(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setNs(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setNucleotide(Long) - Method in class ubic.gemma.model.genome.PhysicalLocation
setNucleotide(Long) - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
setNucleotideEnd(Long) - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject: Deprecated.
setNucleotideLength(Integer) - Method in class ubic.gemma.model.genome.PhysicalLocation
setNucleotideLength(Integer) - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
setNucleotideStart(Long) - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
setNumAnnotations(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: The number of terms (Characteristics) the experiment has to describe it.
setNumberOfAssignedCells(Integer) - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: Indicate how many cells have an assigned cell type, or null if this information is not available.
setNumberOfAssignedCells(Integer) - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject: Indicate how many cells have an assigned characteristic, or null if this information is not available.
setNumberOfAssignedCells(Integer) - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment
setNumberOfAssignedCells(Integer) - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
setNumberOfAssignedCellsByCellType(Map) - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: How many cells carry each cell type, keyed by the id of the entry in CellTypeAssignmentValueObject.cellTypes.
setNumberOfBioAssays(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setNumberOfBioAssays(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setNumberOfCellIds(int) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSample
setNumberOfCellIds(int) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension: Number of cell IDs.
setNumberOfCellIds(int) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject: Number of cells.
setNumberOfCellIds(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Number of cell IDs in the preferred single-cell dimension, or null when there is none.
setNumberOfCells(int[]) - Method in class ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector
setNumberOfCells(int[]) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
setNumberOfCells(int[]) - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
setNumberOfCells(int[]) - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
setNumberOfCells(Integer) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setNumberOfCells(Integer) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setNumberOfCells(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setNumberOfCells(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Total number of cells, or null when this is not a single-cell experiment or the count has not been computed.
setNumberOfCellsByDesignElements(Integer) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setNumberOfCellsByDesignElements(Integer) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setNumberOfCellTypes(int) - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Number of cell types.
setNumberOfCharacteristics(int) - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
setNumberOfDataVectors(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setNumberOfDesignElements(Integer) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setNumberOfDesignElements(Integer) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setNumberOfDiffExpressedProbes(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Number of diffex probes in the Direction.EITHER hit list if available.
setNumberOfDistinctFactorValues(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat: Diversity metric: distinct factor values existing under this category across the corpus.
setNumberOfDistinctTerms(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Annotation-diversity metric: number of distinct ontology-backed terms in use under this category (free-text excluded).
setNumberOfElementsAnalyzed(Integer) - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis
setNumberOfExpressionExperiments(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat: Annotation-burden metric: number of public experiments carrying at least one annotation in this category.
setNumberOfExpressionExperiments(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat: Burden metric: distinct experiments carrying at least one factor under this category.
setNumberOfExpressionExperiments(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat: Distinct public experiments carrying this gene as a perturbation target.
setNumberOfFetchThreads(int) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Number of threads to use for downloading single-cell data.
setNumberOfGenes(int) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSample
setNumberOfGenes(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
setNumberOfGenes(Long) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Distinct genes the platform's elements map to, or null when the caller did not ask.
setNumberOfGenesAnalyzed(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
setNumberOfGenesTested(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setNumberOfMappedElements(Long) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Elements on the platform that map to at least one gene, or null when the caller did not ask.
setNumberOfProbes(int) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setNumberOfProbes(int, int, Integer) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setNumberOfProbes(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
setNumberOfProbes(List) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setNumberOfProbesAnalyzed(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
setNumberOfProbesDiffExpressed(int) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setNumberOfProbesDiffExpressed(int) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setNumberOfProbesDownRegulated(int) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setNumberOfProbesTested(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setNumberOfProbesTotal(int) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setNumberOfProbesUpRegulated(int) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setNumberOfReads(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics: Usually a number, but can take the value "variable".
setNumberOfSamples(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setNumberOfSpots(Long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics: Might be missing if SraRunStatistics.numberOfReads is "variable".
setNumBins(int) - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
setNumBlatHits(Integer) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setNumChannels(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setNumComponentsStored(Integer) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setNumExperimentsInScope(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setNumGenes(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The number of unique genes that this array design maps to.
setNumGenesAnalyzed(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
setNumGenesAnalyzed(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
setNumGenesAnalyzed(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setNumGoTerms(Integer) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Number of GO terms associated with this gene.
setNumGoTerms(Integer) - Method in class ubic.gemma.model.genome.gene.Multifunctionality
setNumMetThreshold(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setNumPopulatedFactors(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: The number of experimental factors the experiment has (counting those that are populated with biomaterials).
setNumProbeAlignments(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The number of probes that have BLAT alignments.
setNumProbes(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setNumProbeSequences(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The number of probes that map to bioSequences.
setNumProbesToGenes(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: The number of probes that map to genes.
setNumResults(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setNumResultSetsIncluded(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setNumSamples(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setNumSamples(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setNumSearchedExperiments(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setNumTimesUsed(int) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
setNumWithCoexpressionAnalysis(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setNumWithDifferentialExpressionAnalysis(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setObj(int, int, Integer) - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
setObject(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setObject(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setObject(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setObject(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setObject(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setObject(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setObject(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
setObjectAlreadyRemoved(boolean) - Method in class ubic.gemma.model.common.BaseValueObject
setObjectCategory(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setObjectCategoryUri(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setObjectClass(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setObjectId(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: A unique ontology identifier (i.e.
setObjectIdClass(Long) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
setObjectIdentityRetrievalStrategy(ObjectIdentityRetrievalStrategy) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter
setObjectTransientnessRetrievalStrategy(ObjectTransientnessRetrievalStrategy) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter: Set the strategy to retrieve the transientness of an object.
setObjectTransientnessRetrievalStrategy(ObjectTransientnessRetrievalStrategy) - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoter: Set the strategy to retrieve the transientness of an object.
setObjectUri(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setObjectUri(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setObjectUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setObjectUri(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setObjectUri(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setObjectUri(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setObjectValue(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setObjectValueUri(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setObsolete(boolean) - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
setOccurredAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
setOccurredAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
setOccurredAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
setOfficialName(String) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setOfficialName(String) - Method in class ubic.gemma.model.genome.Gene
setOfficialSymbol(String) - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject: Official gene symbol, e.g.
setOfficialSymbol(String) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setOfficialSymbol(String) - Method in class ubic.gemma.model.genome.Gene
setOfficialSymbol(String) - Method in class ubic.gemma.rest.HeatmapDataValueObject.GeneRef
setOldStyleCharacteristics(Set) - Method in class ubic.gemma.model.expression.experiment.FactorValue: Deprecated.
setOnBehalfOf(String) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject: The curator an agent acted for, when the credential that authenticated the write is not the person who asked for it.
setOntologyEntry(Characteristic) - Method in class ubic.gemma.model.association.Gene2GOAssociation
setOntologyId(String) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: A unique ontology identifier (i.e.
setOntologyTermCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Total distinct ontology-backed annotation terms in use across all public datasets.
setOntologyTermId(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
setOntologyUsed(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: what Ontology uses this term
setOrder(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setOrderApplied(Integer) - Method in class ubic.gemma.model.expression.biomaterial.Treatment
setOrganism(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setOrganism(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setOrganism(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
setOrganism(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setOrganisms(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setOrganisms(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setOrganisms(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setOrganisms(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
setOrganization(SraOrganization) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
setOrganization(SraOrganization) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
setOrientation(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setOriginalDesignElement(String) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
setOriginalPlatform(ArrayDesign) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setOriginalPlatform(ArrayDesignValueObject) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: The platform this assay was originally run on before a platform switch, or null if it was never switched.
setOriginalPlatforms(List) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: The platforms this dataset's assays were run on BEFORE a platform switch, when one happened.
setOriginalQuery(String) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
setOriginalValue(String) - Method in class ubic.gemma.model.common.description.Characteristic
setOriginalValue(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: The submitter's own wording, as it arrived — before curation replaced CharacteristicValueObject.value with an ontology label, and before a compound field was split.
setOtherIssues(String) - Method in class ubic.gemma.model.expression.experiment.Geeq
setOtherIssues(String) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setOtherKind(String) - Method in class ubic.gemma.model.common.measurement.Measurement
setOtherParts(List) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: The other parts of the study this dataset was split off from, empty when it was not split.
setOtherParts(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setOtherRelevant(List) - Method in class ubic.gemma.rest.DatasetsWebService.CurationPublications
setOtherRelevantPublications(List) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setOtherRelevantPublications(List) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationsUpdateRequest
setOtherRelevantPublications(Set) - Method in class ubic.gemma.model.analysis.Investigation
setOutlier(boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setOutlier(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.SampleOutlierRequest
setOutlier(Boolean) - Method in class ubic.gemma.rest.HeatmapDataValueObject.ColumnMeta: Tri-state outlier flag — boxed so the producer can leave it null when unknown.
setOutliersFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
setOutliersFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setOutputFile(Path) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter
setOutputFile(Path, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedAnnDataTransformation
setOutputFile(Path, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter
setOutputFile(Path, SingleCellDataType) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationPipeline
setOutputFile(Path, SingleCellDataType) - Method in interface ubic.gemma.core.loader.expression.singleCell.transform.SingleCellInputOutputFileTransformation
setOverallDesign(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setOverallDesign(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setOverlap(Integer) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setOwnedByCurrentUser(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
setOwner(Sid) - Method in class ubic.gemma.core.security.acl.domain.AclImpl
setOwner(Securable, String) - Method in interface ubic.gemma.core.security.SecurityService: Change the 'owner' of an object to a specific user.
setOwner(Securable, String) - Method in class ubic.gemma.core.security.SecurityServiceImpl
setOwner(Contact) - Method in class ubic.gemma.model.analysis.Investigation
setOwnerSid(AclSid) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity: Set the owner from an AclSid entity (Hibernate-side).
setOwnerSidFromSpring(Sid) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity: Set the owner from a Spring Security Sid.
setOwningDataset(GeoDataset) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
setP(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setPages(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setPages(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setPageSuffix(String) - Method in class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator: Suffix to append to each page name.
setPaired(Boolean) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
setPaperUrl(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
setParameterValues(Properties) - Method in class ubic.gemma.persistence.hibernate.ByteArrayType
setParameterValues(Properties) - Method in class ubic.gemma.persistence.hibernate.CompressedStringListType
setParamsJson(String) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
setParent(Acl) - Method in class ubic.gemma.core.security.acl.domain.AclImpl
setParent(AnnotationSet) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setParentAcl(Class, Long, AclObjectIdentity) - Method in interface ubic.gemma.core.security.authorization.acl.AclLinterHelperService: Attach the ACL identity of identifier to parentAoi, joining the caller's transaction.
setParentAcl(Class, Long, AclObjectIdentity) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterHelperServiceImpl: This MUST go through MutableAclService.updateAcl(MutableAcl) rather than AclObjectIdentity.setParentObject(AclObjectIdentity).
setParentDescription(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setParentId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setParentLink(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setParentName(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setParentObject(AclObjectIdentity) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
setParentOfParentDescription(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setParentOfParentLink(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setParentOfParentName(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setParents(String[][]) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setParentSubtreeUris(List) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Ontology parent URIs; expanded via OntologyService.getChildren into a full subClassOf descendant set.
setParkedElements(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setParser(NCBIGene2GOAssociationParser) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
setPassword(String) - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceBasedSecurityContextFactory
setPassword(String) - Method in class ubic.gemma.core.util.NetDatasourceUtil
setPassword(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setPassword(String) - Method in class ubic.gemma.rest.AuthWebService.LoginRequest
setPasswordHint(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setPayload(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setPayload(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
setPayload(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
setPayload(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: What the screen that produced this ticket asked, verbatim and opaque.
setPayload(String) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setPayloadJson(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setPayloadJson(String) - Method in class ubic.gemma.model.pipeline.PipelineJobEvent
setPayloadSchemaVersion(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setPayloadSchemaVersion(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject: Which schema TicketValueObject.payload follows; null when the writer declared none.
setPayloadSchemaVersion(Integer) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setPayloadSize(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: Size of the omitted payloadJson in characters.
setPcaAnalysisEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setPendingAssignments(List) - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
setPercent(int) - Method in class ubic.gemma.core.job.progress.ProgressData
setPerformer(String) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setPerformer(String) - Method in class ubic.gemma.rest.DatasetUpdateSummaryValueObject: Username of whoever performed the change, or null when the row has no performer — which is what an unattended batch job leaves behind.
setPermission(Permission) - Method in class ubic.gemma.core.security.acl.domain.AclEntry
setPersist(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Indicate if this analysis should be persisted.
setPersist(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
setPersistJobDetails(Boolean) - Method in class ubic.gemma.core.job.TaskCommand: If true, the jobDetails associated with this task will be persisted in the database.
setPhases(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setPhone(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setPhysicalLocation(PhysicalLocation) - Method in class ubic.gemma.model.genome.ChromosomeFeature
setPipeline(String) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
setPlatform(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setPlatform(GeoPlatform) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setPlatform(SraPlatform) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
setPlatform(ArrayDesign) - Method in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg
setPlatformConstraint(String) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setPlatformConstraint(ArrayDesign) - Method in class ubic.gemma.model.common.search.SearchSettings: Constraint results to be related to the given platform.
setPlatformCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Total public platforms (array designs).
setPlatformCount(Integer) - Method in class ubic.gemma.model.genome.gene.GeneValueObject: Number of platforms carrying at least one probe for this gene.
setPlatformData(List) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setPlatformId(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setPlatforms(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setPlatforms(List) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: The platforms this dataset's assays were run on, as accession + full name.
setPlatformType(GeoDataset.PlatformType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setPlatformUsed(SimplePlatformMetadata) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
setPmid(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
setPollingIntervalMillis(long) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Interval at which events are polled and flushed.
setPolymerType(PolymerType) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setPool(SraPool) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setPoolName(String) - Method in class ubic.gemma.core.metrics.binder.GenericTaskExecutorMetrics
setPoolName(String) - Method in class ubic.gemma.core.metrics.binder.ThreadPoolTaskExecutorMetrics
setPostCode(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setPostProcessOnly(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
setPredicate(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setPredicate(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Predicate label for Statement-backed annotations (e.g.
setPredicate(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setPredicate(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setPredicate(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: The predicate and object halves are absent rather than null when nothing was said.
setPredicate(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setPredicate(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setPredicate(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
setPredicateUri(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setPredicateUri(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setPredicateUri(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setPredicateUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setPredicateUri(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setPredicateUri(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setPredicateUri(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setPredictedOutlier(Boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: Whether the median-correlation algorithm flags this assay as a possible outlier.
setPreExistingFactorIds(Set) - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
setPreExistingFactorValueIds(Set) - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
setPreferred(boolean) - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject: Indicate if this assignment is the preferred one.
setPreferred(boolean) - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: Indicate if this assignment is the preferred one.
setPreferred(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setPreferred(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePreferredRequest
setPrefixes(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setPreflightAtApply(DesignPreflightReport) - Method in class ubic.gemma.model.expression.experiment.DesignApplyOutcome
setPreviousClicks(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord: How many times a curator has already looked at the details.
setPreviousNcbiGeneId(String) - Method in class ubic.gemma.model.genome.Gene
setPrimary(DatasetsWebService.PublicationEntry) - Method in class ubic.gemma.rest.DatasetsWebService.CurationPublications
setPrimaryCitation(CitationValueObject) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setPrimaryId(SraPrimaryId) - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
setPrimaryPublication(BibliographicReference) - Method in class ubic.gemma.model.analysis.Investigation
setPrimaryPublication(PublicationAssertion) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setPrimaryPublication(DatasetsWebService.PublicationEntry) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationsUpdateRequest
setPrimaryTaxon(Taxon) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setPrincipal(String) - Method in class ubic.gemma.core.security.acl.domain.AclPrincipalSid
setPriority(TicketPriority) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setPriority(TicketPriority) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject: The ticket's priority.
setPriority(TicketPriority) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setPriority(TicketPriority) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
setPriority(TicketPriority) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setPriority(TicketPriority) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setPrivateGeneCount(long) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
setProbe(String) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setProbe(CompositeSequence) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setProbe(CompositeSequence) - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
setProbeId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
setProbeId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setProbeIdsAreImageClones(boolean) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: If true, biological characteristics imaging the probes will be created.
setProbeLoadings(Set) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setProbeName(String) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
setProbeResults(Collection) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setProcessedDataVectorComputationEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setProcessedExpressionDataVectors(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setProcessedExpressionVectorCount(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setProcessedVectors(ProcessedVectorComputationPayload) - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: What the processed-vector creation did to the data: which raw quantitation type it started from, which one it produced, how many cells were masked for missing values and for outliers, and whether the result was quantile-normalized.
setProcessImports(boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
setProcessImports(boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
setProcessImports(boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
setProcessImports(boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Allow of forbid this ontology to process imports.
setProcessImports(boolean) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Enable import processing for the ontology.
setProcessingDate(Date) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setProcessingDate(Date) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setProcessPlatformsOnly(boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
setProcessPlatformsOnly(boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParser
setProducerDoneFlag(AtomicBoolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
setProducerDoneFlag(AtomicBoolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
setProducts(Set) - Method in class ubic.gemma.model.genome.Gene
setProgressIncrementToReportInBytes(double) - Method in class ubic.gemma.core.util.AbstractProgressReporter
setProgressIncrementToReportInBytes(double) - Method in interface ubic.gemma.core.util.ProgressReporter: Set the minimum progress increment size to report in bytes.
setProgressIncrementToReportInPercent(double) - Method in class ubic.gemma.core.util.AbstractProgressReporter
setProgressIncrementToReportInPercent(double) - Method in interface ubic.gemma.core.util.ProgressReporter: Set the minimum progress increment size to report in percentage.
setProgressReporterFactory(ProgressReporterFactory) - Method in interface ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderService: Set the progress reporter factory to use for reporting progress during data downloading.
setProgressReporterFactory(ProgressReporterFactory) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderServiceImpl
setProgressReporterFactory(ProgressReporterFactory) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector
setProgressReporterFactory(ProgressReporterFactory) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
setProgressReporterFactory(ProgressReporterFactory) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Set the factory to use to create progress reporter.
setProgressReporterFactory(ProgressReporterFactory) - Method in class ubic.gemma.core.loader.util.fetcher2.AbstractFetcher: Set the progress reporter factory to use for reporting download progress.
setProgressReporterFactory(ProgressReporterFactory) - Method in class ubic.gemma.core.util.SimpleDownloader
setProperty(String, Object) - Static method in class ubic.gemma.core.config.Settings: Deprecated.
setPropertySources(PropertySources) - Method in class ubic.gemma.core.config.BaseCodeConfigurer
setProposalSetId(Long) - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
setProposedDesign(ExperimentalDesignValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setProteinAccession(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setProteinAccessionVersion(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setProteinGI(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setProtocol(ProtocolValueObject) - Method in class ubic.gemma.model.analysis.AnalysisValueObject
setProtocol(Protocol) - Method in class ubic.gemma.model.analysis.Analysis
setPubAccession(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setPubAccession(DatabaseEntry) - Method in class ubic.gemma.model.common.description.BibliographicReference
setPublic(boolean) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setPublic(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
setPublication(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setPublication(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setPublication(BibliographicReference) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setPublicationDate(Date) - Method in class ubic.gemma.model.common.description.BibliographicReference
setPublicationDate(Date) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setPublications(DatasetsWebService.CurationPublications) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setPublicationsCreated(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setPublicationsDeleted(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setPublicationsPresent(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setPublicationsUnchanged(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setPublicGeneCount(long) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: number of occurrences in all genes
setPublicQualityScore(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setPublished(Date) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setPublishedAt(Double) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata: Publication timestamp (seconds since the epoch), or null if not provided.
setPublisher(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setPublisher(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setPubmedAccession(String) - Method in class ubic.gemma.model.common.description.CitationValueObject
setPubmedId(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setPubmedId(String) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
setPubmedId(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: PubMed ID of the primary publication, when it is indexed by PubMed.
setPubMedId(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: PubMed identifier.
setPubMedId(String) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
setPubMedId(String) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
setPubmedIds(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setPubMedIds(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setPubMedIds(List) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setPubmedURL(String) - Method in class ubic.gemma.model.common.description.CitationValueObject
setPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject: The four contrast statistics are rounded to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits on the way out; see DifferentialExpressionAnalysisResultValueObject for why significant digits and why at serialization time rather than in the constructor.
setPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
setPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setPvalue(Double) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: If this vector is associated to a statistical test (i.e.
setPvalue(Double) - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta: Differential-expression p-value, or any single per-row numeric statistic the producer wants the client to know.
setPValue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject: Rounded to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits on the way out.
setPvalueDistribution(PvalueDistribution) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setPythonExecutable(Path) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedTransformation
setPythonExecutable(Path) - Method in interface ubic.gemma.core.loader.expression.singleCell.transform.PythonBasedSingleCellDataTransformation
setPythonExecutable(Path) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationPipeline
setQChtml(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setqScoreBatchConfound(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQScoreBatchConfound(double) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setqScoreBatchEffect(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQScoreBatchEffect(double) - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
setqScoreBatchInfo(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQScoreBatchInfo(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setqScoreOutliers(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQScoreOutliers(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setqScorePlatformsTech(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQScorePlatformsTech(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setQScorePublicBatchConfound(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setQScorePublicBatchEffect(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setqScoreReplicates(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQScoreReplicates(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setqScoreSampleCorrelationVariance(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQScoreSampleCorrelationVariance(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setqScoreSampleMeanCorrelation(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQScoreSampleMeanCorrelation(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setqScoreSampleMedianCorrelation(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQScoreSampleMedianCorrelation(double) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setQualifiers(Set) - Method in class ubic.gemma.model.common.description.MedicalSubjectHeading
setQualityControlDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setQualityControlDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
setQuantitationType(SimpleQuantitationTypeMetadata) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: Required if data is provided.
setQuantitationType(QuantitationType) - Method in class ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector
setQuantitationType(QuantitationType) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setQuantitationType(QuantitationType) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
setQuantitationType(QuantitationType) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
setQuantitationType(QuantitationTypeValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
setQuantitationType(QuantitationTypeValueObject) - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection
setQuantitationType(QuantitationTypeValueObject) - Method in class ubic.gemma.rest.HeatmapDataValueObject: The quantitation type the matrix is in.
setQuantitationTypes(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setQueries(List) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setQuery(String) - Method in class ubic.gemma.model.common.search.SearchSettings: Processed query for performing a search.
setQuery(String) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setQuery(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest.Item
setQueryEnd(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setQueryEnd(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setQueryGapBases(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setQueryGapBases(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setQueryGapCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setQueryGapCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setQuerySequence(BioSequence) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
setQuerySequence(BioSequenceValueObject) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setQueryStart(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setQueryStart(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setQueryStarts(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setQueryStarts(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setQueryString(String) - Method in class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
setQueryString(String) - Method in class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject
setQuickGenes(List) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setQuiet(boolean) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProvider: If set to true, this provider will return null rather than throwing an AccessDeniedException.
setQvalue(int, int, Double) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setqValues(List) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setQvalueThresholdForStorage(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
setRanAt(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
setRanAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setRanAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setRank(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setRank(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
setRank(Double) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
setRank(Double) - Method in class ubic.gemma.model.genome.gene.Multifunctionality
setRank(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setRankByMax(Double) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
setRankByMax(Double) - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector: The relative expression level of this vector in the study.
setRankByMean(Double) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
setRankByMean(Double) - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector: Relative expression level of this vector in the study.
setRatio(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setRawExpressionDataVectors(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setReadCount(Long) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata: The number of reads in the library.
setReadLength(Integer) - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata: The length of the reads.
setReadStatistics(List) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics: Might be missing if SraRunStatistics.numberOfReads is "variable".
setReason(String) - Method in class ubic.gemma.model.blacklist.BlacklistedEntity
setReason(String) - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
setReason(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
setReason(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
setReason(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setReason(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setReason(String) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setReason(String) - Method in class ubic.gemma.rest.WorkflowWebService.AdvanceWorkflowRequest
setReasonCode(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setReasonCode(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setRecentExperiments(List) - Method in class ubic.gemma.core.analysis.report.HomeStats: Most-recently curated public experiments, for the scrolling-names widget.
setRecomputedFromRawData(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setRecordSeparator(String) - Method in class ubic.gemma.core.loader.util.parser.RecordParser
setRecordsMatched(int) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
setRecordsScanned(int) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
setReferencedDatabaseEntry(DatabaseEntry) - Method in class ubic.gemma.model.association.ReferenceAssociation
setRegistryNumber(String) - Method in class ubic.gemma.model.expression.biomaterial.Compound
setRegressedCoexpressionMatrix(SampleCoexpressionMatrix) - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis
setRejectedPublications(List) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationsUpdateRequest
setRelations(Map) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
setRelationshipPersister(RelationshipPersister) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader: Persister-shrink S3: was setPersisterHelper(Persister); now takes the typed RelationshipPersister bean directly.
setReleaseDate(Date) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setReleaseUrl(URL) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setReleaseUrl(URL) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
setReleaseUrl(URL) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setReleaseVersion(String) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setReleaseVersion(String) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
setReleaseVersion(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setRemove(boolean) - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand: If set to true, the annotations passed in will be deleted.
setRemovePrimaryPublication(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
setReorganized(boolean) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: True if the data has been rearranged relative to the bioassay dimension (as a matter of practice the bioassay dimension should be set to null if it is not valid; this boolean is an additional check)
setRepeats(GeoReplication.ReplicationType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
setRepetitiveValuesFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Indicate if the repetitive values filter was applied.
setRepetitiveValuesFilterMode(DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Override the default mode of operation for the RepetitiveValuesFilter.
setReplacedByLabel(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setReplacedByUri(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setReplacementHops(int) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setReplicateDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setReplicateDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
setReplicates(Map) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setReplicatesIssues(byte) - Method in class ubic.gemma.model.expression.experiment.Geeq
setReplicatesIssues(byte) - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
setRepMatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setRepMatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setReporter(Contact) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setReporterId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setReporterName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setReportFrequencyMillis(int) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter: Set the frequency at which to report progress in milliseconds.
setReportFrequencyMillis(int) - Method in class ubic.gemma.cli.util.AbstractCLI: Set the frequency at which the batch task executor should report progress.
setRepresentation(String) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
setRepresentation(String) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setRepresentation(String) - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
setRepresentation(String) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setRepresentation(PrimitiveType) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
setRepresentation(PrimitiveType) - Method in class ubic.gemma.model.common.measurement.Measurement
setRepresentation(PrimitiveType) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setReprocessedFromRawData(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setRequestHeader(String) - Method in class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy: Set the request header used for retrieving the client ID.
setRequireLogin() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI: Indicate that the command requires authentication.
setRequireSequences(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig: Set to true if design elements lacking associated BioSequences for the element should be removed.
setResolutionMillis(long) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Time resolution for regrouping events in the same batch.
setResolvedVia(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setResolvedVia(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage: Which mechanical rule produced ObsoleteTermUsage.replacedByUri.
setRestByDefault() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder
setResultId(long) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult: Not to be confused with resultSetId.
setResultId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
setResultObject(T) - Method in class ubic.gemma.model.common.search.SearchResult: Set the result object.
setResults(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject: Related analysis results.
setResults(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
setResults(Set) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setResults(Set) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
setResultSet(ExpressionAnalysisResultSet) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setResultSetId(Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setResultSetId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
setResultSetId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setResultSetId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setResultSetId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
setResultSetId(Long) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject: The result set ID to which this result belong.
setResultSets(Collection) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
setResultSets(Set) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
setResultSetsIncluded(Set) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
setResultsUsed(Set) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setResultTypes(Set) - Method in class ubic.gemma.model.common.search.SearchSettings: Entities to retrieve.
setResync(ObsoleteTermCorrectionResult.Resync) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
setResyncFailures(List) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync
setRetracted(boolean) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setRetracted(boolean) - Method in class ubic.gemma.model.common.description.CitationValueObject
setRetracted(Boolean) - Method in class ubic.gemma.model.common.description.BibliographicReference
setRetryPolicy(SimpleRetryPolicy) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector
setRetryPolicy(SimpleRetryPolicy) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
setRetryPolicy(SimpleRetryPolicy) - Method in interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector: Set the retry policy to use when downloading single-cell data.
setRevert(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
setRnaNucleotideAccession(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setRnaNucleotideAccessionVersion(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setRnaNucleotideGI(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setRole(String) - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
setRole(AnnotationSetRole) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setRole(AnnotationSetRole) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setRole(PublicationAssociationRole) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setRoot(boolean) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: root of a query
setRow(int, double[]) - Method in class ubic.gemma.core.util.graphics.ColorMatrix: Changes values in a row, clipping if there are more values than columns.
setRow(Integer) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
setRowHeight(int) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
setRowKeys(int[]) - Method in class ubic.gemma.core.util.graphics.ColorMatrix
setRowKeys(int[]) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
setRowName(R, int) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
setRowName(R, int) - Method in interface ubic.gemma.core.util.matrix.Matrix2D: Add a row name associated with a row index.
setRowNameMap(Map) - Method in class ubic.gemma.core.util.matrix.MatrixWriter: Use to customize the labels instead of relying on the toString method of the row object
setRowNames(List) - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
setRowNames(List) - Method in interface ubic.gemma.core.util.matrix.Matrix2D
setRows(List) - Method in class ubic.gemma.rest.HeatmapDataValueObject: Optional.
setRowsCount(int) - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection
setRun(DatasetsWebService.CurationRunRef) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setRunId(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setRunId(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setRunId(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
setRunId(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setRunId(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
setRunningStatus(Boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setRunParentProposal(AnnotationSet) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setRunProvenance(AnnotationSetService.RunProvenance) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setRuns(List) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
setRunSets(List) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
setRunSha(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setRunSha(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setRunSha(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationRunRef
setS2n(double) - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
setSample(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setSample(BioMaterialValueObject) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setSampleCharacteristics(DatasetsWebService.Section) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setSampleCharsCreated(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setSampleCharsDeleted(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setSampleCharsIdMap(Map) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setSampleCharsPresent(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setSampleCharsToAdd(List) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setSampleCharsToDelete(List) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setSampleCharsUnchanged(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setSampleCharsUnchanged(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setSampleColumnName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSortBySample
setSampleCorrespondence(GeoSampleCorrespondence) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSampleCount(int) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setSampleCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Total distinct biomaterials across all public experiments.
setSampleDataProcessing(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleDescriptions(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleDetails(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleExtractProtocols(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleFactorName(String) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: The name of the sample factor under /var.
setSampleGEOAccessions(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleLabelProtocols(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleLabels(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleMolecules(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
setSampleRemovedFlags(Collection) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Details of samples that were removed (or marked as outliers).
setSamples(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
setSamples(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
setSamples(Collection) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata: Samples to be associated with this experiment.
setSamplesAfterMinimumCells(Set) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Number of samples left after filtering for minimum number of cells.
setSamplesAfterOutliers(Set) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
setSamplesByTech(Map) - Method in class ubic.gemma.core.analysis.report.HomeStats: Sample (biomaterial) counts broken down by technology bucket — companion to HomeStats.sampleCount.
setSampleTitle(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
setSampleType(GeoDataset.SampleType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setSampleUsed(BioMaterial) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setScale(String) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setScale(ScaleType) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
setScale(ScaleType) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setScale(ScaleType) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setScaleBarVisible(boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
setScaleType(ScaleType) - Method in interface ubic.gemma.core.datastructure.matrix.io.ExpressionDataMatrixWriter: Set the scale type to use when writing the matrix.
setScaleType(ScaleType) - Method in class ubic.gemma.core.datastructure.matrix.io.JsonMatrixWriter
setScaleType(ScaleType) - Method in class ubic.gemma.core.datastructure.matrix.io.MatrixWriter
setScaleType(ScaleType) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter
setScaleType(ScaleType) - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
setScaleType(ScaleType) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter
setScanFrom(Date) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
setScannedAt(Date) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
setScanProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setScanTo(Date) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
setSchedulerHandle(String) - Method in class ubic.gemma.model.pipeline.PipelineJob
setSchedulerKind(SchedulerKind) - Method in class ubic.gemma.model.pipeline.PipelineJob
setScientificName(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
setScientificName(String) - Method in class ubic.gemma.model.genome.Taxon
setScientificName(String) - Method in class ubic.gemma.model.genome.TaxonValueObject
setScope(int) - Method in class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy: Set the scope to use for retrieving and storing the client ID.
setScope(CurationDecisionScope) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
setScore(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setScore(Double) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setScore(Double) - Method in class ubic.gemma.model.genome.gene.GeneSetMember
setScore(Double) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setScore(Double) - Method in class ubic.gemma.model.genome.gene.Multifunctionality
setScore(Double) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setScoreThreshold(double) - Method in class ubic.gemma.core.loader.genome.BlatResultParser
setScreeningResult(ScreeningResult) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
setScreeningResult(ScreeningResult) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
setScreeningResult(ScreeningResult) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTargetStatusRequest
setScreeningResultReason(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
setScreeningResultReason(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
setScreeningResultReason(String) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTargetStatusRequest
setSearchBibrefs(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchBioSequences(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchedDatabase(ExternalDatabase) - Method in class ubic.gemma.core.loader.genome.BlatResultParser
setSearchedDatabase(ExternalDatabase) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
setSearchEnabled(boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
setSearchEnabled(boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
setSearchEnabled(boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
setSearchEnabled(boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Enable or disable search for this ontology.
setSearchExperiments(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchExperimentSets(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchGenes(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchGeneSets(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchPlatforms(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchProbes(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchTerm(String) - Method in class ubic.gemma.model.genome.gene.GOGroupValueObject
setSecondaryAccession(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject: Identifier in a second database, if available.
setSecondaryExternalDatabase(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setSecondaryExternalUri(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setSecondaryNcbiId(Integer) - Method in class ubic.gemma.model.genome.Taxon
setSecondBaseline(FactorValueBasicValueObject) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
setSecondBaselineGroup(FactorValueBasicValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
setSecondFactorValue(FactorValue) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setSecondFactorValue(FactorValueBasicValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
setSecondFactorValueId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
setSecondFactorValueId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
setSecondObject(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setSecondObject(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setSecondObject(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSecondObject(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setSecondObject(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setSecondObject(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setSecondObject(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
setSecondObjectUri(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setSecondObjectUri(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setSecondObjectUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSecondObjectUri(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setSecondObjectUri(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setSecondObjectUri(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setSecondPredicate(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setSecondPredicate(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setSecondPredicate(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSecondPredicate(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: The second clause of a compound statement (e.g.
setSecondPredicate(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setSecondPredicate(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setSecondPredicate(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit: The second predicate-object pair, for a statement that makes two claims about one subject.
setSecondPredicateUri(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject
setSecondPredicateUri(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setSecondPredicateUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSecondPredicateUri(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setSecondPredicateUri(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setSecondPredicateUri(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setSecurityContext(SecurityContext) - Method in class ubic.gemma.core.scheduler.SecureQuartzJobBean
setSecurityOwner(ExpressionExperiment) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setSecurityOwner(ExpressionExperiment) - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
setSecurityOwner(ExpressionExperiment) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setSecurityOwner(ExpressionExperiment) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setSecurityOwner(ExpressionExperiment) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setSecurityOwner(ExpressionExperiment) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setSeed(long) - Static method in class ubic.gemma.model.analysis.expression.diff.RandomDifferentialExpressionAnalysisUtils
setSeedResolver(ChebiSeedResolver) - Method in class ubic.gemma.core.ontology.providers.ChebiOntologyService
setSeedResolver(MondoSeedResolver) - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService
setSelection(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
setSemanticName(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setSep(String) - Method in class ubic.gemma.core.util.matrix.MatrixWriter
setSeparateSampleFromAssayIdentifiers(boolean) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter: If true, write the sample identifier and the assay identifiers in separate columns.
setSeparateSampleFromAssaysIdentifiers(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriter: If true, write the sample identifier and the assay(s) identifiers in separate columns.
setSequence(String) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Raw probe sequence from the associated BioSequence.sequence.
setSequence(String) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setSequence(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setSequence(BioSequence) - Method in class ubic.gemma.model.genome.Chromosome
setSequenceDatabaseEntry(DatabaseEntry) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setSequenceDatabaseEntry(DatabaseEntryValueObject) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setSequenceField(int) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader: Set the index (starting from zero) of the field where the sequence is found.
setSequenceLength(Long) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject: Pre-computed length from BioSequence.length, exposed alongside sequence.
setSequencePairedReads(Boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setSequencePairedReads(Boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setSequenceReadCount(Long) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setSequenceReadCount(Long) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setSequenceReadLength(Integer) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setSequenceReadLength(Integer) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setSeriesFamilySoftFetcher(GeoFetcher) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator: Wire the resilient (FTP → HTTPS → GEO-generate) series-family SOFT downloader.
setSeriesId(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSeriesType(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setServers(List) - Method in class ubic.gemma.rest.util.OpenApiFactory: A list of servers displayed in the specification.
setServletConfig(ServletConfig) - Method in class ubic.gemma.rest.util.OpenApiFactory: A servlet configuration from which the jax-rs endpoints and resources are discovered.
setShared(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
setShortLabel(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setShortLabel(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setShortLabel(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
setShortLabel(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
setShortName(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
setShortName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
setShortName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
setShortName(String) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
setShortName(String) - Method in class ubic.gemma.model.blacklist.BlacklistedEntity
setShortName(String) - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
setShortName(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setShortName(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: Short name, e.g.
setShortName(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setShortName(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setShortName(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setShortName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setShortName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject: Short name, e.g.
setShortName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setShortName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setShortName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
setShortName(String) - Method in class ubic.gemma.rest.DatasetsWebService.CurationBasics
setShortName(String) - Method in class ubic.gemma.rest.DatasetsWebService.RenameDatasetRequest
setShortNameChangeAllowed(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setShouldSplitOnFactorId(Long) - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit: Curator split advice (factor id, or -1 for "do not split"); recorded in the curation note.
setShouldSplitRationale(String) - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit
setShowMean(boolean) - Method in class ubic.gemma.core.visualization.SingleCellDataBoxplot: Whether to show the mean.
setSid(AclSid) - Method in class ubic.gemma.core.security.acl.domain.AclEntry
setSidRetrievalStrategy(SidRetrievalStrategy) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter
setSignupToken(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setSignupTokenDatestamp(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setSince(Date) - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow: Resolved start of the window — generatedAt - days.
setSince(Date) - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
setSince(Date) - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
setSingle(Boolean) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
setSingleCellCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Number of public experiments that have at least one single-cell dimension recorded (orthogonal to platform-technology type — a single-cell experiment usually rides on a GENELIST platform).
setSingleCellDataTransformationFactory(SingleCellDataTransformationFactory) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.AnnDataDetector
setSingleCellDataTransformationFactory(SingleCellDataTransformationFactory) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector
setSingleCellDataTransformationFactory(SingleCellDataTransformationFactory) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.MexDetector
setSingleCellDimension(SingleCellDimension) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
setSingleCellDimension(SingleCellDimension) - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
setSingleCellExpressionDataVectors(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setSingleCellQuantitationType(QuantitationType) - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap: Quantitation type of the single-cell data this heatmap was generated from, if applicable.
setSingleExperimentMode() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Enable the single-experiment mode.
setSize(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setSize(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setSize(long) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setSize(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setSkip(Integer) - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
setSkip(Integer) - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.

Records to skip at the start of the resolved window; see ScrapeRequest.skip.
setSkipDownload(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader: Set to true to avoid downloading the files, if copies already exist (not recommended if you want an update!)
setSkippedDeferred(List) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
setSkippedNotCorrectable(List) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
setSlackInstance(Slack) - Method in class ubic.gemma.core.logging.log4j.SlackAppender
setSliceNameMap(Map) - Method in class ubic.gemma.core.util.matrix.MatrixWriter
setSlimCacheDir(File) - Method in class ubic.gemma.core.ontology.providers.ChebiOntologyService: Directory under which the slim file and its sidecar meta land.
setSlimCacheDir(File) - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService
setSlimExtractor(OntologySlimExtractor) - Method in class ubic.gemma.core.ontology.providers.ChebiOntologyService
setSlimExtractor(OntologySlimExtractor) - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService
setSlimMaxAge(Duration) - Method in class ubic.gemma.core.ontology.providers.ChebiOntologyService
setSlimMaxAge(Duration) - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService
setSnapshotAnnotationSetId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setSnapshotCreatedBy(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setSnapshotPayloadJson(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setSortKey() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setSortKey(String) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setSource(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat: External-database name (e.g.
setSource(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
setSource(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
setSource(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setSource(String) - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
setSource(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setSource(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setSource(String) - Method in class ubic.gemma.model.expression.experiment.PreboardedExperiment
setSource(String) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
setSource(AnnotationSetSource) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setSource(AnnotationSetSource) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setSource(ExternalDatabase) - Method in class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
setSource(PublicationAssociationSource) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setSourceAccession(DatabaseEntry) - Method in class ubic.gemma.model.genome.gene.GeneSet
setSourceAnalysis(Analysis) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setSourceBioAssayDimension(BioAssayDimensionValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject: If this is a subset, or a padded, BioAssayDimensionValueObject, the sourceBioAssayDimension is the original.
setSourceBioAssayId(Long) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject: If this BioAssay has a parent via BioMaterial.getSourceBioMaterial(), this is the ID.
setSourceBioMaterial(BioMaterial) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setSourceBioMaterialId(Long) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: The BioMaterial this one was derived from, or null if this is a sample in its own right.
setSourceDoneFlag(AtomicBoolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
setSourceExperiment(ExpressionExperiment) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
setSourceExperimentId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
setSourceExperimentId(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject: The ID of the ExpressionExperiment this is a subset of.
setSourceExperimentId(Long) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject: The ID of the source experiment, which differs only if this result is from a subset.
setSourceExperimentShortName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject: The short name of the ExpressionExperiment this is a subset of.
setSourceMetadata(String) - Method in class ubic.gemma.model.analysis.Investigation
setSourceMetadataSchemaVersion(Integer) - Method in class ubic.gemma.model.analysis.Investigation
setSourceName(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setSourceTaxon(Taxon) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setSourceVectorId(Long) - Method in class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject: Obtain the ID of the vector from which this slice is derived from.
setSourceVersion(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setSpecificity(Double) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setSpecificityScore(double) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
setSplitByPlatform(boolean) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
setSplitByPlatform(boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
setSplitByPlatform(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setSplitByPlatform(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setSplitOnFactorId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setSplitRationale(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setSpots(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
setSpots(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
setSraFetcher(SraFetcher) - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector: Set the SraFetcher used to fetch SRA metadata.
setSratoolkit(Boolean) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setStandardizedEnabled(boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
setStartAt(String) - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
setStartAt(String) - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.

GEO accession to resume from; see ScrapeRequest.startAt.
setStartedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJob
setStartedAt(Date) - Method in class ubic.gemma.rest.TaskStatusValueObject
setStartInBioChar(Long) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
setStartingColumns(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setStartingDesignElements(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Starting number of design elements.
setStartingNbiId(Integer) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
setStartingNcbiId(Integer) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
setStartingNcbiId(Integer) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader: Indicate
setStartingRows(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
setStartingSamples(Set) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult: Starting set of samples prior to filtering.
setStartPosition(Long) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setStartTime(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setState(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setState(String) - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: One of PipelineStatusValueObject.PipelineStepValueObject.STATUS_OK, PipelineStatusValueObject.PipelineStepValueObject.STATUS_FAILED, PipelineStatusValueObject.PipelineStepValueObject.STATUS_NOT_RUN, PipelineStatusValueObject.PipelineStepValueObject.STATUS_NOT_APPLICABLE, PipelineStatusValueObject.PipelineStepValueObject.STATUS_STALE.
setState(TicketState) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setState(TicketState) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
setState(TicketState) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setState(TicketState) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setState(JobState) - Method in class ubic.gemma.model.pipeline.PipelineJob
setState(PipelineJobBatch.BatchState) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
setStatementId(Long) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
setStatements(Collection) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: The same annotations as BioMaterialValueObject.characteristics, as statements — carrying the predicate and object when a curator wrote one.
setStatements(List) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: The statements associated with this factor value.
setStatements(DatasetsWebService.Section) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit
setStatements(DatasetsWebService.Section) - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
setStatistics(SraRunStatistics) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setStatus(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setStatus(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setStatus(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setStatus(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setStatus(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setStatus(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: Where a proposal stands with its reviewer.
setStatus(String) - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
setStatus(String) - Method in class ubic.gemma.rest.TaskStatusValueObject: Lower-cased SubmittedTask.Status value: queued, running, completed, failed, cancelling, unknown.
setStatus(TicketTargetStatus) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
setStatus(TicketTargetStatus) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
setStatus(TicketTargetStatus) - Method in class ubic.gemma.rest.TicketsWebService.TicketTargetRequest
setStatus(TicketTargetStatus) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTargetStatusRequest
setStatus(AnnotationRelationStatus) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setStatus(PublicationAssociationStatus) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setStatus(GeoScrapeWatermark.Status) - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark
setStdev(double) - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
setStep(String) - Method in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: Which pipeline step.
setStep(String) - Method in class ubic.gemma.rest.TaskStatusValueObject: Pipeline step the task corresponds to: preprocess, pca, batchInfo, dea, deaRemove.
setSteps(List) - Method in class ubic.gemma.rest.PipelineStatusValueObject
setStolenAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
setStolenFrom(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock
setStoredValue(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setStrand(String) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
setStrand(String) - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
setStrand(String) - Method in class ubic.gemma.model.genome.PhysicalLocation
setStrand(String) - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
setStrand(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setStrand(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setStrategy(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
setStreet(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
setString(String, String) - Static method in class ubic.gemma.core.config.Configuration: Set a configuration by key.
setSubBuckets(List) - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Nested partition.
setSubBuckets(List) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Optional nested partition.
setSubject(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSubject(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setSubject(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
setSubjectCategory(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setSubjectCategoryUri(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setSubjectId(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: A unique ontology identifier (i.e.
setSubjectUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSubjectUri(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
setSubjectValue(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setSubjectValueUri(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setSubmission(SraSubmission) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
setSubmissionComment(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
setSubmissionDate(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setSubmissionDate(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setSubmissionDate(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSubmittedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJob
setSubmittedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
setSubmittedAt(Date) - Method in class ubic.gemma.rest.TaskStatusValueObject
setSubmittedBy(Contact) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch
setSubmitterIds(List) - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
setSubSeries(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSubSeriesOf(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSubsetFactor(ExperimentalFactor) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Factor to subset the analysis on, if non-null.
setSubsetFactor(ExperimentalFactor) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setSubsetFactor(ExperimentalFactorValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
setSubsetFactorId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
setSubsetFactorId(Long) - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialAnalysisRunRequest
setSubsetFactorValue(FactorValue) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: If this is non-null, this is a subset analysis for this factor value.
setSubsetFactorValue(FactorValue) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
setSubsetFactorValue(FactorValueValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
setSubsetFactorValueId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
setSubsetRelevance(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Curator/agent hint about whether a differential expression analysis should SUBSET by this factor.
setSubsetRelevance(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setSubsetRelevance(String) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Curator/agent hint about whether a differential expression analysis should SUBSET by this factor — the write side of ExperimentalFactorValueObject.subsetRelevance.
setSubsetRelevanceReason(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Free-text rationale paired with ExperimentalDesignValueObject.ExperimentalFactorEntry.subsetRelevance.
setSubsetRelevanceReason(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setSubsetRelevanceReason(String) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Free-text rationale paired with DatasetsWebService.FactorCommit.subsetRelevance.
setSubsetsWithStaleAnchor(int) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
setSubsetsWithStaleAnchor(List) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport: Subsets whose definitional factor-value anchors would be deleted.
setSubsumedArrayDesigns(Set) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setSubsumingArrayDesign(ArrayDesign) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setSuitableForDEA(Boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setSummaries(List) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSummary(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSummary(String) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: Human-readable summary of the factor value.
setSummary(DesignPreflightReport.Summary) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport
setSuperSeries(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSupertype(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setSupplementary(boolean) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: True when this candidate came from a flat lexical catalogue (MGI names, Cellosaurus) rather than a conventional ontology.
setSupplementaryFile(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setSupport(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setSupportedTaxa(Collection) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Verbatim provenance backing a curated tag — a JSON array of {quote, source, location, ...} items the curation agents emitted (the agents-side FindingEvidence shape).
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: Verbatim provenance backing a curated characteristic — a JSON array of {quote, source, location, …} items the curation agents emitted.
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject: Verbatim provenance backing this factor VALUE — a JSON array of {quote, source, location, …} items the curation agents emitted.
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry: Verbatim provenance backing this FACTOR — a JSON array of {quote, source, location, …} items the curation agents emitted, stored and served opaquely.
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject: Verbatim provenance backing this statement — a JSON array of {quote, source, location, …} items the curation agents emitted.
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: Verbatim provenance for this FACTOR — a JSON array of {quote, source, location, …} items.
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit: Verbatim provenance for this factor VALUE — a JSON array of {quote, source, location, …} items.
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit: Verbatim provenance for this sample characteristic.
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit: Verbatim provenance for this statement — a JSON array of {quote, source, location, …} items.
setSupportingEvidence(JsonNode) - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit: Verbatim provenance for this tag.
setSupportingEvidence(String) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setSupportingEvidence(String) - Method in class ubic.gemma.model.common.description.Characteristic
setSupportingEvidence(String) - Method in class ubic.gemma.model.common.description.PublicationAssociation
setSupportingEvidence(String) - Method in class ubic.gemma.model.common.description.PublicationAssociationValueObject
setSupportingEvidence(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setSupportingEvidence(String) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setSupportingEvidence(String) - Method in class ubic.gemma.rest.DatasetsWebService.PublicationEntry
setSuppressMatching(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setSuppressMatching(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setSuppressNearMatches(Boolean) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setSuppressPostProcessing(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setSuppressPostProcessing(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.DatasetImportRequest
setSwitchedExpressionExperimentCount(Long) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setSymbolIsFromAuthority(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setSystemWideSalt(String) - Method in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider: Override the system-wide salt used for the pre-2009 fixed-salt fallback.
setTableMaintenanceUtil(TableMaintenanceUtil) - Method in class ubic.gemma.core.scheduler.Ee2AdUpdateJob
setTableMaintenanceUtil(TableMaintenanceUtil) - Method in class ubic.gemma.core.scheduler.Ee2cUpdateJob
setTagCount(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setTagCount(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setTagCount(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject: Derived hint; null means unknown, never zero.
setTagLength(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setTags(DatasetsWebService.Section) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDocument
setTagsCreated(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setTagsDeleted(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setTagsIdMap(Map) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setTagsPresent(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setTagsToAdd(List) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setTagsToDelete(List) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setTagsUnchanged(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
setTagsUnchanged(int) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
setTargetAlignedRegion(PhysicalLocation) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
setTargetArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskCommand
setTargetArrayDesignName(String) - Method in class ubic.gemma.rest.DatasetsWebService.PlatformSwitchRequest
setTargetChromosome(Chromosome) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
setTargetChromosomeName(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setTargetCount(long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject: How many TicketTargets the ticket holds.
setTargetDatabase(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setTargetEnd(Long) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setTargetEnd(Long) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setTargetGapBases(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setTargetGapBases(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setTargetGapCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setTargetGapCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setTargetId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
setTargetId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
setTargetId(Long) - Method in class ubic.gemma.rest.TicketsWebService.AddTargetRequest.TargetRef
setTargetId(Long) - Method in class ubic.gemma.rest.TicketsWebService.TicketTargetRequest
setTargetId(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
setTargets(List) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setTargets(List) - Method in class ubic.gemma.rest.TicketsWebService.AddTargetRequest
setTargets(List) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setTargets(Set) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setTargetSequence(BioSequence) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
setTargetStart(Long) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setTargetStart(Long) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setTargetStarts(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setTargetStarts(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setTargetState(String) - Method in class ubic.gemma.rest.WorkflowWebService.AdvanceWorkflowRequest
setTargetStatus(TicketTargetStatus) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject: This target's status on this ticket.
setTargetType(TicketTargetType) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
setTargetType(TicketTargetType) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
setTargetType(TicketTargetType) - Method in class ubic.gemma.rest.TicketsWebService.AddTargetRequest.TargetRef
setTargetType(TicketTargetType) - Method in class ubic.gemma.rest.TicketsWebService.TicketTargetRequest
setTaskCommand(C) - Method in class ubic.gemma.core.job.AbstractTask
setTaskCommand(C) - Method in interface ubic.gemma.core.job.Task
setTaskExecutor(ExecutorService) - Method in class ubic.gemma.core.loader.util.fetcher2.AbstractFetcher: Set the task executor for parallel downloads.
setTaskExecutor(ExecutorService) - Method in class ubic.gemma.core.util.SimpleDownloader: Set the task executor for performing asynchronous downloads.
setTaskExecutor(TaskExecutor) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Set the task executor used for initializing ontology service in background.
setTaskId(String) - Method in class ubic.gemma.core.job.progress.ProgressData
setTaskId(String) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setTaskId(String) - Method in class ubic.gemma.rest.TaskStatusValueObject
setTaxa(Set) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject: When genes are included, this field is populated.
setTaxId(int) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setTaxId(int) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setTaxon(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat: Lowercase common name of the gene's taxon, matching HomeStats.TaxonStat.commonName.
setTaxon(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
setTaxon(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
setTaxon(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchBatchRequest
setTaxon(SimpleTaxonMetadata) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
setTaxon(Taxon) - Method in class ubic.gemma.core.loader.genome.BlatResultParser
setTaxon(Taxon) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
setTaxon(Taxon) - Method in class ubic.gemma.core.tasks.maintenance.MultifunctionalityTaskCommand
setTaxon(Taxon) - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
setTaxon(Taxon) - Method in class ubic.gemma.model.common.description.AnnotationRelation
setTaxon(Taxon) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setTaxon(Taxon) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setTaxon(Taxon) - Method in class ubic.gemma.model.genome.Chromosome
setTaxon(Taxon) - Method in class ubic.gemma.model.genome.Gene
setTaxon(TaxonValueObject) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setTaxon(TaxonValueObject) - Method in class ubic.gemma.model.genome.gene.GeneValueObject
setTaxon(TaxonValueObject) - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
setTaxon(TaxonValueObject) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setTaxon(TaxonValueObject) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setTaxonConstraint(String) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setTaxonConstraint(Taxon) - Method in class ubic.gemma.model.common.search.SearchSettings: Constraint results to to be related to the given taxon.
setTaxonId(int) - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
setTaxonId(Long) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
setTaxonId(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setTaxonName(String) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
setTaxonName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setTaxonObject(TaxonValueObject) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setTaxonObject(TaxonValueObject) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: FIXME: this should be named simply "taxon", but that field is already taken for Gemma Web, see ExpressionExperimentValueObject.getTaxon().
setTaxonService(TaxonService) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
setTechnology(GeoDataset.PlatformType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setTechnologyType(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject: What kind of platform it is — ONECOLOR, TWOCOLOR, SEQUENCING, GENELIST, OTHER.
setTechnologyType(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
setTechnologyType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setTechnologyType(TechnologyType) - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
setTechnologyType(TechnologyType) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setTempDir(Path) - Method in class ubic.gemma.core.ontology.jena.TdbOntologyService: Set the temporary directory used when opening the TDB in read-only mode.
setTerm(String) - Method in class ubic.gemma.model.common.description.BibRefAnnotation
setTerm(String) - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
setTermCount(long) - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Annotation-diversity metric: distinct URIs that landed in this bucket.
setTerms(List) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult
setTermUri(String) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setTextFname(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setThirdQuartile(double) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
setThreePrimeDistance(Long) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setThreePrimeDistanceMeasurementMethod(ThreePrimeDistanceMethod) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setThreshold(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Threshold applied to the hitlist.
setThresholdQvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
setTicket(Ticket) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
setTicket(Ticket) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
setTicketCountOpen(int) - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
setTicketId(Long) - Method in class ubic.gemma.rest.WorkflowWebService.AdvanceWorkflowRequest
Settings - Class in ubic.gemma.core.config: Deprecated.
This has been replaced with Spring-based configuration SettingsConfig and usage of Value to inject configurations. You can use @Value("${property}") as replacement.
Settings() - Constructor for class ubic.gemma.core.config.Settings: Deprecated.
SettingsCompletionSource - Class in ubic.gemma.cli.completion: Provide completion for all available Gemma settings.
SettingsCompletionSource(boolean) - Constructor for class ubic.gemma.cli.completion.SettingsCompletionSource
SettingsConfig - Class in ubic.gemma.core.config: Beans declaration for making the settings available via the Spring Environment and placeholder substitution.
SettingsConfig() - Constructor for class ubic.gemma.core.config.SettingsConfig
settingsDescriptions() - Static method in class ubic.gemma.core.config.SettingsConfig
settingsPropertySources() - Static method in class ubic.gemma.core.config.SettingsConfig: Property sources populated from various settings files.
setTissue(List) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
setTitle(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
setTitle(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
setTitle(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
setTitle(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setTitle(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
setTitle(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setTitle(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setTitle(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setTitle(String) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
setTitle(String) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setTitle(String) - Method in class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
setTitleInDataset(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: This is used to store the title for the sample as found in the GDS file, if it differs from the one in the GSE file
setToken(String) - Method in class ubic.gemma.core.logging.log4j.SlackAppender.Builder
setToLabel(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setTopLeft(String) - Method in class ubic.gemma.core.util.matrix.MatrixWriter
setTopMarkers(Map) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
setTopPerturbedGenes(List) - Method in class ubic.gemma.core.analysis.report.HomeStats: Per-gene ranking of how many public EEs carry that gene as a perturbation-target annotation — a gene URI whose own category is genotype.
setTopTerms(List) - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat: Top representative terms in this bucket, sorted desc by EE-mention count.
setToRedo(DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setTotalBases(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setTotalCells(long) - Method in class ubic.gemma.core.analysis.report.HomeStats: Total individual cells measured across all single-cell experiments — sum of BioAssay.numberOfCells for assays attached to EEs with a SingleCellDimension.
setTotalSpots(long) - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
setToUri(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
setTransform(boolean) - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
setTranspose(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: Transpose obs/var dataframes.
setTranspose(boolean) - Method in class ubic.gemma.core.visualization.ExpressionDataHeatmap
setTranspose(boolean) - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
setTreatmentProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setTreatments(Set) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setTreatmentSubcategories(List) - Method in class ubic.gemma.core.analysis.report.HomeStats: Treatment-category terms broken down by bucket (see treatment-buckets.json): approved_drug, hormone, vitamin, toxin, vehicle, biologic (PR / NCBI Gene), pathogen (NCBITaxon), control, plus the other_chemical catchall (unbucketed CHEBI) and other catchall (non-CHEBI).
setTriageJudgeKind(String) - Method in class ubic.gemma.rest.PipelineStatusValueObject: Whether PipelineStatusValueObject.triageVerdict came from an agent or a curator; null when nothing has been triaged.
setTriageVerdict(String) - Method in class ubic.gemma.rest.PipelineStatusValueObject: The effective triage ruling across this dataset's annotation sets — fine, wont_fix, might_fix or must_fix — or null when nothing has been triaged.
setTrimNonCanonicalChromosomeHits(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setTroubled(boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setTroubled(boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
setTroubled(boolean) - Method in class ubic.gemma.rest.PipelineStatusValueObject
setTroubled(Boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setTroubled(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
setTroubled(Boolean) - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsUpdateRequest
setTroubleDetails(String) - Method in class ubic.gemma.rest.PipelineStatusValueObject
setTstat(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setTStat(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
setType(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
setType(String) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
setType(String) - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
setType(String) - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
setType(String) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
setType(String) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
setType(String) - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
setType(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
setType(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
setType(String) - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit: "categorical" | "continuous".
setType(String) - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
setType(GeoSampleType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: The sample type (ie.
setType(GeoVariable.VariableType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
setType(GeoVariable.VariableType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
setType(MetaFieldType) - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
setType(TicketEventType) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
setType(TicketEventType) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
setType(TicketType) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setType(TicketType) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
setType(TicketType) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setType(TicketType) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketFromAccessionRequest
setType(TicketType) - Method in class ubic.gemma.rest.TicketsWebService.CreateTicketRequest
setType(DatabaseType) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setType(MeasurementType) - Method in class ubic.gemma.model.common.measurement.Measurement
setType(StandardQuantitationType) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
setType(StandardQuantitationType) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setType(StandardQuantitationType) - Method in class ubic.gemma.rest.DatasetsWebService.QuantitationTypePatchRequest
setType(FactorType) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setType(SequenceType) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setType(SequenceTypeValueObject) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setTypes(Set) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setUnit(String) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
setUnit(String) - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
setUnit(Unit) - Method in class ubic.gemma.model.common.measurement.Measurement
setUnitId(Long) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
setUnitNameCV(String) - Method in class ubic.gemma.model.common.measurement.Unit
setUnknownCellTypeIndicator(String) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: Declare the category that marks cells whose type is unknown.
setUntil(Date) - Method in class ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest: Deprecated.
setUntil(Date) - Method in class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand: Deprecated.
setupBaseAces(MutableAcl, ObjectIdentity, Sid, boolean) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice: Called when objects are first created in the system and need their permissions initialized.
setupBaseAces(MutableAcl, ObjectIdentity, Sid, boolean, boolean) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice
setUpColumnElements() - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix: Note: In the current versions of Gemma, we require that there can be only a single BioAssayDimension.
setUpColumnElements(LinkedHashMap) - Method in class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix
setUpdatedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
setUpdatedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
setUpdatedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
setUpdatedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
setUpdatedAt(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
setUpdateDate(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setUpdatedEEIdsPerTaxon(Map) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setUpdatedObjects(Collection) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setUpperTail(Boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setUpperTail(Boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
setUpregulatedCount(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Number of diffex probes in the Direction.UP hit list if available.
setUri(String) - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat: Ontology URI (CHEBI, OBI, EFO, …).
setUri(String) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setUri(String) - Method in class ubic.gemma.model.common.description.DatabaseEntry
setUri(String) - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
setUri(String) - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
setUri(String) - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject
setUri(String) - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermRef
setUriExactMatches(List) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: Full-URI equality matchers.
setUriPrefixes(List) - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket: valueUri.startsWith(prefix) matchers.
setUrl(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
setUrl(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setUrlId(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: id used by url on the client side
setUsable(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord: Curator judgement about whether this is loadable.
setUseBioAssayIds(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriter: If true, use the IDs of the BioAssays (and BioMaterials.
setUseBioAssayIds(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.MatrixWriter: Use BioAssay IDs (and BioMaterial IDs) in the column names instead of names (or short names).
setUseBioAssayIds(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
setUseBioAssayIds(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.CellLevelCharacteristicsWriter: Use the BioAssay numerical ID instead of its name.
setUseBioAssayIds(boolean) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter: This is only used for the cell ID and does not affect the 'Bioassay', 'Sample' and 'Assay' columns.
setUseBioAssayIds(boolean) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter
setUseCellIdsIfSampleNameIsMissing(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader
setUseCharacteristics(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setUsedAsCategory(boolean) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage: Whether the term is used as a CATEGORY.
setUsedAsTerm(boolean) - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage
setUseDatabase(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Use the database for finding results.
setUseDatabase(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setUseDataFromGEO(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform: Normally only set this if "false".
setUseDoublePrecision(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader: Use double precision (i.e.
setUseEnsembl(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseEnsemblIds(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter: Use Ensembl gene IDs instead of gene symbols.
setUseEsts(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseFullTextIndex(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Use the full-text index for finding results.
setUseGeneOntology(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Include results from the Gene Ontology (GO).
setUseGo(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setUseIndices(boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setUseInferredRelations(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Widen the search into terms Gemma knows are related to the ones matched -- so that ticking "Leigh syndrome" still returns a dataset annotated only as a SURF1 mutant.
setUseKnownGene(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseMiRNA(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseMrnas(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseMultipleRowsForAssays(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriter: Write assays over multiple rows.
setUseOntology(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Use the ontology and ontology inference for finding results.
setUser(User) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setUseRawColumnNames(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriter: If true, use column names as they appear in the database.
setUseRawColumnNames(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.MatrixWriter: Do not make the column names R-friendly.
setUseRawColumnNames(boolean) - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
setUseRawColumnNames(boolean) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter: If true, use column names as they appear in the database.
setUseRawColumnNames(boolean) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter
setUseRawX(Boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader: Use or not the raw.X layer.
setUserCanWrite(boolean) - Method in interface ubic.gemma.core.security.model.SecureValueObject
setUserCanWrite(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setUserCanWrite(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setUserCanWrite(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setUserCanWrite(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setUserCanWrite(boolean) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setUseReferencesIfPossible() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI: Set this to allow reference to be retrieved instead of actual entities.
setUseRefGene(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUserFlaggedOutlier(boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setUserId(Long) - Method in class ubic.gemma.rest.GroupsWebService.MemberAddRequest
setUserIdRetrievalStrategy(UserIdRetrievalStrategy) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Set the strategy used to retrieve user IDs.
setUsername(String) - Method in class ubic.gemma.rest.AuthWebService.LoginRequest
setUsername(String) - Method in class ubic.gemma.rest.GroupsWebService.MemberAddRequest
setUserName(String) - Method in class ubic.gemma.core.security.authentication.LoginDetailsValueObject
setUserName(String) - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceBasedSecurityContextFactory
setUserName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User: The username is immutable.
setUserNotLoggedIn(boolean) - Method in class ubic.gemma.model.common.BaseValueObject
setUserOwned(boolean) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
setUserOwned(boolean) - Method in interface ubic.gemma.core.security.model.SecureValueObject
setUserOwned(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setUserOwned(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setUserOwned(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setUserOwned(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
setUserOwned(boolean) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setUseWeights(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Set true for RNA-seq data sets
setUseWeights(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand: Whether to use weighted regression based on mean-variance relationships (voom)
setValidated(Boolean) - Method in class ubic.gemma.rest.HeatmapDataValueObject.RowMeta: Diffex "validated" highlight flag.
setValue(Double) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
setValue(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraBase
setValue(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject: Label of the annotated term — the value as curated.
setValue(String) - Method in class ubic.gemma.model.common.description.Characteristic
setValue(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
setValue(String) - Method in class ubic.gemma.model.common.measurement.Measurement
setValue(String) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
setValue(String) - Method in class ubic.gemma.model.expression.experiment.FactorValue: Deprecated.
setValue(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject: Deprecated.
use either AbstractFactorValueValueObject.getCharacteristics() or AbstractFactorValueValueObject.getMeasurementObject()
setValue(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setValue(String) - Method in class ubic.gemma.model.expression.experiment.Statement: Deprecated.
use Statement.setSubject(String) instead
setValue(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject
setValue(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setValue(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setValue(String) - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
setValue(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit
setValue(DatasetsWebService.OntologyTermRef) - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
setValueAsDouble(double) - Method in class ubic.gemma.model.common.measurement.Measurement
setValueDefinition(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: The definition of the value, if it is an ontology term, as supplied by the ontology.
setValueId(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject: A unique ontology identifier (i.e.
setValueObject(Serializable) - Method in class ubic.gemma.model.common.BaseValueObject
setValues(Object) - Method in class ubic.gemma.rest.HeatmapDataValueObject.MatrixSection: Either double[][] (encoding=json) or a String holding base64-encoded little-endian Float32 cells (encoding=base64f32).
setValues(Collection) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
setValues(List) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
setValues(GeoValues) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setValueType(GeoDataset.ValueType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setValueUri(String) - Method in class ubic.gemma.model.common.description.AnnotationValueObject: URI of the annotated term.
setValueUri(String) - Method in class ubic.gemma.model.common.description.Characteristic
setValueUri(String) - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
setValueUri(String) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
setValueUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement: Deprecated.
use Statement.setSubjectUri(String) instead
setValueUri(String) - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationDto
setValueUri(String) - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationTagInput
setVarianceFraction(Double) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
setVariances(double[]) - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
setVector(double[]) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
setVectorType(String) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject: Vector type this QT is associated to.
setVerdict(TriageVerdict) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
setVersion(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
setVisualizationValue(int, int, Double) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setVisualizationValues(List) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setVolume(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setVolume(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setWarnedAboutGenePix(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setWarningThresholdMills(int) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
setWebByDefault() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder
setWebLink(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setWebLink(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setWebLinks(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setWebLinks(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setWebUri(String) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setWorkflowState(WorkflowState) - Method in class ubic.gemma.model.analysis.Investigation
setWorkflowStateEnteredAt(Date) - Method in class ubic.gemma.model.analysis.Investigation
setZeroVarianceFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
SEURAT_DISK - Enum constant in enum class ubic.gemma.core.loader.expression.singleCell.SingleCellDataType: SeuratDisk
SeuratDiskDetector - Class in ubic.gemma.core.loader.expression.geo.singleCell
SeuratDiskDetector() - Constructor for class ubic.gemma.core.loader.expression.geo.singleCell.SeuratDiskDetector
sex() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Returns the value of the sex record component.
sha1HexUsernameSalt(CharSequence, String) - Static method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder: Compute the legacy hash.
ShellDelegatingBlat - Class in ubic.gemma.core.analysis.sequence: Class to manage the gfServer and run BLAT searches.
ShellDelegatingBlat() - Constructor for class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat: Create a blat object with settings read from the config file.
ShellDelegatingBlat.BlattableGenome - Enum Class in ubic.gemma.core.analysis.sequence
ShellUtils - Class in ubic.gemma.core.util
ShellUtils() - Constructor for class ubic.gemma.core.util.ShellUtils
shock - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
SHORT - Enum constant in enum class ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType
shortName() - Method in record class ubic.gemma.model.expression.experiment.ExpressionExperimentIdAndShortName: Returns the value of the shortName record component.
shouldBePublic(boolean) - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder: If true, securables should be public.
shouldRun(Date, ArrayDesign, Class) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
showSingleCellExpressionData(QuantitationType, CompositeSequence, List, CellLevelCharacteristics, Characteristic) - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentWebUrl
shutdown() - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
shutdownAndAwaitTermination() - Method in class ubic.gemma.cli.batch.BatchTaskExecutorService
shutdownNow() - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
SID_ALIAS - Static variable in class ubic.gemma.persistence.util.AclQueryUtils: Alias used for the object identity AclObjectIdentity and the owner identity AclSid inside the EXISTS body.
Sids - Class in ubic.gemma.core.security.acl.domain: Utilities for inspecting Sid instances.
sign_j(double, double) - Static method in class ubic.gemma.core.util.math.linalg.Blas: This method implements the FORTRAN sign (not sin) function.
signDatasetCuration(DatasetArg, String, Boolean, Boolean, DatasetsWebService.CurationDocument) - Method in class ubic.gemma.rest.DatasetsWebService
SignificantDigitsSerializer() - Constructor for class ubic.gemma.core.util.RoundingUtils.SignificantDigitsSerializer
signupTokenDate - Variable in class ubic.gemma.rest.AdminWebService.UserValueObject
signupTokenPending - Variable in class ubic.gemma.rest.AdminWebService.UserValueObject: True when a signup token is present and the user is not yet enabled — never-completed signup.
simple - Enum constant in enum class ubic.gemma.core.ontology.GoMetric.Metric
SimpleBioAssayMapper - Class in ubic.gemma.core.loader.util.mapper: A simple strategy for matching BioAssay to sample name.
SimpleBioAssayMapper() - Constructor for class ubic.gemma.core.loader.util.mapper.SimpleBioAssayMapper
SimpleCharacteristic - Class in ubic.gemma.core.loader.expression.simple.model
SimpleCharacteristic(String, String, String, String) - Constructor for class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic
SimpleContactMetadata - Class in ubic.gemma.core.loader.expression.simple.model
SimpleContactMetadata() - Constructor for class ubic.gemma.core.loader.expression.simple.model.SimpleContactMetadata
SimpleDatabaseEntry - Class in ubic.gemma.core.loader.expression.simple.model
SimpleDatabaseEntry() - Constructor for class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
SimpleDesignElementMapper - Class in ubic.gemma.core.loader.util.mapper: A simple design element mapper that simply uses the name as identifier.
SimpleDesignElementMapper(Collection) - Constructor for class ubic.gemma.core.loader.util.mapper.SimpleDesignElementMapper
simpleDownloader - Variable in class ubic.gemma.core.loader.util.fetcher2.AbstractFetcher
SimpleDownloader - Class in ubic.gemma.core.util: A simple downloader for FTP and HTTP(s) URLs.
SimpleDownloader(SimpleRetryPolicy) - Constructor for class ubic.gemma.core.util.SimpleDownloader
SimpleDownloader.URLAndDestination - Class in ubic.gemma.core.util
SimpleExpressionDataLoaderService - Interface in ubic.gemma.core.loader.expression.simple: Load experiment from a flat file.
SimpleExpressionDataLoaderServiceImpl - Class in ubic.gemma.core.loader.expression.simple: Convert a simple matrix and some meta-data into an ExpressionExperiment.
SimpleExpressionDataLoaderServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl
SimpleExpressionExperimentMetadata - Class in ubic.gemma.core.loader.expression.simple.model: Represents the basic data to enter about an expression experiment when starting from a delimited file of data
SimpleExpressionExperimentMetadata() - Constructor for class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
SimpleFastaCmd - Class in ubic.gemma.core.loader.genome: Simple implementation of methods for fetching sequences from blast-formatted databases, using blastdbcmd (aka fastacmd)
SimpleFastaCmd(String) - Constructor for class ubic.gemma.core.loader.genome.SimpleFastaCmd
SimplePlatformMetadata - Class in ubic.gemma.core.loader.expression.simple.model
SimplePlatformMetadata() - Constructor for class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
SimpleQuantitationTypeMetadata - Class in ubic.gemma.core.loader.expression.simple.model
SimpleQuantitationTypeMetadata() - Constructor for class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
SimpleRetry<E> - Class in ubic.gemma.core.util: A simple retry implementation with exponential backoff.
SimpleRetry(SimpleRetryPolicy, Class, String) - Constructor for class ubic.gemma.core.util.SimpleRetry: Create a new simply retry strategy.
SimpleRetryCallable<T,E> - Interface in ubic.gemma.core.util: An interface for work that can be retried.
SimpleRetryContext - Class in ubic.gemma.core.util: Holds the state of a retry attempt.
SimpleRetryContext(int, boolean) - Constructor for class ubic.gemma.core.util.SimpleRetryContext: Creates a new SimpleRetryContext instance.
SimpleRetryPolicy - Class in ubic.gemma.core.util
SimpleRetryPolicy(int, int, double) - Constructor for class ubic.gemma.core.util.SimpleRetryPolicy
SimpleSampleMetadata - Class in ubic.gemma.core.loader.expression.simple.model
SimpleSampleMetadata() - Constructor for class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
SimpleSVDValueObject(SVDResult) - Constructor for class ubic.gemma.rest.DatasetsWebService.SimpleSVDValueObject: Both numeric payloads are rounded to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits, with no opt-out: this is a diagnostic, and nothing recomputes from it.
SimpleTaxonMetadata - Class in ubic.gemma.core.loader.expression.simple.model
SimpleTaxonMetadata() - Constructor for class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
SimpleThreadFactory - Class in ubic.gemma.core.util.concurrent: A simple thread factory based on a preferably unique thread name prefix.
SimpleThreadFactory(String) - Constructor for class ubic.gemma.core.util.concurrent.SimpleThreadFactory
since - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeRequest: Lower bound of the scrape window.
SINGLE_BATCH_SUCCESS - Enum constant in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that there is a single batch and thus there cannot be a batch effect.
SINGLE_CELL_GENOMIC - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoLibrarySource
SINGLE_CELL_RNA_SEQUENCING - Static variable in class ubic.gemma.model.common.description.Values: Deprecated.
use Values.SINGLE_CELL_RNA_SEQUENCING_ASSAY instead
SINGLE_CELL_RNA_SEQUENCING_ASSAY - Static variable in class ubic.gemma.model.common.description.Values
SINGLE_CELL_TRANSCRIPTOMIC - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoLibrarySource
SINGLE_NUCLEUS_RNA_SEQUENCING - Static variable in class ubic.gemma.model.common.description.Values: Deprecated.
use Values.SINGLE_CELL_RNA_SEQUENCING_ASSAY instead
SINGLE_NUCLEUS_RNA_SEQUENCING_ASSAY - Static variable in class ubic.gemma.model.common.description.Values
SingleBatchDeterminationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that we got batch information, but there was (as far as we can tell) just one batch.
SingleBatchDeterminationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SingleBatchDeterminationEvent
singleCell10xMexFilter() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
SingleCell10xMexFilter - Class in ubic.gemma.core.loader.expression.singleCell.transform: Filter 10x Chromium Sequencing data to remove low-quality cells.
SingleCell10xMexFilter() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter
SingleCellAggregationConfig - Class in ubic.gemma.core.analysis.singleCell.aggregate: Configuration for aggregating single-cell data.
SingleCellAggregationConfig.SingleCellAggregationConfigBuilder - Class in ubic.gemma.core.analysis.singleCell.aggregate
SingleCellAggregationException - Exception Class in ubic.gemma.core.analysis.singleCell.aggregate: Exception raised when aggregation fails.
SingleCellAggregationException(String) - Constructor for exception class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationException
SingleCellAggregationPayload - Record Class in ubic.gemma.core.security.audit.payload: Structured payload for the DataAddedEvent written at the end of SingleCellExpressionExperimentAggregateServiceImpl#aggregateVectors.
SingleCellAggregationPayload(String, String, String, List) - Constructor for record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload: Creates an instance of a SingleCellAggregationPayload record class.
SingleCellAggregationPayload.AggregatedAssay - Record Class in ubic.gemma.core.security.audit.payload: Per-assay metrics for an aggregated pseudo-bulk assay.
SingleCellBrainMatcher - Class in ubic.gemma.core.geoscrape: Brain + single-cell intersection matcher.
SingleCellBrainMatcher(BrainKeywordMatcher) - Constructor for class ubic.gemma.core.geoscrape.SingleCellBrainMatcher
SingleCellCellTypeFactorCreatorCli - Class in ubic.gemma.apps
SingleCellCellTypeFactorCreatorCli() - Constructor for class ubic.gemma.apps.SingleCellCellTypeFactorCreatorCli
SingleCellDataAddedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Special case of DataAddedEvent for single-cell data.
SingleCellDataAddedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SingleCellDataAddedEvent
SingleCellDataAggregatorCli - Class in ubic.gemma.apps
SingleCellDataAggregatorCli() - Constructor for class ubic.gemma.apps.SingleCellDataAggregatorCli
SingleCellDataBoxplot - Class in ubic.gemma.core.visualization: Represents a boxplot(s) of single-cell data.
SingleCellDataBoxplot(SingleCellExpressionDataVector) - Constructor for class ubic.gemma.core.visualization.SingleCellDataBoxplot
SingleCellDataDeleterCli - Class in ubic.gemma.apps
SingleCellDataDeleterCli() - Constructor for class ubic.gemma.apps.SingleCellDataDeleterCli
SingleCellDataLoader - Interface in ubic.gemma.core.loader.expression.singleCell: Common interface for all single-cell data loaders.
SingleCellDataLoaderCli - Class in ubic.gemma.apps
SingleCellDataLoaderCli() - Constructor for class ubic.gemma.apps.SingleCellDataLoaderCli
SingleCellDataLoaderConfig - Class in ubic.gemma.core.loader.expression.singleCell: Basic configuration for loading single-cell data.
SingleCellDataLoaderConfig(SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder) - Constructor for class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig
SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C,B> - Class in ubic.gemma.core.loader.expression.singleCell
SingleCellDataLoaderConfigBuilder() - Constructor for class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder
SingleCellDataLoaderConfigurer<T> - Interface in ubic.gemma.core.loader.expression.singleCell: Interface for configuring a single-cell data loader.
SingleCellDataLoaderService - Interface in ubic.gemma.core.loader.expression.singleCell: High-level service for loading single-cell data.
SingleCellDataLoaderServiceImpl - Class in ubic.gemma.core.loader.expression.singleCell
SingleCellDataLoaderServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl
singleCellDataPack() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
SingleCellDataPack - Class in ubic.gemma.core.loader.expression.singleCell.transform: Pack an AnnData object by removing unnecessary zeroes.
SingleCellDataPack() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataPack
SingleCellDataRemovedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
SingleCellDataRemovedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SingleCellDataRemovedEvent
SingleCellDataReplacedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
SingleCellDataReplacedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SingleCellDataReplacedEvent
singleCellDataRewrite() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
SingleCellDataRewrite - Class in ubic.gemma.core.loader.expression.singleCell.transform
SingleCellDataRewrite() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataRewrite
singleCellDataSample() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
SingleCellDataSample - Class in ubic.gemma.core.loader.expression.singleCell.transform
SingleCellDataSample() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSample
singleCellDataSortBySample() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
SingleCellDataSortBySample - Class in ubic.gemma.core.loader.expression.singleCell.transform
SingleCellDataSortBySample() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSortBySample
singleCellDataSparsify() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
SingleCellDataSparsify - Class in ubic.gemma.core.loader.expression.singleCell.transform
SingleCellDataSparsify() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSparsify
SingleCellDataTransformation - Interface in ubic.gemma.core.loader.expression.singleCell.transform: Represents a single-cell data transformation.
singleCellDataTransformationFactory(BeanFactory) - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
SingleCellDataTransformationFactory - Interface in ubic.gemma.core.loader.expression.singleCell.transform
SingleCellDataTransformationFactoryImpl - Class in ubic.gemma.core.loader.expression.singleCell.transform: Factory for obtaining SingleCellDataTransformations.
SingleCellDataTransformationFactoryImpl(BeanFactory, Path) - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactoryImpl
SingleCellDataTransformationPipeline - Class in ubic.gemma.core.loader.expression.singleCell.transform
SingleCellDataTransformationPipeline(List, Path) - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationPipeline
SingleCellDataTransformationUtils - Class in ubic.gemma.core.loader.expression.singleCell.transform
SingleCellDataTransformationUtils() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationUtils
SingleCellDataTransformCli - Class in ubic.gemma.apps: Transform various single-cell formats.
SingleCellDataTransformCli() - Constructor for class ubic.gemma.apps.SingleCellDataTransformCli
singleCellDataTranspose() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
SingleCellDataTranspose - Class in ubic.gemma.core.loader.expression.singleCell.transform: Transpose a single-cell dataset.
SingleCellDataTranspose() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTranspose
SingleCellDataType - Enum Class in ubic.gemma.core.loader.expression.singleCell: Supported single-cell data types.
singleCellDataUnraw() - Method in class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
SingleCellDataUnraw - Class in ubic.gemma.core.loader.expression.singleCell.transform
SingleCellDataUnraw() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataUnraw
SingleCellDataUpdaterCli - Class in ubic.gemma.apps
SingleCellDataUpdaterCli() - Constructor for class ubic.gemma.apps.SingleCellDataUpdaterCli
SingleCellDataVectorAggregatorUtils - Class in ubic.gemma.core.analysis.singleCell.aggregate: Utilities for aggregating single-cell data vectors.
SingleCellDataVectorAggregatorUtils() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils
SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod - Enum Class in ubic.gemma.core.analysis.singleCell.aggregate
SingleCellDataWriterCli - Class in ubic.gemma.apps
SingleCellDataWriterCli() - Constructor for class ubic.gemma.apps.SingleCellDataWriterCli
SingleCellDerivedBulkExpressionDataMatrix<T> - Interface in ubic.gemma.core.datastructure.matrix: A BulkExpressionDataMatrix that was derived from a SingleCellExpressionDataMatrix.
SingleCellDescriptive - Class in ubic.gemma.core.analysis.singleCell: Descriptive statistics for single-cell data.
SingleCellDescriptive() - Constructor for class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
SingleCellDetector - Interface in ubic.gemma.core.loader.expression.geo.singleCell: Interface for single-cell data detectors from GEO.
singleCellDimension() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload: Returns the value of the singleCellDimension record component.
SingleCellDimension - Class in ubic.gemma.model.expression.bioAssayData: Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.
SingleCellDimension() - Constructor for class ubic.gemma.model.expression.bioAssayData.SingleCellDimension
SingleCellDimensionExperiment - Class in ubic.gemma.model.expression.bioAssayData: Denormalized link row that records the SingleCellDimension attached to a given ExpressionExperiment / QuantitationType pair.
SingleCellDimensionExperiment() - Constructor for class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
SingleCellDimensionExperimentDao - Interface in ubic.gemma.persistence.service.expression.experiment: DAO for the denormalized SingleCellDimensionExperiment link table.
SingleCellDimensionExperimentDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment: Hibernate implementation of SingleCellDimensionExperimentDao.
SingleCellDimensionExperimentDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl
SingleCellDimensionUtils - Class in ubic.gemma.model.expression.bioAssayData
SingleCellDimensionUtils() - Constructor for class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionUtils
SingleCellDimensionValueObject - Class in ubic.gemma.model.expression.bioAssayData: Value object for a single-cell dimension.
SingleCellDimensionValueObject(SingleCellDimension, boolean, boolean, boolean) - Constructor for class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject
SingleCellExperimentDesignAuditService - Interface in ubic.gemma.persistence.service.expression.experiment: Co-bean carrying the ExperimentalDesignUpdatedEvent emissions for the cell-type-factor create / remove flows in SingleCellExpressionExperimentServiceImpl.
SingleCellExperimentDesignAuditServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Implementation of SingleCellExperimentDesignAuditService: a thin co-bean that exists so the @Audited aspect can intercept the cell-type-factor create / remove audit emissions previously written imperatively from private helpers in SingleCellExpressionExperimentServiceImpl.
SingleCellExperimentDesignAuditServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.SingleCellExperimentDesignAuditServiceImpl
SingleCellExperimentSubSetsCreationConfig - Class in ubic.gemma.core.analysis.singleCell.aggregate: Configuration for subsetting single-cell expression data in pseudo-bulks.
SingleCellExperimentSubSetsCreationConfig.SingleCellExperimentSubSetsCreationConfigBuilder - Class in ubic.gemma.core.analysis.singleCell.aggregate
SingleCellExpressionDataDoubleMatrix - Class in ubic.gemma.core.datastructure.matrix
SingleCellExpressionDataDoubleMatrix(Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
SingleCellExpressionDataDoubleMatrix(ExpressionExperiment, QuantitationType, SingleCellDimension, List, CompRowMatrix) - Constructor for class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
SingleCellExpressionDataFileOptionValue - Class in ubic.gemma.cli.options: Rows are probes/genes, columns are samples/assays.
SingleCellExpressionDataFileOptionValue(boolean, boolean, Path, Path, boolean, boolean, boolean, ScaleType, boolean, String, boolean) - Constructor for class ubic.gemma.cli.options.SingleCellExpressionDataFileOptionValue
SingleCellExpressionDataFileOptionValue(ExpressionDataFileOptionValue, boolean) - Constructor for class ubic.gemma.cli.options.SingleCellExpressionDataFileOptionValue
SingleCellExpressionDataIntMatrix - Class in ubic.gemma.core.datastructure.matrix
SingleCellExpressionDataIntMatrix(Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
SingleCellExpressionDataMatrix<T> - Interface in ubic.gemma.core.datastructure.matrix: In a single-cell expression data matrix, each column represents a cell.
SingleCellExpressionDataMatrixUtils - Class in ubic.gemma.core.datastructure.matrix
SingleCellExpressionDataMatrixUtils() - Constructor for class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrixUtils
SingleCellExpressionDataMatrixWriter - Interface in ubic.gemma.core.datastructure.matrix.io
SingleCellExpressionDataVector - Class in ubic.gemma.model.expression.bioAssayData: An expression data vector that contains data at the resolution of individual cells.
SingleCellExpressionDataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
SingleCellExpressionDataVectorUtils - Class in ubic.gemma.model.expression.bioAssayData: Utilities for working with SingleCellExpressionDataVector.
SingleCellExpressionDataVectorUtils() - Constructor for class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
SingleCellExpressionExperimentAggregateAuditService - Interface in ubic.gemma.core.analysis.singleCell.aggregate: Co-bean facade for the DataAddedEvent audit emission carried out at the end of SingleCellExpressionExperimentAggregateServiceImpl.aggregateVectors(ExpressionExperiment, QuantitationType, List, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellAggregationConfig).
SingleCellExpressionExperimentAggregateAuditServiceImpl - Class in ubic.gemma.core.analysis.singleCell.aggregate: Implementation of SingleCellExpressionExperimentAggregateAuditService.
SingleCellExpressionExperimentAggregateAuditServiceImpl() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateAuditServiceImpl
SingleCellExpressionExperimentAggregateService - Interface in ubic.gemma.core.analysis.singleCell.aggregate: Aggregate single-cell vectors.
SingleCellExpressionExperimentAggregateServiceImpl - Class in ubic.gemma.core.analysis.singleCell.aggregate
SingleCellExpressionExperimentAggregateServiceImpl() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl
SingleCellExpressionExperimentAggregateServiceImpl.SingleCellExpressionAggregationMethod - Enum Class in ubic.gemma.core.analysis.singleCell.aggregate: Methods for aggregating single-cell expression data.
SingleCellExpressionExperimentCreateSubSetsAndAggregateService - Interface in ubic.gemma.core.analysis.singleCell.aggregate: High-level service for creating subsets and aggregating single-cell expression experiments.
SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl - Class in ubic.gemma.core.analysis.singleCell.aggregate
SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl
singleCellExpressionExperimentService - Variable in class ubic.gemma.apps.DetectQuantitationTypeCli
SingleCellExpressionExperimentService - Interface in ubic.gemma.persistence.service.expression.experiment
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome - Enum Class in ubic.gemma.persistence.service.expression.experiment
SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig - Class in ubic.gemma.persistence.service.expression.experiment
SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder - Class in ubic.gemma.persistence.service.expression.experiment
SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig - Class in ubic.gemma.persistence.service.expression.experiment
SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig.SingleCellVectorInitializationConfigBuilder - Class in ubic.gemma.persistence.service.expression.experiment
SingleCellExpressionExperimentServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
SingleCellExpressionExperimentServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
SingleCellExpressionExperimentSubSetAuditService - Interface in ubic.gemma.core.analysis.singleCell.aggregate: Co-bean facade for the SingleCellSubSetsCreatedEvent audit emission carried out at the end of SingleCellExpressionExperimentSubSetServiceImpl.createSubSets(ExpressionExperiment, SingleCellDimension, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellExperimentSubSetsCreationConfig).
SingleCellExpressionExperimentSubSetAuditServiceImpl - Class in ubic.gemma.core.analysis.singleCell.aggregate: Implementation of SingleCellExpressionExperimentSubSetAuditService.
SingleCellExpressionExperimentSubSetAuditServiceImpl() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetAuditServiceImpl
SingleCellExpressionExperimentSubSetService - Interface in ubic.gemma.core.analysis.singleCell.aggregate: Service to create single-cell expression experiment subsets.
SingleCellExpressionExperimentSubSetServiceImpl - Class in ubic.gemma.core.analysis.singleCell.aggregate
SingleCellExpressionExperimentSubSetServiceImpl() - Constructor for class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceImpl
SingleCellInputOutputFileTransformation - Interface in ubic.gemma.core.loader.expression.singleCell.transform: Simple transformation with input and output files.
SingleCellMaskUtils - Class in ubic.gemma.core.analysis.singleCell: Utility class for handling masks in single-cell analysis.
SingleCellMaskUtils() - Constructor for class ubic.gemma.core.analysis.singleCell.SingleCellMaskUtils
SingleCellSlicerUtils - Class in ubic.gemma.core.analysis.singleCell: Utilities for slicing single-cell data.
SingleCellSlicerUtils() - Constructor for class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtils
SingleCellSparsityHeatmap - Class in ubic.gemma.core.visualization: Heatmap that displays the sparsity of single-cell data.
SingleCellSparsityHeatmap(ExpressionExperiment, SingleCellDimension, BioAssayDimension, Collection, Map, SingleCellSparsityHeatmap.SingleCellHeatmapType) - Constructor for class ubic.gemma.core.visualization.SingleCellSparsityHeatmap
SingleCellSparsityHeatmap.SingleCellHeatmapType - Enum Class in ubic.gemma.core.visualization
SingleCellSparsityMetrics - Class in ubic.gemma.core.analysis.singleCell: Compute sparsity metrics for single-cell data.
SingleCellSparsityMetrics() - Constructor for class ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics
SingleCellSparsityMetricsUpdaterCli - Class in ubic.gemma.apps
SingleCellSparsityMetricsUpdaterCli() - Constructor for class ubic.gemma.apps.SingleCellSparsityMetricsUpdaterCli
SingleCellSubSetsCreatedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted when a collection of ExpressionExperimentSubSet for holding aggregated single-cell data is created.
SingleCellSubSetsCreatedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SingleCellSubSetsCreatedEvent
SingleCellSubSetsCreatedPayload - Record Class in ubic.gemma.core.security.audit.payload: Structured payload for SingleCellSubSetsCreatedEvent writes.
SingleCellSubSetsCreatedPayload(List, String, String, List) - Constructor for record class ubic.gemma.core.security.audit.payload.SingleCellSubSetsCreatedPayload: Creates an instance of a SingleCellSubSetsCreatedPayload record class.
SingleCellTransformationConfig - Class in ubic.gemma.core.loader.expression.singleCell.transform
SingleCellTransformationConfig() - Constructor for class ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
singleChannel - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
singleChannelGenomic - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SingleExperimentAnalysis<T> - Class in ubic.gemma.model.analysis: An analysis of a single experiment or subset.
SingleExperimentAnalysis() - Constructor for class ubic.gemma.model.analysis.SingleExperimentAnalysis
singleton(Supplier) - Static method in interface ubic.gemma.core.context.AsyncFactoryBean: Factory method to create an async singleton bean with a single-thread executor.
SINGLETON_BATCHES_FAILURE - Enum constant in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Batch contains singleton (i.e.
SingletonBatchesException - Exception Class in ubic.gemma.core.analysis.preprocess.batcheffects: Indicates that batches with only a single sample were found, which means we don't form batches at all.
SingletonBatchesException(ExpressionExperiment, String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException
SingletonBatchInvalidEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indiates that there was at least one batch with only one sample.
SingletonBatchInvalidEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SingletonBatchInvalidEvent
SingularValueDecomposition<R,C> - Class in ubic.gemma.core.util.math.linalg: SVD for DoubleMatrix.
SingularValueDecomposition(DoubleMatrix) - Constructor for class ubic.gemma.core.util.math.linalg.SingularValueDecomposition
size() - Method in class ubic.gemma.core.datastructure.sparse.SparseArrayList
size() - Method in class ubic.gemma.core.datastructure.sparse.SparseRangeArrayList
size() - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
size() - Method in interface ubic.gemma.core.loader.util.anndata.Array
size() - Method in class ubic.gemma.core.loader.util.anndata.CategoricalArray
size() - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
size() - Method in class ubic.gemma.core.loader.util.anndata.EnumArray
size() - Method in class ubic.gemma.core.loader.util.anndata.NullableArray
size() - Method in class ubic.gemma.core.loader.util.hdf5.H5Attribute
size() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset.H5Dataspace: Obtain the size of this dataspace.
size() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
size() - Method in class ubic.gemma.core.ontology.relation.OntologyXrefIndex: How many distinct foreign identifiers the index holds.
size() - Method in class ubic.gemma.core.util.matrix.AbstractMatrix
size() - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
size() - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
size() - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
size() - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
size() - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
size() - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
size() - Method in class ubic.gemma.core.util.matrix.StringMatrix
size() - Method in class ubic.gemma.model.common.search.SearchResultSet
size() - Method in class ubic.gemma.model.util.UninitializedCollection
size() - Method in class ubic.gemma.persistence.util.CursorPage
size() - Method in class ubic.gemma.persistence.util.Slice
sized() - Method in class ubic.gemma.model.util.UninitializedCollection
sizeInBytes(String, Charset) - Static method in class ubic.gemma.core.util.StringUtils
sizeWithoutMissingValues(DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
skeletonOf - Static variable in class ubic.gemma.core.ontology.jena.RO
skew(DoubleArrayList, double, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the skew of a data sequence, which is moment(data,3,mean) / standardDeviation3.
skip - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeRequest: Records to skip at the start of the resolved window — record-level resumption.
skip(long) - Method in class ubic.gemma.core.util.ProgressInputStream
SlackAppender - Class in ubic.gemma.core.logging.log4j: Log4j2 appender that report log events to a Slack channel.
SlackAppender.Builder - Class in ubic.gemma.core.logging.log4j
slice(long, long) - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset: Obtain a 1D slice of the dataset.
slice(Collection, List, Class, boolean) - Static method in class ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtils: Slice a collection of bulk data vectors.
slice(Collection, List) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtils
slice(ExpressionExperimentSubsetValueObject, BioAssayDimensionValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
slice(ExpressionExperimentSubsetValueObject, BioAssayDimensionValueObject, int[]) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: Crate a vector that is a slice of this one.
Slice<O> - Class in ubic.gemma.persistence.util: Represents a slice of List.
Slice(List, Sort, Integer, Integer, Long) - Constructor for class ubic.gemma.persistence.util.Slice
sliceBooleans(Collection, List, boolean) - Static method in class ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtils: Slice a collection of bulk data vectors into boolean arrays.
sliceCellIds(SingleCellDimension, List, int[], int[], int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtils
sliceClcs(SingleCellDimension, List, int[], int[], int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtils
sliceColumns(List) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
sliceColumns(List) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
sliceColumns(List) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix: Slice the requested samples (columns) from this matrix.
sliceColumns(List) - Method in class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
sliceColumns(List) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
sliceColumns(List) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
sliceColumns(List) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
sliceColumns(List) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
sliceColumns(List) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
sliceColumns(List, BioAssayDimension) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
sliceColumns(List, BioAssayDimension) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
sliceColumns(List, BioAssayDimension) - Method in interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix: Slice the requested samples (columns) from this matrix.
sliceColumns(List, BioAssayDimension) - Method in class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
sliceColumns(List, BioAssayDimension) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
sliceColumns(List, BioAssayDimension) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
sliceColumns(List, BioAssayDimension) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
sliceColumns(List, BioAssayDimension) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
sliceColumns(List, BioAssayDimension) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
sliceCtas(SingleCellDimension, List, int[], int[], int) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtils
SlicedDoubleVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData
SlicedDoubleVectorValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject
sliceDoubles(Collection, List, boolean) - Static method in class ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtils: Slice a collection of bulk data vectors into double arrays.
sliceNameMap - Variable in class ubic.gemma.core.util.matrix.MatrixWriter
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
sliceRows(List) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Slice the given design elements (rows) from the matrix.
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix
sliceRows(List) - Method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
SLIM_VERSION_SUFFIX - Static variable in class ubic.gemma.core.ontology.providers.OntologySlimExtractor: Appended to a slim's declared version so the artifact identifies itself wherever the version travels — /admin/ontologies, the producer's coverage log, and every ANNOTATION_RELATION.SOURCE_VERSION row.
slimmable - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject: True if the underlying bean implements SlimmableOntologyService — i.e.
SlimmableOntologyService - Interface in ubic.gemma.core.ontology.providers: Marker for an OntologyService that can produce a corpus-tailored slim variant of its source via OWL-API STAR module extraction.
slimSizeBytes - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta
SMALL - Static variable in class ubic.gemma.core.util.math.Constants
SMALLISH - Static variable in class ubic.gemma.core.util.math.Constants
Smooth - Class in ubic.gemma.core.util.math: Methods for moving averages, loess
Smooth() - Constructor for class ubic.gemma.core.util.math.Smooth
SNAPSHOT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetRole
snapshotDatasetCuration(DatasetArg, String) - Method in class ubic.gemma.rest.DatasetsWebService
SNORNA - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
SNP - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
SNRNA - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
SNRNA_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy: GEO's own, not SRA's.
SOFT - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoFormat
softDeleteUser(String, String) - Method in interface ubic.gemma.core.security.authentication.UserManager: Mark the named user as deleted without removing the row.
softDeleteUser(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
solve(DoubleMatrix2D) - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition: Least squares solution of A*X = y; returns X using the stored QR decomposition of A.
some(Class, Collection) - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrlChooser
some(Collection) - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrlChooser
SomeRestEntitiesUrl(String, Class, Collection) - Constructor for class ubic.gemma.persistence.util.EntityUrlBuilder.SomeRestEntitiesUrl
Sort - Class in ubic.gemma.persistence.util: Represents a directed sort by a property.
Sort.Direction - Enum Class in ubic.gemma.persistence.util: Direction of the sort.
Sort.NullMode - Enum Class in ubic.gemma.persistence.util
SortArg<O> - Class in ubic.gemma.rest.util.args: Represents an API argument for sorting.
SortArg.Sort - Class in ubic.gemma.rest.util.args
SortArg.Sort.Direction - Enum Class in ubic.gemma.rest.util.args
SortArg.Sort.NullMode - Enum Class in ubic.gemma.rest.util.args
sortByColumnAbsoluteValues(int, boolean) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
SortValueObject - Class in ubic.gemma.rest.util: Represents Sort as part of a PaginatedResponseDataObject.
SortValueObject(Sort) - Constructor for class ubic.gemma.rest.util.SortValueObject
sortVectorDataByDesign(Collection, ExperimentalFactor) - Method in interface ubic.gemma.core.visualization.ExperimentalDesignVisualizationService: Put data vectors in the order you'd want to display the experimental design.
sortVectorDataByDesign(Collection, ExperimentalFactor) - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl
source - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
source - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetRequest
source - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
source - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
source - Variable in class ubic.gemma.rest.PreboardedWebService.AttachAnnotationSetRequest: Annotation set source; default "agent" for the preboarded surface.
source - Variable in class ubic.gemma.rest.PreboardedWebService.CreatePreboardedRequest
source - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
source(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
SOURCE - Static variable in class ubic.gemma.core.ontology.relation.CellosaurusRelationProducer: As AnnotationRelation.getSource() spells it.
SOURCE - Static variable in class ubic.gemma.core.ontology.relation.ClInferredLocationProducer
SOURCE - Static variable in class ubic.gemma.core.ontology.relation.MgiRelationProducer: As AnnotationRelation.getSource() spells it.
SourceDomainObjectGenerator - Interface in ubic.gemma.core.loader.util.sdo
sourceExperimentId - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
sourceMetadata(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig.GeoUpdateConfigBuilder: Rebuild Investigation.sourceMetadata from the series this refetch parsed.
sourceMetadataSchemaVersion - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse: Which schema PreboardedWebService.PreboardedResponse.identifyingMetadata follows, or null when the writer set none.
sourceQuantitationType() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload: Returns the value of the sourceQuantitationType record component.
sourceUrl - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta
sourceVersion - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta: The release the source ontology declared when this slim was cut, e.g.
sourceVersion(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
SPACE_REPLACEMENT - Static variable in class ubic.gemma.core.analysis.sequence.SequenceWriter: Spaces in the sequence name will cause problems when converting back from some formats (e.g.
sparse(double[][]) - Static method in class ubic.gemma.core.util.matrix.DoubleMatrixFactory
sparse(int, int) - Static method in class ubic.gemma.core.util.matrix.DoubleMatrixFactory
SparseArrayList<T> - Class in ubic.gemma.core.datastructure.sparse: A sparse array backed by an ArrayList.
SparseArrayList() - Constructor for class ubic.gemma.core.datastructure.sparse.SparseArrayList: Create an empty sparse array.
SparseArrayList(Collection) - Constructor for class ubic.gemma.core.datastructure.sparse.SparseArrayList: Create a new sparse array from a given collection, null is used as default value.
SparseArrayList(Collection, T) - Constructor for class ubic.gemma.core.datastructure.sparse.SparseArrayList
SparseArrayList(List, int[], int) - Constructor for class ubic.gemma.core.datastructure.sparse.SparseArrayList: Create a new sparse array, null is used as default value.
SparseArrayList(List, int[], int, T) - Constructor for class ubic.gemma.core.datastructure.sparse.SparseArrayList
SparseDoubleMatrix<R,C> - Class in ubic.gemma.core.util.matrix: A sparse matrix that knows about row and column names.
SparseDoubleMatrix(double[][]) - Constructor for class ubic.gemma.core.util.matrix.SparseDoubleMatrix
SparseDoubleMatrix(int, int) - Constructor for class ubic.gemma.core.util.matrix.SparseDoubleMatrix
SparseDoubleMatrix(int, int, int, double, double) - Constructor for class ubic.gemma.core.util.matrix.SparseDoubleMatrix
SparseList<T> - Interface in ubic.gemma.core.datastructure.sparse: A subclass of List for sparsely stored lists.
SparseListUtils - Class in ubic.gemma.core.datastructure.sparse: Utilities for dealing with sparse List
SparseListUtils() - Constructor for class ubic.gemma.core.datastructure.sparse.SparseListUtils
SparseMatrix - Class in ubic.gemma.core.loader.util.anndata: Represents a sparse AnnData matrix.
SparseMatrix(H5Group) - Constructor for class ubic.gemma.core.loader.util.anndata.SparseMatrix
SparseRangeArrayList<T> - Class in ubic.gemma.core.datastructure.sparse: A sparse range array is a data structure that efficiently stores arrays of repeated elements by encoding their starting offsets.
SparseRangeArrayList() - Constructor for class ubic.gemma.core.datastructure.sparse.SparseRangeArrayList: Create an empty sparse range array.
SparseRangeArrayList(Collection) - Constructor for class ubic.gemma.core.datastructure.sparse.SparseRangeArrayList
SparseRangeArrayList(List, int[], int) - Constructor for class ubic.gemma.core.datastructure.sparse.SparseRangeArrayList
spearmanPvalue(double, int) - Static method in class ubic.gemma.core.util.math.CorrelationStats
spearmanRankCorrelation(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Distance: Convenience function to compute the rank correlation when we just want to know if the values are "in order".
spearmanRankCorrelation(DoubleArrayList, DoubleArrayList) - Static method in class ubic.gemma.core.util.math.Distance: Spearman Rank Correlation.
SpecFunc - Class in ubic.gemma.core.util.math: Assorted special functions, primarily concerning probability distributions.
SpecFunc() - Constructor for class ubic.gemma.core.util.math.SpecFunc
specialCaseToAllowRemovingAcesFromChild(Securable, Acl) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice: For cases in which the object is not a SecuredChild, but we still want to erase ACEs on it when it has a parent.
specialCaseToKeepPrivateOnCreation(Securable) - Method in class ubic.gemma.core.security.acl.BaseAclAdvice: Indicate if the given object should not be made public immediately on creation by administrators.
specialCaseToKeepPrivateOnCreation(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
species - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
species() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Returns the value of the species record component.
specimen - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
split(String) - Static method in class ubic.gemma.core.loader.expression.geo.GeoCharacteristicKey: Divide at the separating colon, which is not always the first.
split(ExpressionExperiment, ExperimentalFactor, boolean) - Method in interface ubic.gemma.core.analysis.preprocess.SplitExperimentService: Split an experiment into multiple experiments based on a factor.
split(ExpressionExperiment, ExperimentalFactor, boolean) - Method in class ubic.gemma.core.analysis.preprocess.SplitExperimentServiceImpl
splitByPlatform - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest
SplitExperimentCli - Class in ubic.gemma.apps: Split an experiment into parts based on an experimental factor
SplitExperimentCli() - Constructor for class ubic.gemma.apps.SplitExperimentCli
SplitExperimentService - Interface in ubic.gemma.core.analysis.preprocess: TODO Document Me
SplitExperimentServiceImpl - Class in ubic.gemma.core.analysis.preprocess: Split an experiment into multiple experiments.
SplitExperimentServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.SplitExperimentServiceImpl
spottedDNAOrcDNA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
spottedOligonucleotide - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SpringContextUtils - Class in ubic.gemma.core.context: Methods to create Spring contexts for Gemma manually.
SpringContextUtils() - Constructor for class ubic.gemma.core.context.SpringContextUtils
Spring Security 6 idiom choices - Section in class ubic.gemma.rest.security.RestSecurityConfig
SQLUtils - Class in ubic.gemma.core.util: SQL helpers.
SQLUtils() - Constructor for class ubic.gemma.core.util.SQLUtils
squeezeVar(DoubleMatrix1D, DoubleMatrix1D, LeastSquaresFit) - Static method in class ubic.gemma.core.util.math.linearmodels.ModeratedTstat: Ignoring robust and covariate for now
squeezeVariances(DoubleMatrix1D, DoubleMatrix1D, double[]) - Static method in class ubic.gemma.core.util.math.linearmodels.ModeratedTstat
SRA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType
SRA - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
SraBase - Class in ubic.gemma.core.loader.expression.sra.model
SraBase() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraBase
SraBases - Class in ubic.gemma.core.loader.expression.sra.model
SraBases() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraBases
SraContact - Class in ubic.gemma.core.loader.expression.sra.model
SraContact() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraContact
SraDateParser - Class in ubic.gemma.core.loader.expression.sra.model
SraDateParser() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraDateParser
SraExperiment - Class in ubic.gemma.core.loader.expression.sra.model
SraExperiment() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraExperiment
SraExperimentDesign - Class in ubic.gemma.core.loader.expression.sra.model
SraExperimentDesign() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
SraExperimentPackage - Class in ubic.gemma.core.loader.expression.sra.model
SraExperimentPackage() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
SraExperimentPackageSet - Class in ubic.gemma.core.loader.expression.sra.model
SraExperimentPackageSet() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackageSet
SraExternalId - Class in ubic.gemma.core.loader.expression.sra.model
SraExternalId() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraExternalId
SraFetcher - Class in ubic.gemma.core.loader.expression.sra
SraFetcher(SimpleRetryPolicy, String) - Constructor for class ubic.gemma.core.loader.expression.sra.SraFetcher
SraFile - Class in ubic.gemma.core.loader.expression.sra.model
SraFile() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraFile
SraFiles - Class in ubic.gemma.core.loader.expression.sra.model
SraFiles() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraFiles
SraIdentifiers - Class in ubic.gemma.core.loader.expression.sra.model
SraIdentifiers() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
SraLibraryDescriptor - Class in ubic.gemma.core.loader.expression.sra.model
SraLibraryDescriptor() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
SraLibraryLayout - Class in ubic.gemma.core.loader.expression.sra.model
SraLibraryLayout() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
SraOrganization - Class in ubic.gemma.core.loader.expression.sra.model
SraOrganization() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraOrganization
SraPlatform - Class in ubic.gemma.core.loader.expression.sra.model
SraPlatform() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraPlatform
SraPool - Class in ubic.gemma.core.loader.expression.sra.model
SraPool() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraPool
SraPoolMember - Class in ubic.gemma.core.loader.expression.sra.model
SraPoolMember() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
SraPrimaryId - Class in ubic.gemma.core.loader.expression.sra.model
SraPrimaryId() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
SraReadStatistics - Class in ubic.gemma.core.loader.expression.sra.model
SraReadStatistics() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
SraRun - Class in ubic.gemma.core.loader.expression.sra.model
SraRun() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraRun
SraRuninfoParser - Class in ubic.gemma.core.loader.expression.sra: Parses SRA runinfo format.
SraRuninfoParser() - Constructor for class ubic.gemma.core.loader.expression.sra.SraRuninfoParser
SraRunSet - Class in ubic.gemma.core.loader.expression.sra.model
SraRunSet() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraRunSet
SraRunStatistics - Class in ubic.gemma.core.loader.expression.sra.model
SraRunStatistics() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics
SraSubmission - Class in ubic.gemma.core.loader.expression.sra.model
SraSubmission() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraSubmission
SraSubmitterId - Class in ubic.gemma.core.loader.expression.sra.model
SraSubmitterId() - Constructor for class ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
SraUtils - Class in ubic.gemma.core.loader.expression.sra
SraUtils() - Constructor for class ubic.gemma.core.loader.expression.sra.SraUtils
SraXmlParser - Class in ubic.gemma.core.loader.expression.sra: Parses SRA XML format.
SraXmlParser() - Constructor for class ubic.gemma.core.loader.expression.sra.SraXmlParser
SSRNA_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
ST - Enum constant in enum class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
stage(String) - Method in class ubic.gemma.cli.pipeline.PipelineJobReporter: Report a stage boundary (e.g.
stages() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Returns the value of the stages record component.
STALE_BASELINE - Enum constant in enum class ubic.gemma.rest.util.CurationCommitConflictException.Reason: The dataset moved since the draft's baseline.
StaleDatasetValueObject(Long, String, List, Date, String) - Constructor for class ubic.gemma.rest.DatasetsWebService.StaleDatasetValueObject
standard - Enum constant in enum class ubic.gemma.rest.PlatformsWebService.AnnotationFileType: Every GO term, including the parents implied by the term's ancestry.
STANDARD_DEVIATION - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
STANDARD_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService: String included in file names for standard (default) annotation files.
STANDARD_LOCATION_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
STANDARD_OUTPUT_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
standardize() - Method in class ubic.gemma.core.util.graphics.ColorMatrix: Normalizes the elements of a matrix to variance one and mean zero, ignoring missing values todo move this to matrixstats or something.
standardize() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
standardize(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Standardize.
standardize(DoubleArrayList, double, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Modifies a data sequence to be standardized.
standardize(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixStats: Scale the rows of the matrix; returns a new matrix.
standardLocation - Variable in class ubic.gemma.cli.options.DataFileOptionValue: Write the file to the standard location in the ${gemma.appdata.home}/dataFiles directory.
standardOutput - Variable in class ubic.gemma.cli.options.DataFileOptionValue: Write the file to standard output.
StandardQuantitationType - Enum Class in ubic.gemma.model.common.quantitationtype
standing(Collection) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition: The standing ruling under each AnnotationSetDisposition.standingKey() — the most recent row per finding, or per target for rows carrying no finding id.
standing(Collection) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision: The standing decision under each key — the most recent per CurationDecision.standingKey().
standingFor(Investigation) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionService: The standing decision under each key.
standingFor(Investigation) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionServiceImpl
standingFor(AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionService: The standing ruling for each finding in one set — the most recent per finding id, or per target id for rows carrying no finding id.
standingFor(AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionServiceImpl
standingForIds(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionService: Batched AnnotationSetDispositionService.standingFor(AnnotationSet), keyed by annotation set id.
standingForIds(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionServiceImpl
standingKey() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition: The key this ruling supersedes others under: the finding when it has one, the target when it does not.
standingKey() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision: What this ruling supersedes: another ruling of the same scope on the same key, or on the same proposal.
startAt - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeRequest: GEO series accession to resume from, e.g.
startingColumns() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Returns the value of the startingColumns record component.
startingRows() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Returns the value of the startingRows record component.
startInitializationThread(boolean, boolean) - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
startInitializationThread(boolean, boolean) - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
startInitializationThread(boolean, boolean) - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
startInitializationThread(boolean, boolean) - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Start the initialization thread.
starts - Static variable in class ubic.gemma.core.ontology.jena.RO
startServer(ShellDelegatingBlat.BlattableGenome, boolean, boolean) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat: Start the server, if the port isn't already being used.
startTime - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
startTimeMillis - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse
StartupLogNoiseFilter - Class in ubic.gemma.rest.servlet: Suppresses a small whitelist of known-benign noisy log records emitted by third-party libraries at startup (and during normal request handling) that aren't actionable from our code.
StartupLogNoiseFilter() - Constructor for class ubic.gemma.rest.servlet.StartupLogNoiseFilter
state - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
state - Variable in class ubic.gemma.rest.PreboardedWebService.PreboardedResponse
STATE_CHANGED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType
Statement - Class in ubic.gemma.model.expression.experiment: A special kind of characteristic that act as a statement.
Statement() - Constructor for class ubic.gemma.model.expression.experiment.Statement
Statement.Factory - Class in ubic.gemma.model.expression.experiment
StatementCommit() - Constructor for class ubic.gemma.rest.DatasetsWebService.StatementCommit
StatementDao - Interface in ubic.gemma.persistence.service.expression.experiment
StatementDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
StatementDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl
StatementUtils - Class in ubic.gemma.model.expression.experiment
StatementUtils() - Constructor for class ubic.gemma.model.expression.experiment.StatementUtils
StatementValueObject - Class in ubic.gemma.model.expression.experiment: Represents a VO for a Statement, typically part of a FactorValueBasicValueObject.
StatementValueObject() - Constructor for class ubic.gemma.model.expression.experiment.StatementValueObject
StatementValueObject(Statement) - Constructor for class ubic.gemma.model.expression.experiment.StatementValueObject
StaticCacheKeyLock - Class in ubic.gemma.persistence.cache: Implementation of the CacheKeyLock interface that uses a static week map to store locks by key.
StaticCacheKeyLock(Cache, Object, boolean) - Constructor for class ubic.gemma.persistence.cache.StaticCacheKeyLock
statisticsEnabled - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
Stats - Class in ubic.gemma.core.util.math: Miscellaneous functions used for statistical analysis.
StatsWebService - Class in ubic.gemma.rest: Public statistics endpoints used by the Gemma home page and similar landing widgets.
StatsWebService() - Constructor for class ubic.gemma.rest.StatsWebService
status - Variable in class ubic.gemma.rest.AdminWebService.CurationAgentHealthResponse: UP, DOWN, or NOT_CONFIGURED.
status - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeWatermarkValueObject
status - Variable in class ubic.gemma.rest.AdminWebService.OntologyRefreshResponse
status - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
status - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
status - Variable in class ubic.gemma.rest.AnnotationSetsWebService.StatusRequest: Where the proposal stands.
status(AnnotationRelationStatus) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
STATUS_FAILED - Static variable in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: The most recent attempt failed.
STATUS_NOT_APPLICABLE - Static variable in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: Not applicable to this experiment -- so "never run" is not a gap.
STATUS_NOT_RUN - Static variable in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: Applicable to this experiment, but never attempted.
STATUS_OK - Static variable in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: The step has completed successfully.
STATUS_STALE - Static variable in class ubic.gemma.rest.PipelineStatusValueObject.PipelineStepValueObject: Ran successfully, and the experimental design has changed since -- so the result is still there but no longer describes the design it was computed from.
StatusRequest() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.StatusRequest
STD_I32BE - Static variable in class ubic.gemma.core.loader.util.hdf5.H5Type
STD_I64BE - Static variable in class ubic.gemma.core.loader.util.hdf5.H5Type
steal() - Method in interface ubic.gemma.core.util.locking.LockedPath: Steal this lock.
stealWithPath(Path) - Method in interface ubic.gemma.core.util.locking.LockedPath: Steal this lock with a different path.
stepSize() - Method in class ubic.gemma.core.util.math.distribution.Histogram
stolenAt - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockResponse
stolenFrom - Variable in class ubic.gemma.rest.DatasetsWebService.CurationLockResponse
stop() - Method in class ubic.gemma.core.logging.log4j.SlackAppender
stopServer() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat: Stop the gfServer, if it was started by this.
StopWatchUtils - Class in ubic.gemma.core.profiling: Utilities for working with StopWatch.
StopWatchUtils() - Constructor for class ubic.gemma.core.profiling.StopWatchUtils
StopWatchUtils.StopWatchRegion - Class in ubic.gemma.core.profiling
storageSize() - Method in class ubic.gemma.core.datastructure.sparse.SparseArrayList
storageSize() - Method in interface ubic.gemma.core.datastructure.sparse.SparseList: The number of elements actually stored.
storageSize() - Method in class ubic.gemma.core.datastructure.sparse.SparseRangeArrayList
strain - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
strainType() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Returns the value of the strainType record component.
stream(Query, Class, int, boolean, boolean) - Static method in class ubic.gemma.persistence.util.QueryUtils: Stream the result of a query with the given fetch size.
streamAll() - Method in class ubic.gemma.persistence.service.AbstractDao
streamAll() - Method in class ubic.gemma.persistence.service.AbstractService
streamAll() - Method in interface ubic.gemma.persistence.service.BaseDao: Stream all entities of T from the persistent storage.
streamAll() - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
streamAll() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
streamAll(boolean) - Method in class ubic.gemma.persistence.service.AbstractDao
streamAll(boolean) - Method in class ubic.gemma.persistence.service.AbstractService
streamAll(boolean) - Method in interface ubic.gemma.persistence.service.BaseDao: Stream all entities of type T from the persistent storage.
streamAll(boolean) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
streamAll(boolean) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
streamAndWriteProcessedExpressionData(ExpressionExperiment, boolean, boolean, Writer, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Stream the processed expression data to the writer while populating the cache file in the same pass.
streamAndWriteProcessedExpressionData(ExpressionExperiment, boolean, boolean, Writer, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
streamAndWriteRawExpressionData(ExpressionExperiment, QuantitationType, boolean, Writer, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Raw sibling of ExpressionDataFileService.streamAndWriteProcessedExpressionData(ExpressionExperiment, boolean, boolean, Writer, boolean).
streamAndWriteRawExpressionData(ExpressionExperiment, QuantitationType, boolean, Writer, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
streamAndWriteTabularSingleCellExpressionData(ExpressionExperiment, QuantitationType, int, boolean, boolean, Writer, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Tabular single-cell sibling of ExpressionDataFileService.streamAndWriteProcessedExpressionData(ExpressionExperiment, boolean, boolean, Writer, boolean) — the payloads here are the largest in the system, so the duplicated cold build this replaces was at its most expensive on this path: two concurrent full scans of the single-cell vectors per cold request.
streamAndWriteTabularSingleCellExpressionData(ExpressionExperiment, QuantitationType, int, boolean, boolean, Writer, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
streamByBatch(Query, String, Collection, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
streamByIdentifiableBatch(Query, String, Collection, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
streamCellIds(SingleCellDimension, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Stream the cell IDs of a dimension.
streamCellIds(SingleCellDimension, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
streamCellIds(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
streamCellIds(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
streamCellIds(ExpressionExperiment, QuantitationType, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
streamCellIds(ExpressionExperiment, QuantitationType, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
streamCellLevelCharacteristics(CellLevelCharacteristics, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
streamCellLevelCharacteristics(CellLevelCharacteristics, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
streamCellLevelCharacteristics(ExpressionExperiment, CellLevelCharacteristics, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
streamCellLevelCharacteristics(ExpressionExperiment, CellLevelCharacteristics, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
streamCellTypes(CellTypeAssignment, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
streamCellTypes(CellTypeAssignment, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
streamCellTypes(ExpressionExperiment, CellTypeAssignment, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
streamCellTypes(ExpressionExperiment, CellTypeAssignment, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
streamQuery(Function, Class, int, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.AbstractDao: Produce a stream over a Query with a new session if desired.
streamSingleCellDataVectors(ExpressionExperiment, List, QuantitationType, int, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
streamSingleCellDataVectors(ExpressionExperiment, List, QuantitationType, int, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
streamSingleCellDataVectors(ExpressionExperiment, List, QuantitationType, int, boolean, boolean, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
streamSingleCellDataVectors(ExpressionExperiment, List, QuantitationType, int, boolean, boolean, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
streamSingleCellDataVectors(ExpressionExperiment, QuantitationType, int, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain a stream over the vectors for a given QT.
streamSingleCellDataVectors(ExpressionExperiment, QuantitationType, int, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
streamSingleCellDataVectors(ExpressionExperiment, QuantitationType, int, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Obtain a stream over single-cell vectors for a given quantitation type.
streamSingleCellDataVectors(ExpressionExperiment, QuantitationType, int, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
streamSingleCellDataVectors(ExpressionExperiment, QuantitationType, int, boolean, boolean, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
streamSingleCellDataVectors(ExpressionExperiment, QuantitationType, int, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
streamSingleCellDataVectors(ExpressionExperiment, QuantitationType, int, boolean, boolean, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
streamSingleCellDataVectors(ExpressionExperiment, QuantitationType, int, boolean, boolean, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
streamWithoutStatementTimeout(Session, Supplier) - Static method in class ubic.gemma.persistence.hibernate.HibernateUtils: Lift the statement timeout for a streamed read, run streamCreator, and register the restore on the resulting stream.
stress - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
STRING - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
STRING - Enum constant in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType
STRING - Static variable in class ubic.gemma.core.loader.util.hdf5.H5Type: Represents a UTF-8 variable-length string.
STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
STRING() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
StringArrayArg - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be an array of strings.
stringArrayToBytes(String[], Charset) - Method in class ubic.gemma.persistence.util.ByteArrayConverter: Note that this method cannot differentiate between empty strings and null strings.
stringArrayToTabbedBytes(String[], Charset) - Method in class ubic.gemma.persistence.util.ByteArrayConverter: Convert an array of strings to a byte array where the delimiter is a tab character.
StringDistance - Class in ubic.gemma.core.util.math: String distance metrics (Levenshtein edit distance and prefix/suffix weighted Hamming variants).
StringDistance() - Constructor for class ubic.gemma.core.util.math.StringDistance
StringMatrix<R,C> - Class in ubic.gemma.core.util.matrix: A NamedMatrix containing String objects.
StringMatrix(int, int) - Constructor for class ubic.gemma.core.util.matrix.StringMatrix
StringMatrixReader - Class in ubic.gemma.core.util.matrix: Reader for StringMatrix.
StringMatrixReader() - Constructor for class ubic.gemma.core.util.matrix.StringMatrixReader
stringPixelWidth(String, FontMetrics) - Static method in class ubic.gemma.core.util.graphics.text.Util
stringsToByteArray(String[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
stringsToByteArray(String[], Charset) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
stringsToTabbedBytes(String[]) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
stringsToTabbedBytes(String[], Charset) - Static method in class ubic.gemma.persistence.util.ByteArrayUtils
StringUtil - Class in ubic.gemma.core.util: String helpers (R-style name munging, common prefix/suffix, CSV split, etc.).
StringUtil() - Constructor for class ubic.gemma.core.util.StringUtil
StringUtils - Class in ubic.gemma.core.util: Various utilities for manipulating strings.
StringUtils() - Constructor for class ubic.gemma.core.util.StringUtils
stripByCriterion(DoubleMatrix1D, DoubleFunction) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
stripNegative(DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
stripNonOK(DoubleMatrix1D, BooleanArrayList) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil
stripPolyAorT(String, int) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Remove a 3' polyA or 5' polyT tail.
SUB_DELIMITER - Static variable in class ubic.gemma.core.util.TsvUtils: Delimiter used when printing a list of strings in a column.
SUB_DELIMITER_STR - Static variable in class ubic.gemma.core.util.TsvUtils
subClause() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
subClause() - Method in class ubic.gemma.rest.util.args.FilterArgParser
subClause(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
SubClauseContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
subclusterOf - Static variable in class ubic.gemma.core.ontology.jena.RO
SUBJECT_IMPLIES_OBJECT - Enum constant in enum class ubic.gemma.model.common.description.RelationInferenceDirection: The subject is the specific end: knowing the subject tells you the object.
SUBJECT_TO_OBJECT - Enum constant in enum class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.Direction: Seed terms are subjects; return objects.
subjectBreadth(long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
subjectCategory(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
subjectCategoryUri(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
subjectCategoryUris(Collection) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
subjectIsADisease(String, String) - Static method in enum class ubic.gemma.model.common.description.RelationTopicality: Whether this row's subject is a disease, by either signal.
subjectValue(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
subjectValues(Collection) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
subjectValueUri(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
subjectValueUris(Collection) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
subList(int, int) - Method in class ubic.gemma.model.util.UninitializedList
submit(Runnable) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextAsyncTaskExecutor
submit(Runnable) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
submit(Runnable, T) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
submit(String, Collection, Contact, String, String) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService: Create a batch + one job per experiment, dispatch each to the configured scheduler.
submit(String, Collection, Contact, String, String) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl
submit(Callable) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextAsyncTaskExecutor
submit(Callable) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
submit(SubmitRequest) - Method in class ubic.gemma.core.pipeline.LuigiPipelineScheduler
submit(SubmitRequest) - Method in class ubic.gemma.core.pipeline.MockPipelineScheduler
submit(SubmitRequest) - Method in class ubic.gemma.core.pipeline.NextflowPipelineScheduler
submit(SubmitRequest) - Method in interface ubic.gemma.core.pipeline.PipelineScheduler: Submit one job to the scheduler.
submitAnnotationSet(DatasetArg, AnnotationSetsWebService.AnnotationSetRequest) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Create or upsert an annotation set on a dataset.
submitBatch(AdminPipelineWebService.SubmitBatchRequest) - Method in class ubic.gemma.rest.AdminPipelineWebService
SubmitBatchRequest() - Constructor for class ubic.gemma.rest.AdminPipelineWebService.SubmitBatchRequest
submitDatasetAnnotationSet(DatasetArg, AnnotationSetsWebService.AnnotationSetRequest) - Method in class ubic.gemma.rest.DatasetsWebService
submitGeoScrape(AdminWebService.GeoScrapeRequest) - Method in class ubic.gemma.rest.AdminWebService: Deprecated.
The curation agent scrapes GEO itself (scrape_geo_and_open_triage.py) and opens its own triage ticket. Still functional; see GeoScrapeService for what an agent-side replacement has to reproduce -- the preboarded rows, the watermark, and ONE batch ticket.
submitMultifunctionalityRecompute(TaxonArg) - Method in class ubic.gemma.rest.AdminWebService: Async port of MultifunctionalityCli: recompute per-gene multifunctionality scores for a single taxon.
submitPlatformReportsRegeneration() - Method in class ubic.gemma.rest.AdminWebService: Submit an async regeneration of the cached reports for EVERY platform.
SubmitRequest - Class in ubic.gemma.core.pipeline: Payload handed to PipelineScheduler.submit(SubmitRequest).
SubmitRequest(Long, String, Long, String) - Constructor for class ubic.gemma.core.pipeline.SubmitRequest
submitTask(T) - Method in interface ubic.gemma.core.job.TaskRunningService
submitTask(T) - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
submitTaskCommand(C) - Method in interface ubic.gemma.core.job.TaskRunningService: Submit a task and track its progress.
submitTaskCommand(C) - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
submittedJobId - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeSubmitResponse
submittedJobId - Variable in class ubic.gemma.rest.AdminWebService.MultifunctionalityRecomputeResponse: Submitted task ID.
submittedJobId - Variable in class ubic.gemma.rest.AdminWebService.ObsoleteTermCorrectionSubmission
submittedJobId - Variable in class ubic.gemma.rest.AdminWebService.SubmittedJobResponse: Poll GET /tasks/{id} with this.
submittedJobIds - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchResponse: Submitted task IDs in the same order as the cleaned accession list.
SubmittedJobResponse() - Constructor for class ubic.gemma.rest.AdminWebService.SubmittedJobResponse
SubmittedTask - Interface in ubic.gemma.core.job: Obtained from the TaskRunningService, can be used to monitor status.
SubmittedTask.Status - Enum Class in ubic.gemma.core.job
SubmittedTasksMaintenance - Class in ubic.gemma.core.job
SubmittedTasksMaintenance() - Constructor for class ubic.gemma.core.job.SubmittedTasksMaintenance
SUBMITTER_INSTUTUTE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
Subquery - Class in ubic.gemma.persistence.util: Represents a subquery right-hand side of a Filter.
Subquery(String, String, List, List) - Constructor for class ubic.gemma.persistence.util.Subquery
Subquery(String, String, List, Filter) - Constructor for class ubic.gemma.persistence.util.Subquery
Subquery.Alias - Class in ubic.gemma.persistence.util
SubqueryMode - Enum Class in ubic.gemma.persistence.util: Mode to use when filtering with a subquery.
SubqueryUtils - Class in ubic.gemma.persistence.util
SubqueryUtils() - Constructor for class ubic.gemma.persistence.util.SubqueryUtils
subSeries - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
subSeriesOf - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
subSeriesStatus(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig.GeoRetrieveConfigBuilder: Fill sub-series status.
subset(int, int, int, int) - Method in interface ubic.gemma.core.util.matrix.ObjectMatrix
subset(int, int, int, int) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
subset(int, int, int, int) - Method in class ubic.gemma.core.util.matrix.StringMatrix
subset(Collection) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: This creates a new GeoValues that has data only for the selected samples.
SUBSET_DESCRIPTION - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
SUBSET_VARIABLE_TYPE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
subsetColumns(List) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
subsetColumns(List) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
subsetColumns(List) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix: Create a copy of this matrix with only the selected columns, in the selected order.
subsetColumns(List) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
subsetColumns(List) - Method in interface ubic.gemma.core.util.matrix.ObjectMatrix
subsetColumns(List) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
subsetColumns(List) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
subsetColumns(List) - Method in class ubic.gemma.core.util.matrix.StringMatrix
SubsetRef(Long, String, List) - Constructor for class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef
subsetRows(List) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
subsetRows(List) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
subsetRows(List) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix: Create a copy of this matrix with only the selected rows, in the selected order.
subsetRows(List) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
subsetRows(List) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
subsets() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellSubSetsCreatedPayload: Returns the value of the subsets record component.
SUCCESS - Static variable in class ubic.gemma.cli.util.AbstractCLI: Exit code used for a successful AbstractCLI.doWork() execution.
suffixWeightedHammingDistance(String, String, double) - Static method in class ubic.gemma.core.util.math.StringDistance: Compute the Hamming distance between two strings of equal length (if they are of unequal length the longer one is trimmed), giving higher weight to characters at the end of the strings.
sum(double[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sum(float[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sum(int[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sum(long[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sum(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the sum of a data sequence.
sum(DataVector) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sum(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
sum(SingleCellExpressionDataVector, CellLevelCharacteristics) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
SUM - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
SUM - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl.SingleCellExpressionAggregationMethod: Aggregate data by summing it.
sumArray(int[]) - Static method in class ubic.gemma.core.util.math.MathUtil
summariesForGroupNames(Collection) - Method in class ubic.gemma.rest.GroupsWebService: Public hook for DatasetsWebService so the dataset-groups route can reuse the GroupSummary projection without duplicating the mapping.
summarize() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
summarize(boolean) - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
summarizeByKeys(boolean) - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
summarizeMapResults(Collection) - Method in interface ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService: Non-HQL version of the composite sequence data summary query.
summarizeMapResults(Collection) - Method in class ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl
summarizeMapResults(ArrayDesign) - Method in interface ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService
summarizeMapResults(ArrayDesign) - Method in class ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl
summary - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
summary(String, String, int, String) - Static method in class ubic.gemma.core.loader.entrez.EutilFetch: Attempts to fetch data via Eutils; failures will be re-attempted several times.
summary(String, EntrezQuery, EntrezRetmode, int, int, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils: Summarize a previous EntrezUtils.search(String, String, EntrezRetmode, String) query.
Summary() - Constructor for class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
sumOfInversions(DoubleArrayList, int, int) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the sum of inversions of a data sequence, which is Sum( 1.0 / data[i]).
sumOfLogarithms(DoubleArrayList, int, int) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the sum of logarithms of a data sequence, which is Sum( Log(data[i]).
sumOfPowerDeviations(DoubleArrayList, int, double) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns Sum( (data[i]-c)k ); optimized for common parameters like c == 0.0 and/or k == -2 .. 4.
sumOfPowerDeviations(DoubleArrayList, int, double, int, int) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns Sum( (data[i]-c)k ) for all i = from .. to; optimized for common parameters like c == 0.0 and/or k == -2 .. 5.
sumOfPowers(DoubleArrayList, int) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the sum of powers of a data sequence, which is Sum ( data[i]k ).
sumOfSquaredDeviations(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Compute the sum of the squared deviations from the mean of a data sequence.
sumOfSquares(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the sum of squares of a data sequence.
sumOfSquares(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixRowStats: Calculates the sum of squares for each row of a matrix
sums(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixRowStats: Calculate the sums of a matrix's rows.
sumUnscaled(double[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive: Calculate the sum of the data in the vector, but keep the result unscaled.
sumUnscaled(float[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sumUnscaled(int[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sumUnscaled(long[], ScaleType) - Static method in class ubic.gemma.core.analysis.stats.DataVectorDescriptive
sumUnscaled(SingleCellExpressionDataVector) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
sumWithUnknown(SingleCellExpressionDataVector, CellLevelCharacteristics) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
superSeries - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
SUPPLEMENTARY_FILES - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
supports(ConfigAttribute) - Method in class ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProvider
supports(ConfigAttribute) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter
supports(ConfigAttribute) - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoter
SuppressArchUnit - Annotation Interface in ubic.gemma.core.architecture: Targeted opt-out marker for ArchUnit production-code rules.
SuppressBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch
SuppressBatchTaskSummaryWriter() - Constructor for class ubic.gemma.cli.batch.SuppressBatchTaskSummaryWriter
suppressMatching - Variable in class ubic.gemma.rest.AdminWebService.ImportGeoBatchRequest
SuspiciousValueResult(int, String, int, String, String) - Constructor for class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult: Creates a new SuspiciousValueResult instance.
SuspiciousValuesForQuantitationException - Exception Class in ubic.gemma.core.analysis.preprocess.detect: Exception raised when suspicious values are detected in an ExpressionDataMatrix.
SuspiciousValuesForQuantitationException(QuantitationType, String, List) - Constructor for exception class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException
SuspiciousValuesForQuantitationException.SuspiciousValueResult - Class in ubic.gemma.core.analysis.preprocess.detect
svd(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService: Compute and update the SVD analysis fo the given experiment.
svd(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
SVDCli - Class in ubic.gemma.apps
SVDCli() - Constructor for class ubic.gemma.apps.SVDCli
SVDException - Exception Class in ubic.gemma.core.analysis.preprocess.svd: Exception raised when the SVD of a given expression data matrix cannot be computed.
SVDException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.svd.SVDException
SVDRelatedPreprocessingException - Exception Class in ubic.gemma.core.analysis.preprocess: Exception raised if a SVD cannot be computed.
SVDRelatedPreprocessingException(ExpressionExperiment, SVDException) - Constructor for exception class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException
SVDResult - Class in ubic.gemma.core.analysis.preprocess.svd: Store information about SVD of expression data and comparisons to factors/batch information.
SVDResult(PrincipalComponentAnalysis) - Constructor for class ubic.gemma.core.analysis.preprocess.svd.SVDResult
SVDService - Interface in ubic.gemma.core.analysis.preprocess.svd: Performs Singular value decomposition on experiment data to get eigengenes, and does comparison of those PCs to factors recorded in the experimental design.
SVDServiceImpl - Class in ubic.gemma.core.analysis.preprocess.svd: Perform SVD on expression data and store the results.
SVDServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
SvdTask - Interface in ubic.gemma.core.tasks.analysis.expression
SvdTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
SvdTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
SvdTaskCommand(ExpressionExperiment, boolean) - Constructor for class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
SvdTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression
SvdTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.SvdTaskImpl
SwissProtParser - Class in ubic.gemma.core.loader.genome.gene: This does a very minimal parse of Swissprot records, just to get mRNAs associated with a single protein.
SwissProtParser() - Constructor for class ubic.gemma.core.loader.genome.gene.SwissProtParser
switchExperimentToArrayDesign(ExpressionExperiment, ArrayDesign) - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService: If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatform
switchExperimentToMergedPlatform(ExpressionExperiment) - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService: Automatically identify an appropriate merged platform
SYMBOL_PREFIX - Enum constant in enum class ubic.gemma.model.common.search.SearchMatchType: Inexact prefix match on an official symbol (SQL LIKE 'foo%').
SymbolFontPua - Class in ubic.gemma.core.util: Repairs Adobe Symbol-font text that was mapped into the Unicode Private Use Area.
SYNAPSE - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
SynapseUtils - Class in ubic.gemma.core.loader.expression.synapse
SynapseUtils() - Constructor for class ubic.gemma.core.loader.expression.synapse.SynapseUtils
SYNCED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.ExternalIssueSyncState: External issue is in agreement with the local ticket.
SYNONYM_TOKENS - Enum constant in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia: Same as AnnotationsWebService.MatchedVia.LABEL_TOKENS but the coverage check passed against a synonym (preferred-label coverage failed).
synonyms() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTerm: Returns the value of the synonyms record component.
SYNTHETIC_LONG_READ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
SYSTEM - Enum constant in enum class ubic.gemma.cli.util.CLI.CommandGroup
SYSTEM_WIDE_SALT - Static variable in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider: Historical SystemWideSaltSource value from build.properties (commit 66f574e926, 2008-10-02).
SystemCLIContext - Class in ubic.gemma.cli.util: A context for the CLI based on System.
SystemCLIContext(String, String[]) - Constructor for class ubic.gemma.cli.util.SystemCLIContext
systemLoadAverage - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse: -1.0 on platforms where the load average is unavailable (e.g.
SystemSnapshotResponse() - Constructor for class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse

T

T__0 - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
T__0 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
T__1 - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
T__1 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
T__2 - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
T__2 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
TableMaintenanceUtil - Interface in ubic.gemma.persistence.service.maintenance
TableMaintenanceUtilImpl - Class in ubic.gemma.persistence.service.maintenance: Functions for maintaining the database.
TableMaintenanceUtilImpl() - Constructor for class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
TABULAR - Enum constant in enum class ubic.gemma.core.analysis.service.ExpressionExperimentDataFileType
TABULAR_BULK_DATA_FILE_SUFFIX - Static variable in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
TABULAR_SC_DATA_SUFFIX - Static variable in class ubic.gemma.core.analysis.service.ExpressionDataFileUtils
TabularMatrixWriter - Class in ubic.gemma.core.datastructure.matrix.io: Write a set of single-cell vectors to a simple tabular format.
TabularMatrixWriter(EntityUrlBuilder, BuildInfo) - Constructor for class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
TAG_LENGTH - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
TagAdd(String, Characteristic) - Constructor for class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.TagAdd
TagAddedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted when a single experiment-level annotation (tag) is added to an ExpressionExperiment via the REST annotation write endpoints.
TagAddedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TagAddedEvent
TagCommit() - Constructor for class ubic.gemma.rest.DatasetsWebService.TagCommit
tagCount - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
tagCount - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
TagRemovedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted when a single experiment-level annotation (tag) is removed from an ExpressionExperiment via the REST annotation write endpoints.
TagRemovedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TagRemovedEvent
TARGET_ADDED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType: An experiment (or other target) was added to the ticket after it was opened — only possible on a ticket whose acceptsTargets flag is set.
TARGET_REMOVED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType: A target was removed from the ticket.
TARGET_STATUS_CHANGED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType
TargetAddition(Ticket, boolean) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService.TargetAddition
TARGETED_CAPTURE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
targetId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionRequest: Which target, in the producer's own numbering.
targetId - Variable in class ubic.gemma.rest.AnnotationSetsWebService.DispositionResponse
TargetRef() - Constructor for class ubic.gemma.rest.TicketsWebService.AddTargetRequest.TargetRef
TAS - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode
Task<C> - Interface in ubic.gemma.core.job
TaskCommand - Class in ubic.gemma.core.job: This command class is used to allow communication of parameters for a task between a client and task running service, which might be on a different computer.
TaskCommand() - Constructor for class ubic.gemma.core.job.TaskCommand
TaskError() - Constructor for class ubic.gemma.rest.TaskStatusValueObject.TaskError
taskExecutor(int) - Method in class ubic.gemma.core.config.ServiceBeansConfig: Local short-lived task executor.
TaskExecutorConfig - Class in ubic.gemma.core.security.concurrent
TaskExecutorConfig() - Constructor for class ubic.gemma.core.security.concurrent.TaskExecutorConfig
taskExecutorSecurityContextDelegatePostProcessor() - Static method in class ubic.gemma.core.security.concurrent.TaskExecutorConfig
TaskExecutorSecurityContextDelegatePostProcessor - Class in ubic.gemma.core.security.concurrent: Post-processor that wraps TaskExecutor, AsyncTaskExecutor and SchedulingTaskExecutor with a DelegatingSecurityContextTaskExecutor.
TaskExecutorSecurityContextDelegatePostProcessor() - Constructor for class ubic.gemma.core.security.concurrent.TaskExecutorSecurityContextDelegatePostProcessor
taskExecutorThreadContextInheritPostProcessor() - Static method in class ubic.gemma.core.logging.log4j.Log4jConfig
TaskExecutorThreadContextInheritPostProcessor - Class in ubic.gemma.core.logging.log4j: Post-process TaskExecutor, AsyncTaskExecutor and SchedulingTaskExecutor such that they inherit the ThreadContext of their callers.
TaskExecutorThreadContextInheritPostProcessor() - Constructor for class ubic.gemma.core.logging.log4j.TaskExecutorThreadContextInheritPostProcessor
TaskMailUtils - Interface in ubic.gemma.core.job.notification
TaskMailUtilsImpl - Class in ubic.gemma.core.job.notification
TaskMailUtilsImpl() - Constructor for class ubic.gemma.core.job.notification.TaskMailUtilsImpl
TaskPostProcessing - Interface in ubic.gemma.core.job.notification: author: anton date: 10/02/13
TaskPostProcessingImpl - Class in ubic.gemma.core.job.notification: author: anton date: 10/02/13
TaskPostProcessingImpl() - Constructor for class ubic.gemma.core.job.notification.TaskPostProcessingImpl
TaskResult - Class in ubic.gemma.core.job: This class describes the result of long-running task.
TaskResult(Serializable) - Constructor for class ubic.gemma.core.job.TaskResult
TaskRunningService - Interface in ubic.gemma.core.job
TaskRunningServiceImpl - Class in ubic.gemma.core.job: Handles the execution of tasks in threads that can be checked by clients later.
TaskRunningServiceImpl() - Constructor for class ubic.gemma.core.job.TaskRunningServiceImpl
tasks - Variable in class ubic.gemma.rest.AdminWebService.JobsListResponse
TaskStatusValueObject - Class in ubic.gemma.rest: Snapshot of a SubmittedTask for the REST API.
TaskStatusValueObject() - Constructor for class ubic.gemma.rest.TaskStatusValueObject
TaskStatusValueObject(SubmittedTask) - Constructor for class ubic.gemma.rest.TaskStatusValueObject
TaskStatusValueObject.TaskError - Class in ubic.gemma.rest: Machine-readable classification of a failed task, so a REST client can react to the failure (link to the existing experiment, correct the accession, retry a transient network error, or surface the raw detail) rather than parsing a free-text message.
TasksWebService - Class in ubic.gemma.rest: RESTful interface for polling background pipeline tasks submitted via the dispatch endpoints on DatasetsWebService (preprocess, diagnostics, batch info fetch, differential analysis run/redo/remove).
TasksWebService() - Constructor for class ubic.gemma.rest.TasksWebService
TaxaWebService - Class in ubic.gemma.rest: RESTful interface for taxa.
TaxaWebService(TaxonService, ExpressionExperimentService, TaxonArgService, DatasetArgService, GeneArgService, GeneService) - Constructor for class ubic.gemma.rest.TaxaWebService: Constructor for service autowiring
Taxon - Class in ubic.gemma.model.genome
Taxon() - Constructor for class ubic.gemma.model.genome.Taxon
Taxon(int, String) - Constructor for record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata.Taxon: Creates an instance of a Taxon record class.
TAXON - Enum constant in enum class ubic.gemma.cli.completion.CompletionType
Taxon.Factory - Class in ubic.gemma.model.genome
TaxonArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for Taxon API
TaxonArg(String, Class, T) - Constructor for class ubic.gemma.rest.util.args.TaxonArg
TaxonArgService - Class in ubic.gemma.rest.util.args
TaxonArgService(TaxonService, ChromosomeService, GeneService) - Constructor for class ubic.gemma.rest.util.args.TaxonArgService
TaxonArrayArg - Class in ubic.gemma.rest.util.args
taxonCommonName(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
taxonConstraint(Taxon) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Constraint results to to be related to the given taxon.
TaxonConstraint(String, Integer, String) - Constructor for class ubic.gemma.core.ontology.model.OntologyTerm.TaxonConstraint
TaxonConstraintValueObject(boolean, String, Integer, String, List) - Constructor for class ubic.gemma.rest.AnnotationsWebService.TaxonConstraintValueObject: Creates a new TaxonConstraintValueObject instance.
TaxonDao - Interface in ubic.gemma.persistence.service.genome.taxon
TaxonDaoImpl - Class in ubic.gemma.persistence.service.genome.taxon
TaxonDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
TaxonFetcher - Class in ubic.gemma.core.loader.genome.taxon: Taxon information from NCBI comes as a tar.gz archive; only the names.dmp file is of interest.
TaxonFetcher() - Constructor for class ubic.gemma.core.loader.genome.taxon.TaxonFetcher
taxonId - Variable in class ubic.gemma.rest.AdminWebService.MultifunctionalityRecomputeResponse: Resolved Gemma taxon ID.
taxonId - Variable in class ubic.gemma.rest.ExperimentSetsWebService.ExperimentSetRequest: Declare the taxon constraint explicitly; omit to derive it from the members.
taxonId(Long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
taxonId(Long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
TaxonIdArg - Class in ubic.gemma.rest.util.args: Long argument type for taxon API, referencing the Taxon ID.
TaxonLoader - Class in ubic.gemma.core.loader.genome.taxon: Load taxa into the system.
TaxonLoader() - Constructor for class ubic.gemma.core.loader.genome.taxon.TaxonLoader
TaxonLoaderCli - Class in ubic.gemma.apps
TaxonLoaderCli() - Constructor for class ubic.gemma.apps.TaxonLoaderCli
taxonName - Variable in class ubic.gemma.rest.AdminWebService.MultifunctionalityRecomputeResponse: Resolved taxon common name (e.g.
TaxonNameArg - Class in ubic.gemma.rest.util.args: String argument type for taxon API, referencing the Taxon scientific name or common name.
taxonNcbiId(Integer) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
TaxonNcbiIdArg - Class in ubic.gemma.rest.util.args: Long argument type for taxon API, referencing the Taxon ID.
TaxonParser - Class in ubic.gemma.core.loader.genome.taxon: Parse the "names.dmp" file from NCBI, ftp://ftp.ncbi.nih.gov/pub/taxonomy/.
TaxonParser() - Constructor for class ubic.gemma.core.loader.genome.taxon.TaxonParser
TaxonReadService - Interface in ubic.gemma.persistence.service.genome.taxon: Read-only retrieval service for Taxon.
TaxonReadServiceImpl - Class in ubic.gemma.persistence.service.genome.taxon: Implementation of TaxonReadService.
TaxonReadServiceImpl(TaxonDao, ExpressionExperimentService, ArrayDesignService) - Constructor for class ubic.gemma.persistence.service.genome.taxon.TaxonReadServiceImpl
TaxonService - Interface in ubic.gemma.persistence.service.genome.taxon
TaxonServiceImpl - Class in ubic.gemma.persistence.service.genome.taxon
TaxonServiceImpl(TaxonDao) - Constructor for class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
TaxonStat() - Constructor for class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
TaxonStat(Long, String, String, long) - Constructor for class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
TaxonUtils - Class in ubic.gemma.persistence.service.genome.taxon: A utility class for taxon.
TaxonUtils() - Constructor for class ubic.gemma.persistence.service.genome.taxon.TaxonUtils
TaxonValueObject - Class in ubic.gemma.model.genome
TaxonValueObject() - Constructor for class ubic.gemma.model.genome.TaxonValueObject
TaxonValueObject(int, String) - Constructor for class ubic.gemma.rest.AnnotationsWebService.TaxonValueObject: Creates a new TaxonValueObject instance.
TaxonValueObject(Long) - Constructor for class ubic.gemma.model.genome.TaxonValueObject
TaxonValueObject(Long, String) - Constructor for class ubic.gemma.model.genome.TaxonValueObject
TaxonValueObject(Taxon) - Constructor for class ubic.gemma.model.genome.TaxonValueObject
TaxonWithUsageStatisticsValueObject(Taxon, Long) - Constructor for class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject
TdbOntologyService - Class in ubic.gemma.core.ontology.jena: An implementation based on Jena TDB.
TdbOntologyService(String, Path, String, boolean, String, boolean) - Constructor for class ubic.gemma.core.ontology.jena.TdbOntologyService
technicalReplicateExtract - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType
technicalReplicateLabeledExtract - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType
TechnologyType - Enum Class in ubic.gemma.model.expression.arrayDesign
temperature - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
TEMPERATURE - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementKind
temporaryPassword - Variable in class ubic.gemma.rest.AdminWebService.CreateUserResponse: Server-generated 16-char temp password.
temporaryPassword - Variable in class ubic.gemma.rest.AdminWebService.ResetPasswordResponse: Server-generated 16-char temp password.
TenXCellRangerUtils - Class in ubic.gemma.core.loader.expression.singleCell: Utilities for detecting 10x Cell Ranger data in GEO series and sample metadata.
TenXCellRangerUtils() - Constructor for class ubic.gemma.core.loader.expression.singleCell.TenXCellRangerUtils
TERM_LEVEL - Enum constant in enum class ubic.gemma.model.common.description.RelationTopicality: The relation says what the subject term IS or where it came from: a disease it models, the patient it derives from, the tissue or organism it came from, the role a compound plays.
TERM_REPLACED_BY_URI - Static variable in class ubic.gemma.core.ontology.OntologyUtils: IAO:0100001 term replaced by — the OBO property an ontology uses to name the exact substitute for a term it has obsoleted.
TermCanonicalization - Class in ubic.gemma.core.ontology: A single in-place rewrite that OntologyTermValidator applied to a slot of a Characteristic while grounding it — the slot still passes (it is not a TermViolation), but what was stored differs from what was submitted, so a client can echo the correction back to its display.
TermCanonicalization(String, String, String, String, String) - Constructor for class ubic.gemma.core.ontology.TermCanonicalization
TermCorrection() - Constructor for class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection
termCount - Variable in class ubic.gemma.rest.AdminWebService.OntologyStatusValueObject: Populated only when the request specifies `includeTermCount=true` AND the ontology is loaded.
termIdOrUriToUri(String) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Normalize any spelling of a term identifier to its URI.
termIdToUri(String) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Converts an OBO term ID to a URI.
termLevelOnly(boolean) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery: Keep only relations that say something about the subject term, dropping per-experiment parameters.
TermStat() - Constructor for class ubic.gemma.core.analysis.report.HomeStats.TermStat
TermStat(String, String, long) - Constructor for class ubic.gemma.core.analysis.report.HomeStats.TermStat
TermViolation - Class in ubic.gemma.core.ontology: A single ontology-term grounding failure found by OntologyTermValidator: one term slot (category / value / predicate / object / …) whose URI does not resolve, or resolves to a term whose label disagrees with the submitted one.
TermViolation(String, String, String, String, TermViolation.Reason) - Constructor for class ubic.gemma.core.ontology.TermViolation
TermViolation.Reason - Enum Class in ubic.gemma.core.ontology
test(DoubleArrayList, IntArrayList) - Static method in class ubic.gemma.core.util.math.KruskalWallis: Perform a Kruskal-Wallis one-way ANOVA.
test(BioAssaySet) - Static method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtils
TEST - Static variable in class ubic.gemma.core.context.EnvironmentProfiles: Mutually-exclusive environment profiles.
TestBootstrapState - Class in ubic.gemma.persistence.initialization: JVM-wide one-shot guard for the integration-test database bootstrap.
TestComponent - Annotation Interface in ubic.gemma.core.context: This will exclude the component or configuration from component scanning.
testDataSource(String, String, String, int, int) - Method in class ubic.gemma.core.config.DataSourceConfig: Test datasource.
testGroupAgentSecurityContext(ManualAuthenticationService, String, String) - Method in class ubic.gemma.core.config.DataSourceConfig: Test-profile variant of DataSourceConfig.groupAgentSecurityContext(ManualAuthenticationService, String, String): same bean id, different credential keys (gemma.testdb.agent.*) so test runs don't authenticate against production credentials.
TETHERED_CHROMATIN_CONFORMATION_CAPTURE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
TEXT - Enum constant in enum class ubic.gemma.core.loader.entrez.EntrezRetmode
TEXT_PLAIN_UTF8 - Static variable in class ubic.gemma.rest.PlatformsWebService
TEXT_PLAIN_UTF8_TYPE - Static variable in class ubic.gemma.rest.PlatformsWebService
TEXT_TAB_SEPARATED_VALUES_UTF8 - Static variable in class ubic.gemma.rest.DatasetsWebService
TEXT_TAB_SEPARATED_VALUES_UTF8 - Static variable in class ubic.gemma.rest.PlatformsWebService
TEXT_TAB_SEPARATED_VALUES_UTF8_Q9 - Static variable in class ubic.gemma.rest.AnalysisResultSetsWebService
TEXT_TAB_SEPARATED_VALUES_UTF8_TYPE - Static variable in class ubic.gemma.rest.DatasetsWebService
TEXT_TAB_SEPARATED_VALUES_UTF8_TYPE - Static variable in class ubic.gemma.rest.PlatformsWebService
TextBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch
TextBatchTaskSummaryWriter(Appendable) - Constructor for class ubic.gemma.cli.batch.TextBatchTaskSummaryWriter
TextResourceToSetOfLinesFactoryBean - Class in ubic.gemma.core.util: Converts a text resource into a set of lines.
TextResourceToSetOfLinesFactoryBean(Resource) - Constructor for class ubic.gemma.core.util.TextResourceToSetOfLinesFactoryBean
TfPerturbationMatcher - Class in ubic.gemma.core.geoscrape: Cheesy v1 transcription-factor perturbation matcher.
TfPerturbationMatcher() - Constructor for class ubic.gemma.core.geoscrape.TfPerturbationMatcher
TGFVO - Class in ubic.gemma.core.ontology.jena: Vocabulary for The Gemma Factor Value Ontology (TGFVO).
TGFVO() - Constructor for class ubic.gemma.core.ontology.jena.TGFVO
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService: Deprecated.
Use BulkExpressionDataVectorService.findAndThaw(QuantitationType), BulkExpressionDataVectorService.findAndThaw(Collection) or BulkExpressionDataVectorService.findAndThaw(BioAssayDimension) instead, it's much more efficient.
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao: Thaw a collection of vectors.
thaw(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService: Thaw a collection of DifferentialExpressionAnalysis for full traversal.
thaw(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
thaw(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
thaw(Collection) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
thaw(Collection) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
thaw(Collection) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Thaw a collection of platforms.
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorService: Thaw both raw and processed vectors.
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl: Deprecated.
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService: Thaw a collection of BioMaterial for full traversal.
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService: Thaw a collection of CompositeSequence for full traversal.
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
thaw(Collection) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
thaw(Collection) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService
thaw(Collection) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
thaw(Collection) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao
thaw(Collection) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao
thaw(Collection) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao
thaw(Collection) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadService
thaw(Collection) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadServiceImpl
thaw(Collection) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService
thaw(Collection) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl
thaw(T) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService
thaw(T) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
thaw(T) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService: Deprecated.
thaw(T) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao: Thaw the given vector.
thaw(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService: Thaw a single DifferentialExpressionAnalysis for full traversal.
thaw(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
thaw(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
thaw(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
thaw(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Initialize the analysis and subset factor vale.
thaw(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
thaw(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
thaw(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
thaw(ExpressionExperimentSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
thaw(ExpressionExperimentSet) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
thaw(ExpressionExperimentSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
thaw(ExpressionExperimentSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
thaw(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
thaw(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
thaw(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
thaw(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl
thaw(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
thaw(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
thaw(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Thaw the given platform as per ArrayDesignDao.thawLite(ArrayDesign) with its probes and genes.
thaw(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
thaw(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
thaw(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
thaw(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Thaw a given platform.
thaw(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
thaw(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
thaw(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl
thaw(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
thaw(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
thaw(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService: Fully thaw a dimension.
thaw(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl
thaw(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService: Thaw a single BioMaterial for full traversal.
thaw(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl
thaw(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
thaw(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
thaw(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
thaw(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
thaw(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService: Thaw a single CompositeSequence for full traversal.
thaw(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl
thaw(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
thaw(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
thaw(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDao
thaw(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl
thaw(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorReadService
thaw(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorReadServiceImpl
thaw(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
thaw(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl
thaw(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Thaw everything.
thaw(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
thaw(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
thaw(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
thaw(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
thaw(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
thaw(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
thaw(BioSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
thaw(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService
thaw(BioSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl
thaw(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
thaw(BioSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
thaw(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
thaw(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
thaw(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
thaw(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
thaw(Gene) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
thaw(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
thaw(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductDao
thaw(GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
thaw(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductReadService
thaw(GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductReadServiceImpl
thaw(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
thaw(GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
thaw(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
thaw(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
thaw(AnnotationAssociation) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao
thaw(AnnotationAssociation) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
thaw(BlatAssociation) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao
thaw(BlatAssociation) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl
thaw(BlatResult) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao
thaw(BlatResult) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl
thaw(BlatResult) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadService
thaw(BlatResult) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadServiceImpl
thaw(BlatResult) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService
thaw(BlatResult) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl
thawAliases(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
thawAliases(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
thawAliases(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
thawAliases(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
thawAliases(Gene) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
thawAliases(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl: Only thaw the Aliases, very light version
thawAll(Collection) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Batch counterpart to ExpressionAnalysisResultSetDao.thaw(ExpressionAnalysisResultSet) for a whole page of result sets.
thawAll(Collection) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
thawBibliographicReference(BibliographicReference) - Static method in class ubic.gemma.persistence.util.Thaws
thawBioAssay(BioAssay) - Static method in class ubic.gemma.persistence.util.Thaws: Thaw the given BioAssay.
thawBioAssayDimension(BioAssayDimension) - Static method in class ubic.gemma.persistence.util.Thaws
thawBioAssayPlatforms(BioAssay) - Static method in class ubic.gemma.persistence.util.Thaws: Thaw the platform-side associations of a BioAssay without walking its sampleUsed BioMaterial chain.
thawBioAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService: Narrow thaw used by the /samples REST endpoint: initializes only the bioAssays collection and applies Thaws.thawBioAssay(BioAssay) to each assay (which warms the array design, original platform, and biomaterial-with-factor-values shape that BioAssayValueObject reads).
thawBioAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
thawBioAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
thawBioAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
thawBioMaterial(BioMaterial) - Static method in class ubic.gemma.persistence.util.Thaws: Thaw the given BioMaterial.
thawBioMaterialsForBioAssays(Collection) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao: Batched counterpart to the per-BioMaterial Thaws.thawBioMaterial(BioMaterial) pattern: warm the source-BioMaterial chain plus the per-row lazy associations (sourceTaxon, treatments, factorValues.experimentalFactor) for the BioMaterials referenced by every BioAssay in bas, using a small constant number of SQL round-trips instead of the per-BA, per-chain-level Hibernate.initialize pattern.
thawBioMaterialsForBioAssays(Collection) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
thawCellTypeAssignment(CellTypeAssignment) - Static method in class ubic.gemma.persistence.util.Thaws
thawCompositeSequences(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
thawCompositeSequences(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
thawCompositeSequences(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
thawCompositeSequences(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
thawCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Only thaw the design elements of a given platform.
thawCompositeSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
thawCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
thawCompositeSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
thawCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Thaw the composite sequences of a given platform
thawCompositeSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
thawCurationDetails(Curatable) - Static method in class ubic.gemma.persistence.util.Thaws: Thaw the CurationDetails of a curatable entity, including the three last*Event associations hanging off it.
thawDatabaseEntry(DatabaseEntry) - Static method in class ubic.gemma.persistence.util.Thaws
thawFully(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService: Thaw a single DifferentialExpressionAnalysis including all its result sets, results and contrasts.
thawFully(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl
thawFully(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
thawFully(DifferentialExpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
thawLite(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
thawLite(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
thawLite(Collection) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
thawLite(Collection) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
thawLite(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
thawLite(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
thawLite(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
thawLite(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
thawLite(Collection) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
thawLite(Collection) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
thawLite(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Lightly thaw the given platform.
thawLite(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
thawLite(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
thawLite(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl
thawLite(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Perform a less intensive thaw of an array design: not the composite sequences.
thawLite(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
thawLite(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService: Lightly thaw a dimension.
thawLite(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl
thawLite(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Thaw experiment metadata and bioassays.
thawLite(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
thawLite(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
thawLite(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
thawLite(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
thawLite(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
thawLite(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
thawLite(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
thawLite(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
thawLite(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
thawLite(Gene) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
thawLite(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
thawLiter(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Thaw experiment metadata.
thawLiter(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
thawLiter(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
thawLiter(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl
thawLiter(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
thawLiter(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
thawLiter(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneReadService
thawLiter(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl
thawLiter(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
thawLiter(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
thawLiter(Gene) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
thawLiter(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
Thaws - Class in ubic.gemma.persistence.util: Consistent initialization logic for the entity graph.
Thaws() - Constructor for class ubic.gemma.persistence.util.Thaws
thawSingleCellDimension(SingleCellDimension) - Static method in class ubic.gemma.persistence.util.Thaws: Thaw a single-cell dimension.
The Gsec secure entity data model - Section in package ubic.gemma.core.security
The rule - Section in class ubic.gemma.core.loader.expression.geo.GeoCharacteristicKey
The table is precomputed, not derived at runtime - Section in class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService
THIRD_PARTY_REANALYSIS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
ThreadBlock() - Constructor for class ubic.gemma.rest.AdminWebService.ThreadBlock
ThreadBlock(int, int, int) - Constructor for class ubic.gemma.rest.AdminWebService.ThreadBlock
ThreadContextPopulator - Interface in ubic.gemma.core.logging.log4j: Interface for populating the Log4j ThreadContext with custom information.
ThreadPoolExecutorMetrics - Class in ubic.gemma.core.metrics.binder
ThreadPoolExecutorMetrics(ThreadPoolExecutor, String) - Constructor for class ubic.gemma.core.metrics.binder.ThreadPoolExecutorMetrics
ThreadPoolTaskExecutorMetrics - Class in ubic.gemma.core.metrics.binder
ThreadPoolTaskExecutorMetrics(ThreadPoolTaskExecutor) - Constructor for class ubic.gemma.core.metrics.binder.ThreadPoolTaskExecutorMetrics
threads - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse
threadsAwaitingConnection - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
ThreadUtils - Class in ubic.gemma.core.util.concurrent: Utilities for creating Thread objects.
ThreadUtils() - Constructor for class ubic.gemma.core.util.concurrent.ThreadUtils
ThreePrimeDistanceMethod - Enum Class in ubic.gemma.model.genome.sequenceAnalysis
Three reports, one precedence order - Section in class ubic.gemma.core.ontology.relation.MgiRelationProducer
tick() - Method in class ubic.gemma.core.pipeline.JobReconciler: Every 5 minutes by default (matches prompt-cache TTL).
Ticket - Class in ubic.gemma.model.common.auditAndSecurity.curation: A curation ticket targeting one or more entities (initially TicketTargetType.EXPRESSION_EXPERIMENT and TicketTargetType.ARRAY_DESIGN).
Ticket() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.Ticket
Ticket.Factory - Class in ubic.gemma.model.common.auditAndSecurity.curation
TicketAssignedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted on the inherited audit trail when a Ticket's assignee is set or cleared.
TicketAssignedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TicketAssignedEvent
ticketCountOpen - Variable in class ubic.gemma.rest.WorkflowWebService.WorkflowQueueEntryResponse
TicketDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Persistence operations for Ticket (Phase B-1 of AUDIT_AS_WORKFLOW_RECCE.md).
TicketDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Hibernate implementation of TicketDao.
TicketDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl
TicketEvent - Class in ubic.gemma.model.common.auditAndSecurity.curation: An append-only entry in a Ticket's workflow event log.
TicketEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
TicketEvent.Factory - Class in ubic.gemma.model.common.auditAndSecurity.curation
TicketEventType - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Kind of a workflow event appended to a Ticket's events log.
TicketEventValueObject - Class in ubic.gemma.model.common.auditAndSecurity.curation: Value object projection of TicketEvent for the REST surface (Phase B-2 of AUDIT_AS_WORKFLOW_RECCE.md).
TicketEventValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
TicketMetadataChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted on the inherited audit trail when a Ticket's non-workflow metadata changes — priority, dueDate, title, body, or mode.
TicketMetadataChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TicketMetadataChangedEvent
TicketMode - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: How a Ticket advances between actions.
TicketOpenedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted on the inherited audit trail when a new Ticket is created.
TicketOpenedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TicketOpenedEvent
TicketPriority - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Priority of a Ticket.
tickets - Variable in class ubic.gemma.rest.AdminWebService.CurationStatusResponse
TicketsBlock() - Constructor for class ubic.gemma.rest.AdminWebService.TicketsBlock
TicketSearchHitValueObject - Class in ubic.gemma.model.common.auditAndSecurity.curation: One row of GET /tickets/search — enough of a ticket to pick it out of a list with confidence, and nothing more.
TicketSearchHitValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
TicketSearchHitValueObject(Long, String, TicketState, TicketType, long, Date, TicketPriority) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
TicketService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Service-layer API for the Phase B-1 Ticket layer (AUDIT_AS_WORKFLOW_RECCE.md).
TicketService.TargetAddition - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: What TicketService.addTarget(Ticket, TicketTargetType, Long, Contact) did: the saved ticket, and whether the target was new to it.
TicketServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Implementation of TicketService.
TicketServiceImpl(TicketDao, AuditTrailService) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
TicketState - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Lifecycle state of a Ticket.
TicketStateChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted on the inherited audit trail when a Ticket transitions to a different TicketState (OPEN / IN_PROGRESS / RESOLVED / CANCELLED).
TicketStateChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TicketStateChangedEvent
TicketSummaryForTargetValueObject - Class in ubic.gemma.model.common.auditAndSecurity.curation: One open ticket as it bears on ONE target — the per-ticket summary plus that target's own TicketTargetStatus.
TicketSummaryForTargetValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject
TicketSummaryForTargetValueObject(Long, String, TicketState, TicketType, long, Date, TicketPriority, TicketTargetStatus) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject
TicketsWebService - Class in ubic.gemma.rest: RESTful interface for curation tickets (Phase B-2 of AUDIT_AS_WORKFLOW_RECCE.md).
TicketsWebService(TicketService, UserManager, UserReadService, ExpressionExperimentService, PreboardedExperimentService) - Constructor for class ubic.gemma.rest.TicketsWebService
TicketsWebService.AddTargetRequest - Class in ubic.gemma.rest: Body of POST /tickets/{id}/targets.
TicketsWebService.AddTargetRequest.TargetRef - Class in ubic.gemma.rest
TicketsWebService.AddTargetsResult - Class in ubic.gemma.rest: Result of adding targets: which ids landed and which were already there.
TicketsWebService.CreateTicketFromAccessionRequest - Class in ubic.gemma.rest
TicketsWebService.CreateTicketRequest - Class in ubic.gemma.rest: Body for TicketsWebService.createTicket(CreateTicketRequest).
TicketsWebService.MyQueueResponse - Class in ubic.gemma.rest
TicketsWebService.MyQueueSummaryResponse - Class in ubic.gemma.rest
TicketsWebService.OpenTicketSummaryResponse - Class in ubic.gemma.rest
TicketsWebService.RemovedTargetResult - Class in ubic.gemma.rest: Result of removing a target: what went, and what state it was in.
TicketsWebService.ResponseDataObjectTicketValueObject - Class in ubic.gemma.rest: The 201 body of TicketsWebService.createTicketFromAccession(CreateTicketFromAccessionRequest).
TicketsWebService.TicketTargetRequest - Class in ubic.gemma.rest
TicketsWebService.UpdateTargetStatusRequest - Class in ubic.gemma.rest: Body for TicketsWebService.updateTargetStatus(Long, Long, UpdateTargetStatusRequest).
TicketsWebService.UpdateTicketRequest - Class in ubic.gemma.rest: Body for TicketsWebService.updateTicket(Long, UpdateTicketRequest).
TicketTarget - Class in ubic.gemma.model.common.auditAndSecurity.curation: A single target of a Ticket.
TicketTarget() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
TicketTarget.Factory - Class in ubic.gemma.model.common.auditAndSecurity.curation
TicketTargetRequest() - Constructor for class ubic.gemma.rest.TicketsWebService.TicketTargetRequest
TicketTargetStatus - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Per-target progress through a Ticket's work.
TicketTargetStatusChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted on the inherited audit trail when one of a Ticket's TicketTargets changes status (NOT_DONE / UNDERWAY / DONE).
TicketTargetStatusChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TicketTargetStatusChangedEvent
TicketTargetType - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Type of entity a TicketTarget points at.
TicketTargetValueObject - Class in ubic.gemma.model.common.auditAndSecurity.curation: Value object projection of TicketTarget for the REST surface (Phase B-2 of AUDIT_AS_WORKFLOW_RECCE.md).
TicketTargetValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
TicketType - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: Domain category of a Ticket.
TicketValueObject - Class in ubic.gemma.model.common.auditAndSecurity.curation: Value object projection of Ticket for the REST surface (Phase B-2 of AUDIT_AS_WORKFLOW_RECCE.md).
TicketValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
time - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
TIME - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementKind
timedAspect(MeterRegistry) - Method in class ubic.gemma.core.config.MetricsConfig: Enables @Timed-annotated method timing.
timeoutMillis - Variable in class ubic.gemma.rest.AdminWebService.CurationAgentHealthResponse
TIMEPOINT - Static variable in class ubic.gemma.model.common.description.Categories
timestamp(Date) - Method in class ubic.gemma.rest.util.BuildInfoValueObject.BuildInfoValueObjectBuilder
TINY - Static variable in class ubic.gemma.core.util.math.Constants
title - Variable in class ubic.gemma.rest.AdminWebService.GeoRecordValueObject
TITLE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
TN_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
toArray() - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix1D: WARNING unlike the superclass, this returns the actual underlying array, not a copy.
toArray() - Method in class ubic.gemma.model.util.UninitializedCollection
toArray(T1[]) - Method in class ubic.gemma.model.util.UninitializedCollection
toBatchObject(T) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI: Convert the given object to a serializable object for batch processing.
toBatchObject(ArrayDesign) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
toBatchObject(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI
toBeSet(String) - Static method in class ubic.gemma.cli.util.OptionsUtils: Make sure that the given option is present.
toBeUnset(String) - Static method in class ubic.gemma.cli.util.OptionsUtils: Make sure that the given option is missing.
toBooleanArray() - Method in class ubic.gemma.core.loader.util.anndata.NullableBoolArray
toBooleanVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Attribute
toBooleanVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset.H5Dataspace
toBooleanVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
toBulkVectors(Collection) - Static method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObjectUtils: Convert a collection of DoubleVectorValueObject.
toByteVector(byte[], long, long, long) - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset.H5Dataspace: Write the dataspace into a slice of a target.
toByteVector(long) - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset.H5Dataspace
TODO - Section in package ubic.gemma.core.security
toDoubleVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset.H5Dataspace
toDoubleVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
toExclusive() - Method in interface ubic.gemma.core.util.locking.LockedPath: Convert this lock to an exclusive lock.
toExclusive(long, TimeUnit) - Method in interface ubic.gemma.core.util.locking.LockedPath: Try to convert this lock to an exclusive lock.
toIdentifiableMap(Function, Function) - Static method in class ubic.gemma.persistence.util.IdentifiableUtils: Collect results into an identifiable map.
toIdentifiableSet() - Static method in class ubic.gemma.persistence.util.IdentifiableUtils: Collect results into an identifiable set.
toIntegerArray() - Method in class ubic.gemma.core.loader.util.anndata.NullableIntArray
toIntegerVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Attribute
toIntegerVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset.H5Dataspace
toIntegerVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
TokenCoverageRankingStrategy - Class in ubic.gemma.rest.ranking: Re-orders hits by what fraction of the query tokens appear in the hit's lowercased value.
TokenCoverageRankingStrategy() - Constructor for class ubic.gemma.rest.ranking.TokenCoverageRankingStrategy
tokenNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer: Deprecated.
Use FilterArgLexer.VOCABULARY instead.
tokenNames - Static variable in class ubic.gemma.rest.util.args.FilterArgParser: Deprecated.
Use FilterArgParser.VOCABULARY instead.
TokenStore - Class in ubic.gemma.rest.security: In-memory bearer-token store backing the /rest/v2/login flow used by the curation-UI SPA (see AUTH_FOR_SPA_RECCE.md Option C).
TokenStore() - Constructor for class ubic.gemma.rest.security.TokenStore
toList() - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap
toList(DoubleMatrix1D) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil: Makes a copy
toLongVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
TooFewDistinctValuesFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Remove rows that have a low diversity of values (equality judged based on tolerance set in RowLevelFilter).
TooFewDistinctValuesFilter(double) - Constructor for class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilter
toOriginalString() - Method in class ubic.gemma.persistence.util.Filter
toOriginalString() - Method in class ubic.gemma.persistence.util.Filters
toOriginalString() - Method in interface ubic.gemma.persistence.util.PropertyMapping: Render this with its original property.
toOriginalString() - Method in class ubic.gemma.persistence.util.Sort
TOOSMALL - Static variable in class ubic.gemma.core.util.math.linearmodels.ModeratedTstat
TooSmallDatasetLinkAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that the data set had too few samples or probes to be analyzed (after filtering), and was skipped
TooSmallDatasetLinkAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TooSmallDatasetLinkAnalysisEvent
top(List, Filters, String[], Sort, Integer) - Static method in class ubic.gemma.rest.util.Responders: Produce top results.
topLeft - Variable in class ubic.gemma.core.util.matrix.MatrixWriter
toResponse(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper
toShared() - Method in interface ubic.gemma.core.util.locking.LockedPath: Convert this lock to a shared lock.
toSid() - Method in class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
toSid() - Method in class ubic.gemma.core.security.acl.domain.AclPrincipalSid
toSid() - Method in class ubic.gemma.core.security.acl.domain.AclSid: Convert this Hibernate-mapped row to a Spring Security Sid for use in the security path (ACL equality checks, owner comparisons, ACE construction).
toString() - Method in class ubic.gemma.cli.batch.BatchTaskProcessingResult
toString() - Method in class ubic.gemma.cli.completion.CompletionSource.Completion
toString() - Method in class ubic.gemma.cli.completion.ConfluenceWikiHtmlGenerator.CommandMeta
toString() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
toString() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter
toString() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
toString() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
toString() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
toString() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
toString() - Method in class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.LowVarianceFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.OutliersFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.RowsWithSequencesFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.filter.ZeroVarianceFilter
toString() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
toString() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition
toString() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.RunMetrics
toString() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics
toString() - Method in class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics
toString() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats.AddedInWindow
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats.CategoryStat
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats.TaxonStat
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats.TermStat
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats
toString() - Method in class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat
toString() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket
toString() - Method in class ubic.gemma.core.analysis.report.TreatmentBucketsConfig
toString() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
toString() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
toString() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder
toString() - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExperimentSubSetsCreationConfig.SingleCellExperimentSubSetsCreationConfigBuilder
toString() - Method in class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix
toString() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
toString() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder
toString() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
toString() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
toString() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
toString() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
toString() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.Link
toString() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
toString() - Method in class ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder
toString() - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
toString() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
toString() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
toString() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
toString() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
toString() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
toString() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig.GeoRetrieveConfigBuilder
toString() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig
toString() - Method in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
toString() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig.GeoUpdateConfigBuilder
toString() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder
toString() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata.SequencingMetadataBuilder
toString() - Method in class ubic.gemma.core.loader.expression.sequencing.SequencingMetadata
toString() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic
toString() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleContactMetadata
toString() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry
toString() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata
toString() - Method in class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata
toString() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata
toString() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata
toString() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata
toString() - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
toString() - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder
toString() - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraBase
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraBases
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraContact
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperimentPackageSet
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraExternalId
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFile
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraFiles
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraOrganization
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPlatform
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPool
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPoolMember
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRun
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunSet
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraRunStatistics
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmission
toString() - Method in class ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
toString() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
toString() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
toString() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
toString() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
toString() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
toString() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
toString() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
toString() - Method in class ubic.gemma.core.loader.util.anndata.AnnData
toString() - Method in class ubic.gemma.core.loader.util.anndata.CategoricalArray
toString() - Method in class ubic.gemma.core.loader.util.anndata.Layer
toString() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
toString() - Method in class ubic.gemma.core.loader.util.hdf5.H5Type
toString() - Method in class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper
toString() - Method in class ubic.gemma.core.loader.util.mapper.AbstractGeneIdentifierBasedDesignElementMapper
toString() - Method in class ubic.gemma.core.loader.util.mapper.EntityMapper.MappingStatistics
toString() - Method in class ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper
toString() - Method in class ubic.gemma.core.ontology.chembl.ChemblCompound
toString() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.Annotation
toString() - Method in class ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
toString() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
toString() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
toString() - Method in record class ubic.gemma.core.ontology.lexical.LexicalOntologyIndex.Hit: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTerm: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata.Taxon: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTermMetadata: Returns a string representation of this record class.
toString() - Method in class ubic.gemma.core.ontology.model.OntologyTerm.TaxonConstraint
toString() - Method in class ubic.gemma.core.ontology.model.OntologyXref
toString() - Method in class ubic.gemma.core.ontology.ols.OlsTerm
toString() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
toString() - Method in class ubic.gemma.core.ontology.providers.OntologySlimExtractor.ExtractResult
toString() - Method in class ubic.gemma.core.ontology.search.OntologySearchService.Result
toString() - Method in class ubic.gemma.core.ontology.TermViolation
toString() - Method in class ubic.gemma.core.pipeline.JobSnapshot
toString() - Method in class ubic.gemma.core.pipeline.SchedulerHandle
toString() - Method in class ubic.gemma.core.pipeline.SubmitRequest
toString() - Method in class ubic.gemma.core.search.SearchContext
toString() - Method in class ubic.gemma.core.security.acl.domain.AclEntry
toString() - Method in class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
toString() - Method in class ubic.gemma.core.security.acl.domain.AclImpl
toString() - Method in class ubic.gemma.core.security.acl.domain.AclObjectIdentity
toString() - Method in class ubic.gemma.core.security.acl.domain.AclPrincipalSid
toString() - Method in record class ubic.gemma.core.security.audit.AuditEventPayload.None: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.DifferentialExpressionAnalysisPayload: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.ReleaseDetailsUpdatePayload: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.SampleRemovalPayload: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload: Returns a string representation of this record class.
toString() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellSubSetsCreatedPayload: Returns a string representation of this record class.
toString() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl
toString() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder
toString() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterService.LintResult
toString() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
toString() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
toString() - Method in class ubic.gemma.core.util.BuildInfo
toString() - Method in class ubic.gemma.core.util.locking.FileLockInfo
toString() - Method in class ubic.gemma.core.util.math.linalg.QRDecomposition: Returns a String with (propertyName, propertyValue) pairs.
toString() - Method in class ubic.gemma.core.util.math.linalg.SingularValueDecomposition
toString() - Method in class ubic.gemma.core.util.math.linearmodels.AnovaEffect
toString() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix
toString() - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
toString() - Method in class ubic.gemma.core.util.matrix.IntegerMatrix
toString() - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
toString() - Method in class ubic.gemma.core.util.matrix.StringMatrix
toString() - Method in record class ubic.gemma.core.util.runtime.CpuInfo: Returns a string representation of this record class.
toString() - Method in class ubic.gemma.core.util.runtime.FileLockInfo
toString() - Method in record class ubic.gemma.core.util.runtime.MemInfo: Returns a string representation of this record class.
toString() - Method in class ubic.gemma.core.util.SimpleDownloader.URLAndDestination
toString() - Method in class ubic.gemma.core.util.SimpleRetryContext
toString() - Method in class ubic.gemma.core.util.SimpleRetryPolicy
toString() - Method in class ubic.gemma.model.analysis.CellTypeAssignmentValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.Baseline
toString() - Method in class ubic.gemma.model.analysis.expression.diff.Contrast
toString() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
toString() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
toString() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
toString() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
toString() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
toString() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
toString() - Method in class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject
toString() - Method in class ubic.gemma.model.analysis.ProtocolValueObject
toString() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
toString() - Method in class ubic.gemma.model.association.Gene2GOAssociation
toString() - Method in class ubic.gemma.model.common.AbstractDescribable
toString() - Method in class ubic.gemma.model.common.AbstractIdentifiable
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
toString() - Method in record class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject.LastEventTriple: Returns a string representation of this record class.
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType
toString() - Method in class ubic.gemma.model.common.BaseValueObject
toString() - Method in class ubic.gemma.model.common.description.AnnotationRelation
toString() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
toString() - Method in class ubic.gemma.model.common.description.Category
toString() - Method in class ubic.gemma.model.common.description.Characteristic
toString() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
toString() - Method in class ubic.gemma.model.common.description.DatabaseEntry
toString() - Method in class ubic.gemma.model.common.description.DatabaseEntryValueObject
toString() - Method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
toString() - Method in class ubic.gemma.model.common.description.PublicationAssociation
toString() - Method in class ubic.gemma.model.common.description.Value
toString() - Method in class ubic.gemma.model.common.IdentifiableValueObject
toString() - Method in class ubic.gemma.model.common.measurement.Measurement
toString() - Method in class ubic.gemma.model.common.measurement.Unit
toString() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
toString() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
toString() - Method in class ubic.gemma.model.common.search.SearchResult
toString() - Method in class ubic.gemma.model.common.search.SearchResultValueObject
toString() - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder
toString() - Method in class ubic.gemma.model.common.search.SearchSettings
toString() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
toString() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
toString() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject
toString() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
toString() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector
toString() - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment
toString() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics
toString() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimension
toString() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
toString() - Method in class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject
toString() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
toString() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef
toString() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker
toString() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef
toString() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef
toString() - Method in class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary
toString() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
toString() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
toString() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
toString() - Method in record class ubic.gemma.model.expression.experiment.ExpressionExperimentIdAndShortName: Returns a string representation of this record class.
toString() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
toString() - Method in enum class ubic.gemma.model.expression.experiment.FactorType
toString() - Method in class ubic.gemma.model.expression.experiment.FactorValue
toString() - Method in class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
toString() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.
toString() - Method in class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
toString() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
toString() - Method in class ubic.gemma.model.expression.experiment.Statement
toString() - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
toString() - Method in class ubic.gemma.model.genome.Chromosome
toString() - Method in class ubic.gemma.model.genome.gene.GeneProduct
toString() - Method in class ubic.gemma.model.genome.gene.GeneReferenceValueObject
toString() - Method in class ubic.gemma.model.genome.gene.GeneSetMember
toString() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
toString() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
toString() - Method in class ubic.gemma.model.genome.gene.Multifunctionality
toString() - Method in class ubic.gemma.model.genome.Gene
toString() - Method in class ubic.gemma.model.genome.PhysicalLocation
toString() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
toString() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
toString() - Method in class ubic.gemma.model.genome.Taxon
toString() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder
toString() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
toString() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
toString() - Method in class ubic.gemma.persistence.service.common.description.PublicationAssertion
toString() - Method in record class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao.BioSequenceLite: Returns a string representation of this record class.
toString() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
toString() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm
toString() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder
toString() - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig.SingleCellVectorInitializationConfigBuilder
toString() - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
toString() - Method in class ubic.gemma.persistence.util.Cursor
toString() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.AllEntitiesUrl
toString() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl
toString() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.SomeEntitiesUrl
toString() - Method in class ubic.gemma.persistence.util.FactorValueVector
toString() - Method in class ubic.gemma.persistence.util.Filter
toString() - Method in class ubic.gemma.persistence.util.Filters
toString() - Method in interface ubic.gemma.persistence.util.PropertyMapping: Render this with its PropertyMapping.getObjectAlias() and PropertyMapping.getPropertyName().
toString() - Method in enum class ubic.gemma.persistence.util.Sort.Direction
toString() - Method in class ubic.gemma.persistence.util.Sort
toString() - Method in class ubic.gemma.persistence.util.Subquery.Alias
toString() - Method in class ubic.gemma.persistence.util.Subquery
toString() - Method in class ubic.gemma.rest.AdminWebService.ReindexAcceptedResponse
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationCategoryValueObject
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationRelationValueObject
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationReplaceReport
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.ExampleUsageValueObject
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.LexicalTermMetadataValueObject
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSimpleValueObject
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermSynonymValueObject
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.OntologyTermValueObject
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonConstraintValueObject
toString() - Method in class ubic.gemma.rest.AnnotationsWebService.TaxonValueObject
toString() - Method in class ubic.gemma.rest.AuthWebService.LoginResponse
toString() - Method in class ubic.gemma.rest.CompletionsWebService.CompletionValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.BatchEffectStatisticsValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.CurationDetailsCommit
toString() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetMetadataFileValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.DatasetSearchHitValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.DesignCommit
toString() - Method in class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.EntityRef
toString() - Method in class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.FactorCommit
toString() - Method in class ubic.gemma.rest.DatasetsWebService.FactorValueCommit
toString() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject.Fit
toString() - Method in class ubic.gemma.rest.DatasetsWebService.MeanVarianceValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.MeasurementRef
toString() - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermRef
toString() - Method in class ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject.Row
toString() - Method in class ubic.gemma.rest.DatasetsWebService.PcLoadingsValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.QcMetricDefinitionValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.RunQcMetricsValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCharacteristicCommit
toString() - Method in class ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.SampleQcMetricsValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.Section
toString() - Method in class ubic.gemma.rest.DatasetsWebService.SequencingQcMetricsValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.SimpleSVDValueObject
toString() - Method in class ubic.gemma.rest.DatasetsWebService.StatementCommit
toString() - Method in class ubic.gemma.rest.DatasetsWebService.TagCommit
toString() - Method in class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject
toString() - Method in class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject
toString() - Method in class ubic.gemma.rest.GeneWebService.GeneDifferentialExpressionGroupValueObject
toString() - Method in class ubic.gemma.rest.GoTermsWebService.GoTermGeneCountValueObject
toString() - Method in class ubic.gemma.rest.monitoring.HealthWebService.ComponentValueObject
toString() - Method in class ubic.gemma.rest.monitoring.HealthWebService.HealthValueObject
toString() - Method in class ubic.gemma.rest.monitoring.InfoWebService.BuildBlock
toString() - Method in class ubic.gemma.rest.monitoring.InfoWebService.InfoValueObject
toString() - Method in class ubic.gemma.rest.monitoring.InfoWebService.JavaBlock
toString() - Method in class ubic.gemma.rest.monitoring.InfoWebService.OsBlock
toString() - Method in class ubic.gemma.rest.monitoring.InfoWebService.UptimeBlock
toString() - Method in class ubic.gemma.rest.RootWebService.ApiInfoValueObject
toString() - Method in class ubic.gemma.rest.RootWebService.UserValueObject
toString() - Method in class ubic.gemma.rest.SearchWebService.SearchResultValueObject
toString() - Method in class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
toString() - Method in class ubic.gemma.rest.util.args.AbstractArg
toString() - Method in class ubic.gemma.rest.util.args.SortArg.Sort
toString() - Method in class ubic.gemma.rest.util.BuildInfoValueObject.BuildInfoValueObjectBuilder
toString() - Method in class ubic.gemma.rest.util.BuildInfoValueObject
toString() - Method in class ubic.gemma.rest.util.ResponseErrorObject.ResponseErrorObjectBuilder
toString() - Method in class ubic.gemma.rest.util.ResponseErrorObject
toString() - Method in class ubic.gemma.rest.util.Sendfile
toString() - Method in class ubic.gemma.rest.util.SortValueObject
toString() - Method in class ubic.gemma.rest.util.WellComposedError
toString() - Method in class ubic.gemma.rest.util.WellComposedError.WellComposedErrorBuilder
toString() - Method in class ubic.gemma.rest.util.WellComposedErrorBody
toString() - Method in class ubic.gemma.rest.util.WellComposedErrorBody.WellComposedErrorBodyBuilder
toString() - Method in class ubic.gemma.rest.util.WellComposedWarning
toString() - Method in class ubic.gemma.rest.util.WellComposedWarning.WellComposedWarningBuilder
toString(T, Class) - Static method in class ubic.gemma.persistence.util.IdentifiableUtils: Converts an identifiable to string, avoiding its initialization of it is a proxy.
toStringVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Attribute
toStringVector() - Method in class ubic.gemma.core.loader.util.hdf5.H5Dataset
total - Variable in class ubic.gemma.rest.AdminWebService.BlacklistListResponse: Total number of blacklist entries (independent of paging).
total - Variable in class ubic.gemma.rest.AdminWebService.JobsListResponse
total - Variable in class ubic.gemma.rest.AdminWebService.UsersListResponse
totalCells() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns the value of the totalCells record component.
totalConnections - Variable in class ubic.gemma.rest.AdminWebService.DbPoolResponse
totalCount - Variable in class ubic.gemma.rest.TicketsWebService.MyQueueSummaryResponse
totalDocumentCount - Variable in class ubic.gemma.rest.AdminWebService.SearchIndicesResponse
totalDocumentCountExact - Variable in class ubic.gemma.rest.AdminWebService.SearchIndicesResponse: False if any per-index count failed; the total is then a lower bound.
totalLast24h - Variable in class ubic.gemma.rest.AdminWebService.ProposalsBlock
totalLast7d - Variable in class ubic.gemma.rest.AdminWebService.ProposalsBlock
totalOpen - Variable in class ubic.gemma.rest.TicketsWebService.OpenTicketSummaryResponse: Open tickets across the corpus, EXCLUDING TicketType.SCRATCHPAD.
totalRNA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
totalRNA - Enum constant in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule
totalSize(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
toText() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.AllEntitiesUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.AllRestEntitiesUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.AllWebEntitiesUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ArrayDesignWebUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExperimentalDesignWebUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentWebUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExternalEntityUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.OntologyEntityUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.RestEntityUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.SomeEntitiesUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.SomeWebEntitiesUrl
toUri() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.WebEntityUrl
toUriString() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.AllEntitiesUrl
toUriString() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl
toUriString() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.SomeEntitiesUrl
toVectors(BulkExpressionDataMatrix, Class) - Static method in class ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrixUtils: Convert a BulkExpressionDataMatrix to a collection of BulkExpressionDataVector.
toVectors(SingleCellExpressionDataMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrixUtils
transactionalMethod() - Method in class ubic.gemma.persistence.util.Pointcuts: A transactional method, public and annotated with Transactional.
transactionCount - Variable in class ubic.gemma.rest.AdminWebService.HibernateStatsResponse
transactionManager(SessionFactory, DataSource) - Method in class ubic.gemma.persistence.hibernate.HibernateConfig
TRANSCRIPTOMIC - Enum constant in enum class ubic.gemma.core.loader.expression.geo.GeoLibrarySource
transformedCount - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
transformExecutor - Variable in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig: Executor service to use to transform single-cell data.
transformExecutor(ExecutorService) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: Executor service to use to transform single-cell data.
transformList(List) - Method in interface ubic.gemma.persistence.hibernate.TypedResultTransformer
transformListTyped(List) - Method in interface ubic.gemma.persistence.hibernate.TypedResultTransformer: Legacy name for the ResultListTransformer.transformList(List) hook.
transformTuple(Object[], String[]) - Method in interface ubic.gemma.persistence.hibernate.TypedResultTransformer
transition(Ticket, TicketState, Contact, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Transition the ticket to a new state.
transition(Ticket, TicketState, Contact, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
TRANSITIVE - Enum constant in enum class ubic.gemma.core.ontology.providers.OntologyService.InferenceMode: Only basic inference is supported for rdfs:subClassOf and rdfs:subPropertyOf.
transpose() - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
transpose() - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
transpose() - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
transpose() - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
transpose() - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
transpose(Boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
TransposedHeatMapDataset - Class in ubic.gemma.core.visualization
TransposedHeatMapDataset(HeatMapDataset) - Constructor for class ubic.gemma.core.visualization.TransposedHeatMapDataset
TRANSPOSON - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
treatment - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
Treatment - Class in ubic.gemma.model.expression.biomaterial
Treatment() - Constructor for class ubic.gemma.model.expression.biomaterial.Treatment
TREATMENT - Static variable in class ubic.gemma.model.common.description.Categories
Treatment.Factory - Class in ubic.gemma.model.expression.biomaterial
TreatmentBucketsConfig - Class in ubic.gemma.core.analysis.report: Externalised bucket spec for /stats/home treatmentSubcategories.
TreatmentBucketsConfig() - Constructor for class ubic.gemma.core.analysis.report.TreatmentBucketsConfig
TreatmentBucketsConfig.Bucket - Class in ubic.gemma.core.analysis.report
TreatmentBucketStat() - Constructor for class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat
TreatmentBucketStat(String, String) - Constructor for class ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat
triage - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageRequest
triage - Variable in class ubic.gemma.rest.AnnotationSetsWebService.TriageResponse
triageAnnotationSet(Long, String, AnnotationSetsWebService.TriageRequest) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Record or replace the caller's triage ruling on an annotation set.
TriageJudgeKind - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: What kind of judge produced an AnnotationSet triage ruling.
TriageRequest() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.TriageRequest
TriageResponse() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.TriageResponse
TriageVerdict - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation: One judge's ruling on how much an AnnotationSet matters.
trigammaInverse(double) - Static method in class ubic.gemma.core.util.math.SpecFunc
trigammaInverse(DoubleMatrix1D) - Static method in class ubic.gemma.core.util.math.SpecFunc: Ported from limma
triggerSlimRebuildAsync() - Method in class ubic.gemma.core.ontology.providers.ChebiOntologyService: Build the slim cache from the currently-loaded source + the live corpus seed set, asynchronously.
triggerSlimRebuildAsync() - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService
triggerSlimRebuildAsync() - Method in interface ubic.gemma.core.ontology.providers.SlimmableOntologyService: Spawn a daemon thread to rebuild the slim cache from the current corpus seed set.
trimmedMean(DoubleArrayList, int, int) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the trimmed mean of a data sequence.
trimToSize() - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
trimToSize() - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
TRNA - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
troubled() - Method in record class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject.LastEventTriple: Returns the value of the troubled record component.
troubled(Curatable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService: Deprecated.

Convenience overload — resolves target type from the entity.
troubled(Curatable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImpl
troubled(TicketTargetType, Long) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService: Deprecated.

Whether the given target has at least one open ticket of type QUALITY_REVIEW.
troubled(TicketTargetType, Long) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImpl
TroubledStatusFlagAlteringEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
see CurationDetailsEvent — the trouble flag is being replaced by open QUALITY_REVIEW tickets.
TroubledStatusFlagAlteringEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagAlteringEvent: Deprecated.
TroubledStatusFlagEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Deprecated.
open a QUALITY_REVIEW ticket via TicketService.openTicket(Contact, TicketType, String, Collection) instead. See CurationDetailsEvent for the full migration map.
TroubledStatusFlagEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent: Deprecated.
TruncatedH5FileException - Exception Class in ubic.gemma.core.loader.util.hdf5
TruncatedH5FileException(String) - Constructor for exception class ubic.gemma.core.loader.util.hdf5.TruncatedH5FileException
truncateInBytes(String, int, Charset) - Static method in class ubic.gemma.core.util.StringUtils
tryAcquirePathLock(Path, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.util.locking.FileLockManager: Attempt to lock a path.
tryAcquirePathLock(Path, boolean, long, TimeUnit) - Method in class ubic.gemma.core.util.locking.FileLockManagerImpl
TSV - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoFormat
TsvBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch
TsvBatchTaskSummaryWriter(Appendable) - Constructor for class ubic.gemma.cli.batch.TsvBatchTaskSummaryWriter
TsvUtils - Class in ubic.gemma.core.util: Bunch of utilities for writing data to TSV.
TsvUtils() - Constructor for class ubic.gemma.core.util.TsvUtils
TTEST - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.AnalysisType
TTL - Static variable in class ubic.gemma.rest.security.TokenStore: Sliding TTL: a token is invalidated 8 hours after its last successful lookup.
TWO_WAY_ANOVA_NO_INTERACTION - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.AnalysisType
TWO_WAY_ANOVA_WITH_INTERACTION - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.AnalysisType
TwoChannelExpressionDataMatrixBuilder - Class in ubic.gemma.core.datastructure.matrix: Utility methods for taking an ExpressionExperiment and returning various types of ExpressionDataMatrices, such as the processed data, preferred data, background, etc.
TwoChannelExpressionDataMatrixBuilder(Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
TwoChannelExpressionDataMatrixBuilder(Collection, Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
TwoChannelMissingValueHelperService - Interface in ubic.gemma.core.analysis.preprocess
TwoChannelMissingValues - Interface in ubic.gemma.core.analysis.preprocess
TwoChannelMissingValuesImpl - Class in ubic.gemma.core.analysis.preprocess: Computes a missing value matrix for ratiometric data sets.
TwoChannelMissingValuesImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl
TwoChannelMissingValueTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
TwoChannelMissingValueTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
TwoChannelMissingValueTaskCommand(ExpressionExperiment, double, Collection) - Constructor for class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
TwoChannelMissingValueTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression: Space task for computing two channel missing values.
TwoChannelMissingValueTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskImpl
TWOCOLOR - Enum constant in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType: Indicates this platform uses two channels and expression measurements are ratios.
Two constraints the measurement imposed - Section in class ubic.gemma.rest.ranking.CommonalityRankingStrategy
TwoWayAnovaResult - Interface in ubic.gemma.core.util.math.linearmodels
TypedResultTransformer<T> - Interface in ubic.gemma.persistence.hibernate: Lightweight type-safe row-and-list transformer.
typeStringToGeneType(String) - Static method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo: Convert string to GeneType.
🛑 These numbers describe the sample-correlation filter, not the download filter - Section in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload

U

U - Enum constant in enum class ubic.gemma.model.analysis.expression.diff.Direction: Up
U - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Update
UberonOntologyService - Class in ubic.gemma.core.ontology.providers: Uberon multi-species anatomy ontology
UberonOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.UberonOntologyService
uberonOntologyServiceOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig
ubic.gemma.apps - package ubic.gemma.apps: This package contains built-in Gemma CLI applications.
ubic.gemma.cli.audit - package ubic.gemma.cli.audit
ubic.gemma.cli.authentication - package ubic.gemma.cli.authentication
ubic.gemma.cli.batch - package ubic.gemma.cli.batch: Utilities for executing batch jobs via the CLI.
ubic.gemma.cli.completion - package ubic.gemma.cli.completion: This package provides completion support for the Gemma CLI.
ubic.gemma.cli.config - package ubic.gemma.cli.config
ubic.gemma.cli.logging - package ubic.gemma.cli.logging
ubic.gemma.cli.logging.log4j - package ubic.gemma.cli.logging.log4j
ubic.gemma.cli.main - package ubic.gemma.cli.main
ubic.gemma.cli.metrics - package ubic.gemma.cli.metrics
ubic.gemma.cli.options - package ubic.gemma.cli.options: This package contains reusable command line options.
ubic.gemma.cli.pipeline - package ubic.gemma.cli.pipeline
ubic.gemma.cli.util - package ubic.gemma.cli.util
ubic.gemma.core.analysis.expression - package ubic.gemma.core.analysis.expression
ubic.gemma.core.analysis.expression.diff - package ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess - package ubic.gemma.core.analysis.preprocess: This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.preprocess.batcheffects - package ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.convert - package ubic.gemma.core.analysis.preprocess.convert: Convert data from one QuantitationType to another.
ubic.gemma.core.analysis.preprocess.detect - package ubic.gemma.core.analysis.preprocess.detect: This package contains classes for detecting and linting expression data.
ubic.gemma.core.analysis.preprocess.filter - package ubic.gemma.core.analysis.preprocess.filter: This package contains classes for filtering expression data.
ubic.gemma.core.analysis.preprocess.normalize - package ubic.gemma.core.analysis.preprocess.normalize
ubic.gemma.core.analysis.preprocess.qc - package ubic.gemma.core.analysis.preprocess.qc
ubic.gemma.core.analysis.preprocess.slice - package ubic.gemma.core.analysis.preprocess.slice: This package provides capabilities for slicing BulkExpressionDataVector.
ubic.gemma.core.analysis.preprocess.svd - package ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.report - package ubic.gemma.core.analysis.report
ubic.gemma.core.analysis.sequence - package ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.service - package ubic.gemma.core.analysis.service
ubic.gemma.core.analysis.singleCell - package ubic.gemma.core.analysis.singleCell: This package contains classes for analysing single-cell expression data.
ubic.gemma.core.analysis.singleCell.aggregate - package ubic.gemma.core.analysis.singleCell.aggregate: This package contains classes for subsetting and aggregating single-cell data.
ubic.gemma.core.analysis.stats - package ubic.gemma.core.analysis.stats: This package contains classes for computing various statistics.
ubic.gemma.core.architecture - package ubic.gemma.core.architecture
ubic.gemma.core.config - package ubic.gemma.core.config: This package contains classes that are used to manage Gemma's Spring context.
ubic.gemma.core.context - package ubic.gemma.core.context: This package contains classes that are used to manage Gemma's Spring context.
ubic.gemma.core.datastructure.matrix - package ubic.gemma.core.datastructure.matrix: This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.datastructure.matrix.io - package ubic.gemma.core.datastructure.matrix.io: This package contains I/O utilities for reading and writing expression data matrices.
ubic.gemma.core.datastructure.sparse - package ubic.gemma.core.datastructure.sparse: This package contains sparse data structures implementations and utilities.
ubic.gemma.core.geoscrape - package ubic.gemma.core.geoscrape
ubic.gemma.core.goldenpath - package ubic.gemma.core.goldenpath
ubic.gemma.core.job - package ubic.gemma.core.job: Provides functionalities for running background tasks.
ubic.gemma.core.job.notification - package ubic.gemma.core.job.notification
ubic.gemma.core.job.progress - package ubic.gemma.core.job.progress
ubic.gemma.core.loader.association - package ubic.gemma.core.loader.association
ubic.gemma.core.loader.crossref - package ubic.gemma.core.loader.crossref
ubic.gemma.core.loader.entrez - package ubic.gemma.core.loader.entrez
ubic.gemma.core.loader.entrez.pubmed - package ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.loader.expression - package ubic.gemma.core.loader.expression: This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.arrayDesign - package ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.arrayExpress - package ubic.gemma.core.loader.expression.arrayExpress
ubic.gemma.core.loader.expression.arrayExpress.util - package ubic.gemma.core.loader.expression.arrayExpress.util
ubic.gemma.core.loader.expression.cellxgene - package ubic.gemma.core.loader.expression.cellxgene: This package contains classes for loading expression data from CELLxGENE.
ubic.gemma.core.loader.expression.cellxgene.model - package ubic.gemma.core.loader.expression.cellxgene.model
ubic.gemma.core.loader.expression.geo - package ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.fetcher - package ubic.gemma.core.loader.expression.geo.fetcher
ubic.gemma.core.loader.expression.geo.fetcher2 - package ubic.gemma.core.loader.expression.geo.fetcher2: Provides classes for fetching data from various sources.
ubic.gemma.core.loader.expression.geo.model - package ubic.gemma.core.loader.expression.geo.model
ubic.gemma.core.loader.expression.geo.service - package ubic.gemma.core.loader.expression.geo.service
ubic.gemma.core.loader.expression.geo.singleCell - package ubic.gemma.core.loader.expression.geo.singleCell: This package contains specific logic for dealing with single-cell data from GEO.
ubic.gemma.core.loader.expression.geo.util - package ubic.gemma.core.loader.expression.geo.util
ubic.gemma.core.loader.expression.sequencing - package ubic.gemma.core.loader.expression.sequencing: This package contains interfaces and classes for loading sequencing data.
ubic.gemma.core.loader.expression.simple - package ubic.gemma.core.loader.expression.simple
ubic.gemma.core.loader.expression.simple.model - package ubic.gemma.core.loader.expression.simple.model: Model classes for loading simple expression data.
ubic.gemma.core.loader.expression.singleCell - package ubic.gemma.core.loader.expression.singleCell: This package contains classes for loading single-cell expression data.
ubic.gemma.core.loader.expression.singleCell.metadata - package ubic.gemma.core.loader.expression.singleCell.metadata: This package contains classes for loading single-cell metadata such as cell type assignment and cell-level characteristics.
ubic.gemma.core.loader.expression.singleCell.transform - package ubic.gemma.core.loader.expression.singleCell.transform: This package contains classes for transforming single-cell expression data.
ubic.gemma.core.loader.expression.sra - package ubic.gemma.core.loader.expression.sra
ubic.gemma.core.loader.expression.sra.model - package ubic.gemma.core.loader.expression.sra.model
ubic.gemma.core.loader.expression.synapse - package ubic.gemma.core.loader.expression.synapse: This package contains interfaces and classes for loading expression data from Synapse.
ubic.gemma.core.loader.expression.ucsc.cellbrowser - package ubic.gemma.core.loader.expression.ucsc.cellbrowser: This package contains utilities for loading and interacting with the UCSC Cell Browser.
ubic.gemma.core.loader.expression.ucsc.cellbrowser.model - package ubic.gemma.core.loader.expression.ucsc.cellbrowser.model
ubic.gemma.core.loader.expression.zenodo - package ubic.gemma.core.loader.expression.zenodo: This package contains interfaces and classes for loading expression data from Zenodo.
ubic.gemma.core.loader.genome - package ubic.gemma.core.loader.genome
ubic.gemma.core.loader.genome.gene - package ubic.gemma.core.loader.genome.gene
ubic.gemma.core.loader.genome.gene.ncbi - package ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.genome.gene.ncbi.homology - package ubic.gemma.core.loader.genome.gene.ncbi.homology
ubic.gemma.core.loader.genome.gene.ncbi.model - package ubic.gemma.core.loader.genome.gene.ncbi.model
ubic.gemma.core.loader.genome.taxon - package ubic.gemma.core.loader.genome.taxon
ubic.gemma.core.loader.util - package ubic.gemma.core.loader.util
ubic.gemma.core.loader.util.anndata - package ubic.gemma.core.loader.util.anndata
ubic.gemma.core.loader.util.biomart - package ubic.gemma.core.loader.util.biomart
ubic.gemma.core.loader.util.converter - package ubic.gemma.core.loader.util.converter
ubic.gemma.core.loader.util.fetcher - package ubic.gemma.core.loader.util.fetcher
ubic.gemma.core.loader.util.fetcher2 - package ubic.gemma.core.loader.util.fetcher2: Provides classes for fetching data from various sources.
ubic.gemma.core.loader.util.ftp - package ubic.gemma.core.loader.util.ftp: Utilities for working with FTP.
ubic.gemma.core.loader.util.hdf5 - package ubic.gemma.core.loader.util.hdf5: Minimalistic read-only wrapper around HDF5 native library.
ubic.gemma.core.loader.util.mapper - package ubic.gemma.core.loader.util.mapper: Utilities for mapping Identifiable entities to external identifiers.
ubic.gemma.core.loader.util.parser - package ubic.gemma.core.loader.util.parser
ubic.gemma.core.loader.util.sdo - package ubic.gemma.core.loader.util.sdo
ubic.gemma.core.logging.log4j - package ubic.gemma.core.logging.log4j
ubic.gemma.core.mail - package ubic.gemma.core.mail
ubic.gemma.core.metrics - package ubic.gemma.core.metrics
ubic.gemma.core.metrics.binder - package ubic.gemma.core.metrics.binder
ubic.gemma.core.metrics.binder.database - package ubic.gemma.core.metrics.binder.database
ubic.gemma.core.metrics.binder.jpa - package ubic.gemma.core.metrics.binder.jpa
ubic.gemma.core.ontology - package ubic.gemma.core.ontology
ubic.gemma.core.ontology.chembl - package ubic.gemma.core.ontology.chembl
ubic.gemma.core.ontology.jena - package ubic.gemma.core.ontology.jena: Jena-based ontology implementation: OntologyService concrete classes, Lucene indexer, OWL/OBO/RO/IAO helpers.
ubic.gemma.core.ontology.lexical - package ubic.gemma.core.ontology.lexical
ubic.gemma.core.ontology.model - package ubic.gemma.core.ontology.model
ubic.gemma.core.ontology.ols - package ubic.gemma.core.ontology.ols
ubic.gemma.core.ontology.providers - package ubic.gemma.core.ontology.providers: This package contains baseCode built-in ontologies and a ubic.basecode.ontology.providers.GenericOntologyService to implement your own ontologies.
ubic.gemma.core.ontology.providers.chebi - package ubic.gemma.core.ontology.providers.chebi
ubic.gemma.core.ontology.providers.mondo - package ubic.gemma.core.ontology.providers.mondo
ubic.gemma.core.ontology.relation - package ubic.gemma.core.ontology.relation
ubic.gemma.core.ontology.search - package ubic.gemma.core.ontology.search: In-Gemma ontology full-text search subsystem.
ubic.gemma.core.ontology.simple - package ubic.gemma.core.ontology.simple: Simple ontology implementation.
ubic.gemma.core.pipeline - package ubic.gemma.core.pipeline
ubic.gemma.core.profiling - package ubic.gemma.core.profiling: Classes and utilities for profiling the performance of Gemma.
ubic.gemma.core.scheduler - package ubic.gemma.core.scheduler
ubic.gemma.core.search - package ubic.gemma.core.search
ubic.gemma.core.search.indexer - package ubic.gemma.core.search.indexer: Mass-indexer driver around Hibernate Search 7's MassIndexer.
ubic.gemma.core.search.lucene - package ubic.gemma.core.search.lucene
ubic.gemma.core.search.source - package ubic.gemma.core.search.source
ubic.gemma.core.security - package ubic.gemma.core.security: Gsec is an attempt to generalise the security framework of Gemma to make it usable in other projects such as ASPIREdb.
ubic.gemma.core.security.acl - package ubic.gemma.core.security.acl
ubic.gemma.core.security.acl.afterinvocation - package ubic.gemma.core.security.acl.afterinvocation: Provides various implementations of AbstractAclProvider for filtering method return values for ACLS.
ubic.gemma.core.security.acl.annotation - package ubic.gemma.core.security.acl.annotation
ubic.gemma.core.security.acl.domain - package ubic.gemma.core.security.acl.domain
ubic.gemma.core.security.acl.voter - package ubic.gemma.core.security.acl.voter
ubic.gemma.core.security.audit - package ubic.gemma.core.security.audit
ubic.gemma.core.security.audit.payload - package ubic.gemma.core.security.audit.payload
ubic.gemma.core.security.authentication - package ubic.gemma.core.security.authentication
ubic.gemma.core.security.authorization.acl - package ubic.gemma.core.security.authorization.acl
ubic.gemma.core.security.concurrent - package ubic.gemma.core.security.concurrent
ubic.gemma.core.security.model - package ubic.gemma.core.security.model
ubic.gemma.core.security.util - package ubic.gemma.core.security.util
ubic.gemma.core.tasks - package ubic.gemma.core.tasks: This package contains task definitions.
ubic.gemma.core.tasks.analysis.diffex - package ubic.gemma.core.tasks.analysis.diffex
ubic.gemma.core.tasks.analysis.expression - package ubic.gemma.core.tasks.analysis.expression
ubic.gemma.core.tasks.analysis.sequence - package ubic.gemma.core.tasks.analysis.sequence
ubic.gemma.core.tasks.maintenance - package ubic.gemma.core.tasks.maintenance
ubic.gemma.core.tasks.visualization - package ubic.gemma.core.tasks.visualization
ubic.gemma.core.util - package ubic.gemma.core.util
ubic.gemma.core.util.concurrent - package ubic.gemma.core.util.concurrent
ubic.gemma.core.util.graphics - package ubic.gemma.core.util.graphics
ubic.gemma.core.util.graphics.text - package ubic.gemma.core.util.graphics.text
ubic.gemma.core.util.locking - package ubic.gemma.core.util.locking: Utilities for locking files.
ubic.gemma.core.util.math - package ubic.gemma.core.util.math
ubic.gemma.core.util.math.distribution - package ubic.gemma.core.util.math.distribution
ubic.gemma.core.util.math.linalg - package ubic.gemma.core.util.math.linalg
ubic.gemma.core.util.math.linearmodels - package ubic.gemma.core.util.math.linearmodels
ubic.gemma.core.util.math.metaanalysis - package ubic.gemma.core.util.math.metaanalysis
ubic.gemma.core.util.matrix - package ubic.gemma.core.util.matrix: Labelled-axis matrix types ported in-tree from baseCode's ubic.basecode.dataStructure.matrix subsystem as part of the Phase 3 baseCode retirement (see BASECODE_MATRIX_RECCE.md and BASECODE_DEP_AUDIT.md).
ubic.gemma.core.util.matrix.datafilter - package ubic.gemma.core.util.matrix.datafilter
ubic.gemma.core.util.runtime - package ubic.gemma.core.util.runtime: Utilities for accessing extended runtime information.
ubic.gemma.core.visualization - package ubic.gemma.core.visualization
ubic.gemma.core.visualization.cellbrowser - package ubic.gemma.core.visualization.cellbrowser: This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.analysis - package ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression - package ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.coexpression - package ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.diff - package ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.analysis.expression.pca - package ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.analysis.sequence - package ubic.gemma.model.analysis.sequence
ubic.gemma.model.annotations - package ubic.gemma.model.annotations
ubic.gemma.model.association - package ubic.gemma.model.association
ubic.gemma.model.blacklist - package ubic.gemma.model.blacklist
ubic.gemma.model.common - package ubic.gemma.model.common
ubic.gemma.model.common.auditAndSecurity - package ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.auditAndSecurity.curation - package ubic.gemma.model.common.auditAndSecurity.curation
ubic.gemma.model.common.auditAndSecurity.eventType - package ubic.gemma.model.common.auditAndSecurity.eventType
ubic.gemma.model.common.description - package ubic.gemma.model.common.description
ubic.gemma.model.common.measurement - package ubic.gemma.model.common.measurement
ubic.gemma.model.common.protocol - package ubic.gemma.model.common.protocol
ubic.gemma.model.common.quantitationtype - package ubic.gemma.model.common.quantitationtype
ubic.gemma.model.common.search - package ubic.gemma.model.common.search
ubic.gemma.model.expression.arrayDesign - package ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay - package ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData - package ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial - package ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.designElement - package ubic.gemma.model.expression.designElement
ubic.gemma.model.expression.experiment - package ubic.gemma.model.expression.experiment
ubic.gemma.model.genome - package ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence - package ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.gene - package ubic.gemma.model.genome.gene
ubic.gemma.model.genome.sequenceAnalysis - package ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.model.pipeline - package ubic.gemma.model.pipeline
ubic.gemma.model.util - package ubic.gemma.model.util
ubic.gemma.persistence.audit - package ubic.gemma.persistence.audit
ubic.gemma.persistence.cache - package ubic.gemma.persistence.cache
ubic.gemma.persistence.hibernate - package ubic.gemma.persistence.hibernate: This package contains Hibernate-related classes and utilities for persisting entities.
ubic.gemma.persistence.initialization - package ubic.gemma.persistence.initialization
ubic.gemma.persistence.persister - package ubic.gemma.persistence.persister
ubic.gemma.persistence.retry - package ubic.gemma.persistence.retry
ubic.gemma.persistence.service - package ubic.gemma.persistence.service
ubic.gemma.persistence.service.analysis - package ubic.gemma.persistence.service.analysis
ubic.gemma.persistence.service.analysis.expression - package ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.analysis.expression.diff - package ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.analysis.expression.pca - package ubic.gemma.persistence.service.analysis.expression.pca
ubic.gemma.persistence.service.analysis.expression.sampleCoexpression - package ubic.gemma.persistence.service.analysis.expression.sampleCoexpression
ubic.gemma.persistence.service.association - package ubic.gemma.persistence.service.association
ubic.gemma.persistence.service.blacklist - package ubic.gemma.persistence.service.blacklist: Service for managing blacklisted entities.
ubic.gemma.persistence.service.common.auditAndSecurity - package ubic.gemma.persistence.service.common.auditAndSecurity
ubic.gemma.persistence.service.common.auditAndSecurity.curation - package ubic.gemma.persistence.service.common.auditAndSecurity.curation
ubic.gemma.persistence.service.common.description - package ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.common.measurement - package ubic.gemma.persistence.service.common.measurement
ubic.gemma.persistence.service.common.protocol - package ubic.gemma.persistence.service.common.protocol
ubic.gemma.persistence.service.common.quantitationtype - package ubic.gemma.persistence.service.common.quantitationtype
ubic.gemma.persistence.service.expression.arrayDesign - package ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssay - package ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData - package ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.biomaterial - package ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.designElement - package ubic.gemma.persistence.service.expression.designElement
ubic.gemma.persistence.service.expression.experiment - package ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome - package ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.biosequence - package ubic.gemma.persistence.service.genome.biosequence
ubic.gemma.persistence.service.genome.gene - package ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.genome.sequenceAnalysis - package ubic.gemma.persistence.service.genome.sequenceAnalysis
ubic.gemma.persistence.service.genome.taxon - package ubic.gemma.persistence.service.genome.taxon
ubic.gemma.persistence.service.maintenance - package ubic.gemma.persistence.service.maintenance: Contains classes related to database maintenance.
ubic.gemma.persistence.service.pipeline - package ubic.gemma.persistence.service.pipeline
ubic.gemma.persistence.util - package ubic.gemma.persistence.util
ubic.gemma.rest - package ubic.gemma.rest
ubic.gemma.rest.analytics - package ubic.gemma.rest.analytics
ubic.gemma.rest.analytics.ga4 - package ubic.gemma.rest.analytics.ga4
ubic.gemma.rest.annotations - package ubic.gemma.rest.annotations
ubic.gemma.rest.context - package ubic.gemma.rest.context
ubic.gemma.rest.monitoring - package ubic.gemma.rest.monitoring
ubic.gemma.rest.monitoring.health - package ubic.gemma.rest.monitoring.health
ubic.gemma.rest.providers - package ubic.gemma.rest.providers
ubic.gemma.rest.ranking - package ubic.gemma.rest.ranking
ubic.gemma.rest.security - package ubic.gemma.rest.security
ubic.gemma.rest.serializers - package ubic.gemma.rest.serializers
ubic.gemma.rest.servlet - package ubic.gemma.rest.servlet
ubic.gemma.rest.startup - package ubic.gemma.rest.startup
ubic.gemma.rest.swagger.resolver - package ubic.gemma.rest.swagger.resolver
ubic.gemma.rest.util - package ubic.gemma.rest.util
ubic.gemma.rest.util.args - package ubic.gemma.rest.util.args
UCSC_CELL_BROWSER - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
UcscCellBrowserGrabberCli - Class in ubic.gemma.apps: Lists available datasets from the UCSC Cell Browser.
UcscCellBrowserGrabberCli() - Constructor for class ubic.gemma.apps.UcscCellBrowserGrabberCli
UcscCellBrowserUtils - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser
UcscCellBrowserUtils() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils
uMatrixAsExpressionData() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
unadjustedLibrarySize() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay: Returns the value of the unadjustedLibrarySize record component.
UNCATEGORIZED - Static variable in class ubic.gemma.model.common.description.Categories: Indicate an uncategorized term.
UNCATEGORIZED - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Special indicator for an uncategorized term.
UNCATEGORIZED - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Special indicator for uncategorized terms.
UNCHANGED - Enum constant in enum class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome: No change were made.
UNDECIDED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.ScreeningResult: Reviewed but could not be resolved — a curator or agent looked and could not decide.
underflow() - Method in class ubic.gemma.core.util.math.distribution.Histogram: The height of the underflow bin.
UNDERWAY - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetStatus
UNDETERMINED - Enum constant in enum class ubic.gemma.model.util.ModelUtils.EqualityOutcome: Equality could not be determined.
unFisherTransform(double) - Static method in class ubic.gemma.core.util.math.CorrelationStats: Reverse the Fisher z-transform of Pearson correlations
UNGROUNDED_NOT_DECLARED - Enum constant in enum class ubic.gemma.core.ontology.TermViolation.Reason: The term carries no URI at all and the caller did not declare that it meant to leave it as free text.
unGzipFile(String) - Static method in class ubic.gemma.core.util.FileTools: Given the path to a gzipped file, unzip it into the same directory.
UnhandledExceptionMapper - Class in ubic.gemma.rest.providers: Render unhandled exceptions.
UnhandledExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.UnhandledExceptionMapper
unifiedOntologyService(boolean, Path, Path) - Method in class ubic.gemma.core.ontology.OntologyConfig: This ontology encompasses all the ontologies declared below.
UnifiedOntologyUpdaterCli - Class in ubic.gemma.apps
UnifiedOntologyUpdaterCli() - Constructor for class ubic.gemma.apps.UnifiedOntologyUpdaterCli
UNINFORMATIVE_HEADERS_FAILURE - Enum constant in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Batch information is uninformative.
UninformativeFASTQHeadersForBatchingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that FASTQ headers were present, but they were not usable for determining batches, typically because of invalid formatting or lack of information.
UninformativeFASTQHeadersForBatchingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.UninformativeFASTQHeadersForBatchingEvent
UninitializedCollection<T> - Class in ubic.gemma.model.util: A collection that is intentionally not initialized.
UninitializedCollection() - Constructor for class ubic.gemma.model.util.UninitializedCollection
UninitializedCollection(int) - Constructor for class ubic.gemma.model.util.UninitializedCollection
UninitializedCollectionException - Exception Class in ubic.gemma.model.util: Exception raised when an operation is performed on an intentionally uninitialized collection.
UninitializedCollectionException(String) - Constructor for exception class ubic.gemma.model.util.UninitializedCollectionException
uninitializedException() - Method in class ubic.gemma.model.util.UninitializedCollection
UninitializedList<T> - Class in ubic.gemma.model.util: A list that is intentionally not initialized.
UninitializedList() - Constructor for class ubic.gemma.model.util.UninitializedList
UninitializedList(int) - Constructor for class ubic.gemma.model.util.UninitializedList
UninitializedSet<T> - Class in ubic.gemma.model.util: A set that is intentionally not initialized.
UninitializedSet() - Constructor for class ubic.gemma.model.util.UninitializedSet
UninitializedSet(int) - Constructor for class ubic.gemma.model.util.UninitializedSet
UNIQUE_STRING - Enum constant in enum class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaFieldType
uniqueResult(Query) - Method in interface ubic.gemma.persistence.hibernate.TypedResultTransformer: Execute the query with this transformer wired in, returning the single typed row (or null).
uniqueResult(Query) - Static method in class ubic.gemma.persistence.util.QueryUtils
uniqueValues() - Method in interface ubic.gemma.core.loader.util.anndata.Dataframe.Column
Unit - Class in ubic.gemma.model.common.measurement
Unit() - Constructor for class ubic.gemma.model.common.measurement.Unit
Unit.Factory - Class in ubic.gemma.model.common.measurement
UnitDao - Interface in ubic.gemma.persistence.service.common.measurement
UnitDaoImpl - Class in ubic.gemma.persistence.service.common.measurement: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.common.measurement.Unit.
UnitDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.measurement.UnitDaoImpl
UnitsOntologyService - Class in ubic.gemma.core.ontology.providers: Units of measurement ontology
UnitsOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.UnitsOntologyService
unknown - Variable in class ubic.gemma.rest.AdminWebService.JobsListResponse
unknown() - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCounts: Both counts unknown — what an unparseable, absent or unrecognized payload yields.
UNKNOWN - Enum constant in enum class ubic.gemma.core.job.SubmittedTask.Status
UNKNOWN - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
UNKNOWN - Enum constant in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus
UNKNOWN - Enum constant in enum class ubic.gemma.model.common.quantitationtype.GeneralType: Indicate an unknown type.
UNKNOWN_CELL_TYPE - Static variable in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment: A special indicator for CellTypeAssignment.cellTypeIndices when the cell type is unknown.
UNKNOWN_CHARACTERISTIC - Static variable in interface ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics: Indicator for an unknown characteristic.
unknownCellTypeIndicator(String) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
UnknownQueryParameterException - Exception Class in ubic.gemma.rest.util: Thrown when a request carries a query parameter the matched resource method cannot bind.
UnknownQueryParameterException(Collection, Collection) - Constructor for exception class ubic.gemma.rest.util.UnknownQueryParameterException
UnknownQueryParameterExceptionMapper - Class in ubic.gemma.rest.providers: Maps an UnknownQueryParameterException to a 400 whose errors[] carries one entry per rejected parameter, each naming the parameter in location with locationType LocationType.QUERY.
UnknownQueryParameterExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.UnknownQueryParameterExceptionMapper
UnknownQueryParameterFilter - Class in ubic.gemma.rest.providers: Rejects a request that carries a query parameter the matched resource method cannot bind, rather than ignoring it.
UnknownQueryParameterFilter(boolean) - Constructor for class ubic.gemma.rest.providers.UnknownQueryParameterFilter: The inline default matters: the mocked REST test contexts resolve placeholders from a fixed list rather than from default.properties, so a bare ${...} here fails container startup for every JerseyTest in the module, not just a test of this filter.
unlock() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition: Release the lock on the cache key previously acquired with CacheKeyLock.lock() or CacheKeyLock.lockInterruptibly().
unLogTransform(DoubleMatrix) - Static method in class ubic.gemma.core.util.math.MatrixStats: Undo log2 transform.
unmappable(String) - Static method in class ubic.gemma.core.util.SymbolFontPua: The private-use codepoints in s that SymbolFontPua.repair(String) would leave in place.
unmark - Variable in class ubic.gemma.rest.DatasetsWebService.BatchOutlierRequest
unmarkAsMissing(Collection) - Method in interface ubic.gemma.core.analysis.service.OutlierFlaggingService: Reverts the action of markAsMissing.
unmarkAsMissing(Collection) - Method in class ubic.gemma.core.analysis.service.OutlierFlaggingServiceImpl
unmarkedCount - Variable in class ubic.gemma.rest.DatasetsWebService.BatchOutlierResponse
unmarshal(String) - Method in class ubic.gemma.core.loader.expression.sra.model.SraDateParser
unnestSubquery(Filter) - Static method in class ubic.gemma.persistence.util.FiltersUtils: Unnest a filter from a subquery.
unPack(File) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
unregisterEntity(String, Class) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer: Unregister an entity at a given prefix previously registered via AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer.registerEntity(String, Class, int).
unregisterProperties(Predicate) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer: Unregister all the properties matching the given predicate.
unregisterProperty(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
UNSCALED - Enum constant in enum class ubic.gemma.model.common.quantitationtype.ScaleType: An unscaled measurement is one that has no inherent scale; e.g., a categorical value.
UNSPECIFIED - Enum constant in enum class ubic.gemma.core.ontology.model.OntologyXref.Strength: A bare oboInOwl:hasDbXref with no qualifying axiom annotation.
UNSPECIFIED - Enum constant in enum class ubic.gemma.rest.util.CurationCommitConflictException.Reason: The write refused this as a conflict without saying which kind — e.g.
UnsuitableForDifferentialExpressionAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that the associated Experiment is NOT suitable for differential expression analysis.
UnsuitableForDifferentialExpressionAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.UnsuitableForDifferentialExpressionAnalysisEvent
UnsupportedEntityUrlException - Exception Class in ubic.gemma.persistence.util
UnsupportedEntityUrlException(String, Class) - Constructor for exception class ubic.gemma.persistence.util.UnsupportedEntityUrlException
UnsupportedQuantitationRepresentationConversionException - Exception Class in ubic.gemma.core.analysis.preprocess.convert: Exception raised when data in a given representation cannot be converted to another representation.
UnsupportedQuantitationRepresentationConversionException(PrimitiveType, PrimitiveType) - Constructor for exception class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationRepresentationConversionException
UnsupportedQuantitationScaleConversionException - Exception Class in ubic.gemma.core.analysis.preprocess.convert: Exception raised when data from a given scale cannot be converted to another scale.
UnsupportedQuantitationScaleConversionException(ScaleType, ScaleType) - Constructor for exception class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationScaleConversionException
UnsupportedQuantitationTypeConversionException - Exception Class in ubic.gemma.core.analysis.preprocess.convert: Exception raised when data from a given quantitation type cannot be converted to another quantitation type.
UnsupportedQuantitationTypeConversionException(String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationTypeConversionException
UnsupportedRawdataFileFormatException - Exception Class in ubic.gemma.core.analysis.preprocess.batcheffects: Used to indicate failure was due to the format being unusable, but the files are available.
UnsupportedRawdataFileFormatException(ExpressionExperiment, String) - Constructor for exception class ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException
UnsupportedScaleTypeForSingleCellAggregationException - Exception Class in ubic.gemma.core.analysis.singleCell.aggregate: Exception raised when a ScaleType is not suitable for aggregating.
UnsupportedScaleTypeForSingleCellAggregationException(ScaleType) - Constructor for exception class ubic.gemma.core.analysis.singleCell.aggregate.UnsupportedScaleTypeForSingleCellAggregationException
until - Variable in class ubic.gemma.rest.AdminWebService.GeoScrapeRequest: Upper bound of the scrape window (publication date inclusive).
UNTRIAGED - Enum constant in enum class ubic.gemma.model.annotations.WithheldFromApi.Reason: Real data that a client might legitimately want, withheld only because Gemma Web was once the consumer, and not yet traced far enough to expose safely.
UNVERIFIED_OLS_UNAVAILABLE - Enum constant in enum class ubic.gemma.core.ontology.TermViolation.Reason: The URI is unknown locally and OLS could not be reached to check it — unverified, not proven bad.
unZipFiles(String) - Static method in class ubic.gemma.core.util.FileTools: Unzip every entry of a zip archive next to the archive.
up() - Static method in class ubic.gemma.rest.monitoring.health.HealthResult
up(Map) - Static method in class ubic.gemma.rest.monitoring.health.HealthResult
UP - Enum constant in enum class ubic.gemma.rest.monitoring.health.HealthResult.Status
UP - Static variable in enum class ubic.gemma.model.analysis.expression.diff.Direction: Aliases for readability.
update(C) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService
update(String, String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
update(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService
update(Collection) - Method in class ubic.gemma.persistence.service.AbstractService
update(Collection) - Method in interface ubic.gemma.persistence.service.BaseService
update(Collection) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService
update(Collection) - Method in class ubic.gemma.persistence.service.AbstractDao
update(Collection) - Method in interface ubic.gemma.persistence.service.BaseDao: Update the given entities.
update(Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
update(Collection) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
update(Collection) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
update(Collection) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
update(Collection) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
update(Collection) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
update(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
update(O) - Method in class ubic.gemma.persistence.service.AbstractService
update(O) - Method in interface ubic.gemma.persistence.service.BaseService
update(O) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService
update(MutableAcl) - Method in interface ubic.gemma.core.security.acl.domain.AclDao
update(MutableAcl) - Method in class ubic.gemma.core.security.acl.domain.AclDaoImpl: This is an important method, and one that causes problems in the default JDBC-based service from spring-security.
update(T) - Method in class ubic.gemma.persistence.service.AbstractDao
update(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Update the given entity.
update(User) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
update(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
update(UserGroup) - Method in interface ubic.gemma.core.security.authentication.BaseUserService
update(UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
update(ExpressionExperimentSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
update(UserGroup) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
update(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
update(Characteristic) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
update(ExternalDatabase) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
update(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
update(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
update(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
update(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper: Update corresponding entity based on value object
update(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
update(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
update(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
UPDATE - Static variable in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Aliases, for readability.
UPDATE_DATE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField
updateAce(int, Permission) - Method in class ubic.gemma.core.security.acl.domain.AclImpl
updateAcl(MutableAcl) - Method in class ubic.gemma.core.security.acl.domain.AclServiceImpl
updateAnnotationRelationEntries(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Rebuild the ANNOTATION_RELATION rows a curator already wrote.
updateAnnotationRelationEntries(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl: Removes the CURATED rows.
updateAnnotations(ExpressionExperiment, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Replace the experiment-level characteristic set on ee with the supplied desired collection (idempotent set semantics).
updateAnnotations(ExpressionExperiment, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Idempotent set-replace for an EE's direct characteristic set.
updateAnnotations(ExpressionExperiment, BioMaterial, Collection) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Idempotent set-replace for a biomaterial's direct characteristic set, the sample-level counterpart of ExpressionExperimentService.updateAnnotations(ExpressionExperiment, Collection).
updateAnnotations(ExpressionExperiment, BioMaterial, Collection) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
updateAnnotationSetProvenance(Long, AnnotationSetsWebService.ProvenanceRequest) - Method in class ubic.gemma.rest.AnnotationSetsWebService
updateBioMaterials(Collection) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Update the biomaterials that are described by the given valueObjects.
updateBioMaterials(Collection) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent: Deprecated.

This method should be overloaded in all of the extensions of this class to do the specific actions they wre designed for.
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent: Deprecated.
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent: Deprecated.
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionEvent: Deprecated.
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent: Deprecated.
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent: Deprecated.
updateCurationDetailsFromAuditEvent(C, AuditEvent) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
updateCurationDetailsFromAuditEvent(C, AuditEvent) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao: Update the curation details of a given curatable entity.
updateCurationDetailsFromAuditEvent(Curatable, AuditEvent) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDaoImpl
updated - Variable in class ubic.gemma.rest.util.args.DatasetArgService.DesignChangeResult
updatedAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetResponse
updatedAt - Variable in class ubic.gemma.rest.AnnotationSetsWebService.AnnotationSetSummaryResponse
UpdateDatabaseCli - Class in ubic.gemma.apps: Update the database.
UpdateDatabaseCli() - Constructor for class ubic.gemma.apps.UpdateDatabaseCli
updateDatabaseEntity(Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: AJAX Updates the database entity (permission permitting) with the fields of the param value object
updateDatabaseEntity(Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
updateDatabaseEntityMembers(Long, Collection) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: Updates the database record for the param gene set value object (permission permitting) with the members specified of the set, not the name or description etc.
updateDatabaseEntityMembers(Long, Collection) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService: AJAX Updates the database entity (permission permitting) with the name and description fields of the param value object
updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
updateDatasetAnnotations(DatasetArg, DatasetsWebService.AnnotationsUpdateRequest) - Method in class ubic.gemma.rest.DatasetsWebService
updateDatasetBasics(DatasetArg, DatasetsWebService.DatasetBasicsUpdateRequest) - Method in class ubic.gemma.rest.DatasetsWebService
updateDatasetCurationDetails(DatasetArg, DatasetsWebService.CurationDetailsUpdateRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Deprecated.
per Decision 1 of AUDIT_AS_WORKFLOW_RECCE.md the troubled / needsAttention flips are now backed by TicketService: a troubled=true flip opens a TicketType.QUALITY_REVIEW ticket, troubled=false resolves the matching open ticket(s), and analogously for needsAttention (mapped to TicketType.GENERIC on open). Clients should migrate to POST /tickets + PUT /tickets/{id} on TicketsWebService. The endpoint is retained for back-compat while the UI moves over. The curationNote field is still routed through CurationNoteUpdateEvent pending the note-to-ticket-comment migration (see CURATION_DETAILS_RETIREMENT.md).
updateDatasetPermissions(DatasetArg, DatasetsWebService.PermissionsUpdateRequest) - Method in class ubic.gemma.rest.DatasetsWebService
updateDatasetPublications(DatasetArg, DatasetsWebService.PublicationsUpdateRequest) - Method in class ubic.gemma.rest.DatasetsWebService
UpdateEe2AdCli - Class in ubic.gemma.apps
UpdateEe2AdCli() - Constructor for class ubic.gemma.apps.UpdateEe2AdCli
UpdateEE2CCli - Class in ubic.gemma.apps
UpdateEE2CCli() - Constructor for class ubic.gemma.apps.UpdateEE2CCli
UpdateEEDetailsCommand - Class in ubic.gemma.core.tasks.analysis.expression
UpdateEEDetailsCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
updateExperimentSet(Long, ExperimentSetsWebService.ExperimentSetRequest) - Method in class ubic.gemma.rest.ExperimentSetsWebService
updateExperimentSetMembers(Long, ExperimentSetsWebService.ExperimentSetMembersRequest) - Method in class ubic.gemma.rest.ExperimentSetsWebService
updateExpressionExperiment2ArrayDesignEntries(Date, boolean) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Update the EXPRESSION_EXPERIMENT2_ARRAY_DESIGN table.
updateExpressionExperiment2ArrayDesignEntries(Date, boolean) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
updateExpressionExperiment2ArrayDesignEntries(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
updateExpressionExperiment2ArrayDesignEntries(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
updateExpressionExperiment2CharacteristicEntries(Class, Date, boolean) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Update a specific level of the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
updateExpressionExperiment2CharacteristicEntries(Class, Date, boolean) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
updateExpressionExperiment2CharacteristicEntries(Date, boolean) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Update the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
updateExpressionExperiment2CharacteristicEntries(Date, boolean) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
updateExpressionExperiment2CharacteristicEntries(ExpressionExperiment, Class) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Update the EXPRESSION_EXPERIMENT2CHARACTERISTIC table for a specific experiment.
updateExpressionExperiment2CharacteristicEntries(ExpressionExperiment, Class) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
updateExternalRelationEntries() - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Rebuild the AnnotationRelationBasis.EXTERNAL rows that MGI's genotype-to-disease reports assert — and the ones they deny.
updateExternalRelationEntries() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl: Not @Transactional, for the same reason as the ontology pass: the fetch and the parse happen before there is a row to write, and the producer's own transaction wraps only the delete-and-insert.
UpdateExternalRelationsCli - Class in ubic.gemma.apps: Rebuilds the EXTERNAL rows of ANNOTATION_RELATION from the third-party resources that state relations Gemma cannot derive itself.
UpdateExternalRelationsCli() - Constructor for class ubic.gemma.apps.UpdateExternalRelationsCli
updateFromGEO(String, GeoService.GeoUpdateConfig) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService: Refetch and reprocess the GEO series, updating select information.
updateFromGEO(String, GeoService.GeoUpdateConfig) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
updateFromGEO(ExpressionExperiment, GeoService.GeoUpdateConfig) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService: Refetch and reprocess a given experiment.
updateFromGEO(ExpressionExperiment, GeoService.GeoUpdateConfig) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
updateGene(Gene, Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneWriteService: Update-path body for an already-persistent gene.
updateGene(Gene, Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl
UpdateGene2CsCli - Class in ubic.gemma.apps
UpdateGene2CsCli() - Constructor for class ubic.gemma.apps.UpdateGene2CsCli
updateGene2CsEntries() - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: If necessary, update the GENE2CS table.
updateGene2CsEntries() - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
updateGene2CsEntries(Date, boolean, boolean) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Update the GENE2CS table.
updateGene2CsEntries(Date, boolean, boolean) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
updateGene2CsEntries(ArrayDesign, boolean) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Update the GENE2CS table for a specific ArrayDesign.
updateGene2CsEntries(ArrayDesign, boolean) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
updateGeneProduct(GeneProduct, GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneWriteService: Update mutable fields on an existing gene product from incoming info.
updateGeneProduct(GeneProduct, GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl
updateGenesUsable(Taxon, boolean) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
updateGenesUsable(Taxon, boolean) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
UpdateGeoSourceMetadataCli - Class in ubic.gemma.apps: Housekeeping: store the GEO record each experiment was built from.
UpdateGeoSourceMetadataCli() - Constructor for class ubic.gemma.apps.UpdateGeoSourceMetadataCli
updateGroup(Long, GroupsWebService.GroupUpdateRequest) - Method in class ubic.gemma.rest.GroupsWebService: Partial update — currently name (rename) and description.
updateIgnoreAcl(FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Deprecated.
do not use this, it is only a workaround to make FV migration faster
updateIgnoreAcl(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
updateMeanVarianceRelation(ExpressionExperiment, MeanVarianceRelation) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
updateMeanVarianceRelation(ExpressionExperiment, MeanVarianceRelation) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
updateMeanVarianceRelation(ExpressionExperiment, MeanVarianceRelation) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
updateMeanVarianceRelation(ExpressionExperiment, MeanVarianceRelation) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
updateMeanVarianceRelation(ExpressionExperiment, MeanVarianceRelation) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService
updateMeanVarianceRelation(ExpressionExperiment, MeanVarianceRelation) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl
updateMembers(Long, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper: Updates the database record for the param experiment set value object (permission permitting) with the members specified of the set, not the name or description etc.
updateMembers(Long, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
updateMetadata(Ticket, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Persist metadata-only edits (priority, dueDate, title, body, mode, etc.) to a ticket.
updateMetadata(Ticket, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
updateMultifunctionality() - Method in interface ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationService: Update for all taxa
updateMultifunctionality() - Method in class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceImpl
updateMultifunctionality(Taxon) - Method in interface ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationService
updateMultifunctionality(Taxon) - Method in class ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceImpl
updateNameAndDescription(ExpressionExperiment, String, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Update the curator-editable "basics" of ee: its name (title) and/or description.
updateNameAndDescription(ExpressionExperiment, String, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
updateNameAndDescription(ExpressionExperimentSetValueObject, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper: Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.
updateNameAndDescription(ExpressionExperimentSetValueObject, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
updateOntologyRelationEntries(Collection) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil: Rebuild the ANNOTATION_RELATION rows a loaded ontology asserts.
updateOntologyRelationEntries(Collection) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl: Not @Transactional: the producer spends minutes walking Jena models before it has a row to write, and its own transaction wraps only the delete-and-insert.
UpdateOntologyRelationsCli - Class in ubic.gemma.apps: Rebuilds the ONTOLOGY rows of ANNOTATION_RELATION from the relations CLO and CHEBI assert.
UpdateOntologyRelationsCli() - Constructor for class ubic.gemma.apps.UpdateOntologyRelationsCli
updatePassword(UserDetails, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl: Spring Security 6's password-upgrade hook.
updateProvenance(Long, AnnotationSetService.RunProvenance) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: Correct the run-provenance envelope on an existing row in place, so a mis-stamped agentVersion / model / agentName / runSha / ranAt is fixed without the delete-and-recreate that mints a new id.
updateProvenance(Long, AnnotationSetService.RunProvenance) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
updatePublications(ExpressionExperiment, BibliographicReference, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Replace the publications associated with ee: set (or clear) its primary publication and replace its other-relevant-publication set in one shot (idempotent set semantics).
updatePublications(ExpressionExperiment, BibliographicReference, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Replace an EE's primary + other-relevant publications, recording every one as a bare curator assertion.
updatePublications(ExpressionExperiment, PublicationAssertion, Collection, Collection) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Replace ee's publications and the evidence behind them in one transaction, including the record of which publications have been ruled out.
updatePublications(ExpressionExperiment, PublicationAssertion, Collection, Collection) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Replace an EE's publications and the evidence behind them.
UpdatePubMedCli - Class in ubic.gemma.apps: Identify experiments in Gemma that have no publication Fetch their GEO records and check for pubmed IDs Add the publications where we find them.
UpdatePubMedCli() - Constructor for class ubic.gemma.apps.UpdatePubMedCli
UpdatePubMedCommand - Class in ubic.gemma.core.tasks.analysis.expression
UpdatePubMedCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
UpdatePubMedCommand(Long) - Constructor for class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
updateQuantitationType(ExpressionExperiment, QuantitationType, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Update a quantitation type.
updateQuantitationType(ExpressionExperiment, QuantitationType, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
updateQuantitationType(ExpressionExperiment, QuantitationType, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService
updateQuantitationType(ExpressionExperiment, QuantitationType, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl
updateRanks(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Update the ranks of the processed vectors for the given experiment.
updateRanks(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
updateReleaseDetails(ExternalDatabase, String, URL, String, Date) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
updateReleaseDetails(ExternalDatabase, String, URL, String, Date) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
updateReleaseLastUpdated(ExternalDatabase, String, Date) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
updateReleaseLastUpdated(ExternalDatabase, String, Date) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
updateSampleCharacteristics(DatasetArg, Long, DatasetsWebService.AnnotationsUpdateRequest) - Method in class ubic.gemma.rest.DatasetsWebService
updateSingleCellDimension(ExpressionExperiment, SingleCellDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Update a single-cell dimensino for a given experiment.
updateSingleCellDimension(ExpressionExperiment, SingleCellDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
updateSparsityMetrics(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService: Update the sparsity metrics.
updateSparsityMetrics(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl
updateStatus(AnnotationSet, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: Record where a proposal stands with its reviewer, and return the updated set.
updateStatus(AnnotationSet, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
updateSubsumingStatus(ArrayDesign, ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
updateSubsumingStatus(ArrayDesign, ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
updateSubsumingStatus(ArrayDesign, ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Test whether the candidateSubsumer subsumes the candidateSubsumee.
updateSubsumingStatus(ArrayDesign, ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
updateTargetScreeningResult(Ticket, Long, ScreeningResult, String, boolean, Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService: Record a ScreeningResult on one target (by its row id).
updateTargetScreeningResult(Ticket, Long, ScreeningResult, String, boolean, Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
updateTargetStatus(Long, Long, TicketsWebService.UpdateTargetStatusRequest) - Method in class ubic.gemma.rest.TicketsWebService
updateTargetStatus(Ticket, Long, TicketTargetStatus, Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
updateTargetStatus(Ticket, Long, TicketTargetStatus, Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl
UpdateTargetStatusRequest() - Constructor for class ubic.gemma.rest.TicketsWebService.UpdateTargetStatusRequest
updateTaxaWithGenesUsable(Collection) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader: Method to update taxon to indicate that genes have been loaded for that taxon are are usable.
updateTicket(Long, TicketsWebService.UpdateTicketRequest) - Method in class ubic.gemma.rest.TicketsWebService: Update mutable fields of a ticket.
UpdateTicketRequest() - Constructor for class ubic.gemma.rest.TicketsWebService.UpdateTicketRequest
updateUser(UserDetails) - Method in interface ubic.gemma.core.security.authentication.UserManager
updateUser(UserDetails) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
updateUserGroups(UserDetails, Collection) - Method in interface ubic.gemma.core.security.authentication.UserManager: Update the groups a user belong to.
updateUserGroups(UserDetails, Collection) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
UpdateUserRequest() - Constructor for class ubic.gemma.rest.AdminWebService.UpdateUserRequest
upgradeEncoding(String) - Method in class ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder
upsert(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneWriteService: Find-or-update entry point for the gene-curation path.
upsert(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl
upsertDatasetDraftAnnotationSet(DatasetArg, String, AnnotationSetsWebService.UpsertDraftRequest) - Method in class ubic.gemma.rest.DatasetsWebService
upsertDraft(Investigation, String, String, String, AnnotationSet) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService: Convenience overload for the common DRAFT-upsert path used by the curation-UI: ensures one DRAFT per (investigation, curator) by deriving runId as "draft-{createdBy}".
upsertDraft(Investigation, String, String, String, AnnotationSet) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl
upsertDraftForDataset(DatasetArg, String, AnnotationSetsWebService.UpsertDraftRequest) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Upsert a curator's DRAFT for the given dataset.
UpsertDraftRequest() - Constructor for class ubic.gemma.rest.AnnotationSetsWebService.UpsertDraftRequest
UptimeBlock(long, long) - Constructor for class ubic.gemma.rest.monitoring.InfoWebService.UptimeBlock
uptimeMillis - Variable in class ubic.gemma.rest.AdminWebService.SystemSnapshotResponse
URGENT - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketPriority
uri() - Method in record class ubic.gemma.core.ontology.lexical.LexicalOntologyIndex.Hit: Returns the value of the uri record component.
uri() - Method in record class ubic.gemma.core.ontology.lexical.LexicalTerm: Returns the value of the uri record component.
URI_PREFIX - Static variable in class ubic.gemma.core.ontology.providers.CellosaurusOntologyService: Canonical, resolvable Cellosaurus URI prefix; <prefix>CVCL_1234.
URI_PREFIX - Static variable in class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService: Every URI served here is a MONDO term; nothing else is admitted.
URI_PREFIX - Static variable in class ubic.gemma.core.ontology.providers.MgiStrainOntologyService: Canonical, resolvable MGI strain URI prefix; <prefix>MGI:2160170.
URI_UNRESOLVED - Enum constant in enum class ubic.gemma.core.ontology.TermViolation.Reason: The URI resolves in neither Gemma's loaded ontologies nor OLS, and is not an allow-listed non-ontology URI — a fabricated / ungrounded term.
uris - Variable in class ubic.gemma.rest.AdminWebService.ObsoleteTermCorrectionSubmission
uriToTermId(String) - Static method in class ubic.gemma.core.ontology.OntologyUtils: Converts a URI to an OBO term ID.
url - Variable in class ubic.gemma.rest.AdminWebService.CurationAgentHealthResponse
URLAndDestination(URL, Path) - Constructor for class ubic.gemma.core.util.SimpleDownloader.URLAndDestination
urlEncode(String) - Static method in class ubic.gemma.core.util.StringUtils: Encode the given string for use in a URL.
UrlOntologyService - Class in ubic.gemma.core.ontology.jena: An ontology service that loads an ontology from a URL.
UrlOntologyService(String, String, boolean, String) - Constructor for class ubic.gemma.core.ontology.jena.UrlOntologyService
UsageExample(Class, String, String, String, String, String, String, String, String, String, String, String, String, long) - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
UsageWeightedRankingStrategy - Class in ubic.gemma.rest.ranking: Blends Lucene rank with the per-URI usage count.
UsageWeightedRankingStrategy(double, double) - Constructor for class ubic.gemma.rest.ranking.UsageWeightedRankingStrategy: Convenience constructor that defaults presence-floor and usage-saturation to the production values (0.2 / 100).
UsageWeightedRankingStrategy(double, double, double, int) - Constructor for class ubic.gemma.rest.ranking.UsageWeightedRankingStrategy
USE_BIO_ASSAY_IDS_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
USE_ENSEMBL_IDS_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
USE_MULTIPLE_ROWS_FOR_ASSAYS_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
USE_RAW_COLUMN_NAMES_OPTION - Static variable in class ubic.gemma.cli.options.DataFileOptionsUtils
use10xChemistry(String) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder: Chemistry used for single-cell sequencing.
useBioAssayIds - Variable in class ubic.gemma.cli.options.ExpressionDataFileOptionValue
useCellIdsIfSampleNameIsMissing(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder: When parsing SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder.cellTypeAssignmentFile and SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder.otherCellLevelCharacteristicsFile, allow for a missing sample_id column, in which case barcodes are used to infer the sample a cell belongs to.
useCursorFetchIfSupported(boolean) - Method in class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder
useDatabase(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Use the database for finding results.
useDataFromGeo() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
usedBytes - Variable in class ubic.gemma.rest.AdminWebService.MemoryBlock
useDoublePrecision(boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder: Use double precision for loading MEX data.
usedToBe(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
Use esummary, not elink - Section in ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder.locatePubMedIds(String)
useFullTextIndex(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Use the full-text index for finding results.
useGeneOntology(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Include results from the Gene Ontology (GO).
useInferredRelations(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Widen the search into terms Gemma knows are related to the ones matched -- so that ticking "Leigh syndrome" still returns a dataset annotated only as a SURF1 mutant.
useOntology(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder: Use the ontology and ontology inference for finding results.
user - Variable in class ubic.gemma.rest.AdminWebService.CreateUserResponse
User - Class in ubic.gemma.model.common.auditAndSecurity: A user of the software system, who is authenticated.
User - Interface in ubic.gemma.core.security.model: TODO Document Me
User() - Constructor for class ubic.gemma.model.common.auditAndSecurity.User
USER_GROUP_AUTHORITY - Static variable in class ubic.gemma.core.security.AuthorityConstants: The name of the default user group authority.
USER_GROUP_NAME - Static variable in class ubic.gemma.core.security.AuthorityConstants
USER_ID_MDC_KEY - Static variable in class ubic.gemma.rest.servlet.RequestIdMdcFilter
User.Factory - Class in ubic.gemma.model.common.auditAndSecurity
useRawColumnNames - Variable in class ubic.gemma.cli.options.ExpressionDataFileOptionValue
useRawX(Boolean) - Method in class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder
UserDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
UserDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity: DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.common.auditAndSecurity.User.
UserDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
UserDetailsImpl - Class in ubic.gemma.core.security.authentication: Implementation for Spring Security.
UserDetailsImpl(String, String, boolean, Collection, String, String, Date) - Constructor for class ubic.gemma.core.security.authentication.UserDetailsImpl
UserDetailsImpl(User) - Constructor for class ubic.gemma.core.security.authentication.UserDetailsImpl: Create a user details object from a User object.
UserDetailsManager - Interface in ubic.gemma.core.security.authentication: Extension of UserDetailsManager.
UserDetailsThreadContextPopulator - Class in ubic.gemma.cli.logging.log4j: Populate user details in the Log4j ThreadContext.
UserDetailsThreadContextPopulator() - Constructor for class ubic.gemma.cli.logging.log4j.UserDetailsThreadContextPopulator
userExists(String) - Method in interface ubic.gemma.core.security.authentication.UserManager
userExists(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
UserExistsException - Exception Class in ubic.gemma.core.security.authentication: Exception raised when a user with a given username already exist.
UserExistsException(String) - Constructor for exception class ubic.gemma.core.security.authentication.UserExistsException
UserGroup - Class in ubic.gemma.model.common.auditAndSecurity: An organized group of researchers with an identifiable leader and group members.
UserGroup - Interface in ubic.gemma.core.security.model: Represents a group of users whom are conferred a set of GrantedAuthority.
UserGroup() - Constructor for class ubic.gemma.model.common.auditAndSecurity.UserGroup: No-arg constructor added to satisfy javabean contract
UserGroup.Factory - Class in ubic.gemma.model.common.auditAndSecurity
UserGroupDao - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
UserGroupDaoImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
UserGroupDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
UserIdRetrievalStrategy - Interface in ubic.gemma.rest.analytics.ga4: Strategy for retrieving a user ID.
UserManager - Interface in ubic.gemma.core.security.authentication: Overrides gsec's UserManager to provide Gemma-specific types.
userManagerAliases() - Static method in class ubic.gemma.core.security.SecurityConfig: Register the userDetailsManager and groupManager aliases for the userManager bean (UserManagerImpl).
UserManagerImpl - Class in ubic.gemma.core.security.authentication: Implementation for Spring Security, plus some other handy methods.
UserManagerImpl() - Constructor for class ubic.gemma.core.security.authentication.UserManagerImpl
username - Variable in class ubic.gemma.rest.AdminWebService.CreateUserRequest
username - Variable in class ubic.gemma.rest.AdminWebService.SessionPrincipalValueObject
username - Variable in class ubic.gemma.rest.AdminWebService.UserValueObject
username - Variable in class ubic.gemma.rest.AuthWebService.LoginRequest
UsernamePasswordFTPClientAuthenticator - Class in ubic.gemma.core.loader.util.ftp: Simple username/password authenticator.
UsernamePasswordFTPClientAuthenticator(String, String) - Constructor for class ubic.gemma.core.loader.util.ftp.UsernamePasswordFTPClientAuthenticator
UserReadService - Interface in ubic.gemma.core.security.authentication: Read-only retrieval service for User / UserGroup / GroupAuthority.
UserReadServiceImpl - Class in ubic.gemma.core.security.authentication: Read-only implementation of the UserService read cluster.
UserReadServiceImpl(UserDao, UserGroupDao) - Constructor for class ubic.gemma.core.security.authentication.UserReadServiceImpl
users - Variable in class ubic.gemma.rest.AdminWebService.UsersListResponse
UserService - Interface in ubic.gemma.core.security.authentication: Override a few definition from gsec so that we can use Gemma-specific implementations safely.
UserServiceImpl - Class in ubic.gemma.core.security.authentication
UserServiceImpl() - Constructor for class ubic.gemma.core.security.authentication.UserServiceImpl
UsersListResponse() - Constructor for class ubic.gemma.rest.AdminWebService.UsersListResponse
UserValueObject() - Constructor for class ubic.gemma.rest.AdminWebService.UserValueObject
UserValueObject(User, String, List) - Constructor for class ubic.gemma.rest.RootWebService.UserValueObject
userWithEmailExists(String) - Method in interface ubic.gemma.core.security.authentication.UserDetailsManager
userWithEmailExists(String) - Method in interface ubic.gemma.core.security.authentication.UserManager
userWithEmailExists(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
usesSubquery(boolean) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder: Indicate if the property uses a subquery for filtering.
Using Gsec - Section in package ubic.gemma.core.security
Util - Class in ubic.gemma.core.util.graphics.text
Util() - Constructor for class ubic.gemma.core.util.graphics.text.Util

V

validate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: This method can only be called once a sample has been completely processed, and before a new sample has been started.
validateAndCanonicalize(Characteristic) - Method in interface ubic.gemma.core.ontology.OntologyTermValidator: Validate every URI-bearing slot of a characteristic, rewriting accepted case/whitespace near-matches to their canonical labels in place, discarding the record of which labels were rewritten.
validateAndCanonicalize(Characteristic, List) - Method in interface ubic.gemma.core.ontology.OntologyTermValidator: As OntologyTermValidator.validateAndCanonicalize(Characteristic), but also records every label rewrite it applied (accepted near-match or blank-label fill-in) into canonicalizations so the caller can echo the correction back to its client — the report obligation the hard-reject contract promises.
validateAndCanonicalize(Characteristic, List) - Method in class ubic.gemma.core.ontology.OntologyTermValidatorImpl
validateMask(CellLevelCharacteristics) - Static method in class ubic.gemma.core.analysis.singleCell.SingleCellMaskUtils: Validate a mask.
validateSignupToken(String, String) - Method in interface ubic.gemma.core.security.authentication.UserDetailsManager: Validate the token previously generated by UserDetailsManager.generateSignupToken(String).
validateSignupToken(String, String) - Method in interface ubic.gemma.core.security.authentication.UserManager
validateSignupToken(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
validateSparseArray(List, int[], int, T) - Static method in class ubic.gemma.core.datastructure.sparse.SparseListUtils
validateSparseRangeArray(List, int[], int) - Static method in class ubic.gemma.core.datastructure.sparse.SparseListUtils: Validate a sparse range array.
validateTaxaForBlatFile(ArrayDesign, Taxon) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService: If no taxon is supplied then infer it from array.
validateTaxaForBlatFile(ArrayDesign, Taxon) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
validateTaxon(Taxon, ArrayDesign) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
validateTaxon(Taxon, ArrayDesign) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl: If taxon is null then it has not been provided on the command line, then deduce the taxon from the arrayDesign.
VALIDATION - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
value - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.PriorCurationUsage
value - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
value() - Element in annotation interface ubic.gemma.core.architecture.SuppressArchUnit: Name of the ArchUnit rule being suppressed.
value() - Element in annotation interface ubic.gemma.core.security.audit.Audited: The concrete AuditEventType subclass to record.
value() - Element in annotation interface ubic.gemma.core.security.audit.AuditedConditional: The concrete AuditEventType subclass to record.
value() - Element in annotation interface ubic.gemma.core.security.audit.AuditedOnError: The concrete AuditEventType subclass to record.
value() - Element in annotation interface ubic.gemma.core.security.audit.AuditedOnErrors
value() - Element in annotation interface ubic.gemma.model.annotations.WithheldFromApi: Why this member is withheld.
value() - Element in annotation interface ubic.gemma.rest.annotations.CacheControls
value() - Element in annotation interface ubic.gemma.rest.annotations.GZIPs
Value - Class in ubic.gemma.model.common.description: Represents a value.
Value(String, String) - Constructor for class ubic.gemma.model.common.description.Value
valueId - Variable in class ubic.gemma.model.common.description.CharacteristicValueObject: A unique ontology identifier (i.e.
ValueObject - Annotation Interface in ubic.gemma.model.common: Annotate class representing value objects.
ValueObjectConfig - Class in ubic.gemma.persistence.util
ValueObjectConfig() - Constructor for class ubic.gemma.persistence.util.ValueObjectConfig
valueObjectConversionService(ArrayDesignService, BibliographicReferenceService, BioSequenceService, CompositeSequenceService, ExpressionExperimentService, ExpressionExperimentSetService, GeneService, GeneSetService, BlacklistedEntityService) - Method in class ubic.gemma.persistence.util.ValueObjectConfig
valueOf(int) - Static method in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.cli.completion.CompletionType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.cli.util.CLI.CommandGroup: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.analysis.expression.diff.AnalysisType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter.Mode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat.BlattableGenome: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.analysis.service.ExpressionExperimentDataFileType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl.SingleCellExpressionAggregationMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.job.SubmittedTask.Status: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.entrez.EntrezRetmode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.cellxgene.FileType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.GeoLibrarySource: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoAmount: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoFormat: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoRecordType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoScope: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoSource: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.singleCell.SingleCellDataType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaFieldType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.ontology.GoMetric.Metric: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.ontology.model.OntologyCardinalityRestriction.CardinalityType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.ontology.model.OntologyXref.Strength: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.ontology.providers.OntologyService.InferenceMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.ontology.providers.OntologyService.LanguageLevel: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.ontology.TermViolation.Reason: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.core.visualization.SingleCellSparsityHeatmap.SingleCellHeatmapType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.analysis.expression.diff.Direction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.annotations.WithheldFromApi.Reason: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.association.GOEvidenceCode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetRole: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSource: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionScope: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions.Disposition: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.ExternalIssueSyncState: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.FindingDisposition: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.ScreeningResult: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketPriority: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketState: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageJudgeKind: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdict: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.description.AnnotationRelationBasis: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.description.AnnotationRelationStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.description.DatabaseType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.description.PublicationAssociationRole: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.description.PublicationAssociationSource: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.description.PublicationAssociationStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.description.RelationInferenceDirection: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.description.RelationTopicality: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.measurement.MeasurementKind: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.measurement.MeasurementType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.quantitationtype.GeneralType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.search.SearchMatchType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.common.search.SearchSettings.SearchMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.expression.experiment.AgentCurationKind: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.expression.experiment.FactorType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.expression.experiment.GeoScrapeWatermark.Status: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.expression.experiment.WorkflowState: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.genome.biosequence.PolymerType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.genome.biosequence.SequenceType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.pipeline.JobState: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.pipeline.PipelineJobBatch.BatchState: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.pipeline.SchedulerKind: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.model.util.ModelUtils.EqualityOutcome: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao.SummarySort: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.Direction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.util.Cursor.Direction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.util.Filter.Operator: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.util.Sort.Direction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.util.Sort.NullMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.persistence.util.SubqueryMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.rest.DatasetsWebService.CorrelationMatrixChoice: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.rest.DatasetsWebService.PcLoadingDirection: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.rest.monitoring.health.HealthResult.Status: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.rest.PlatformsWebService.AnnotationFileType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.CompositeSequenceArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.CursorArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatabaseEntryArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatabaseEntryArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatasetArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatasetArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.ExcludeArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.ExpLevelConsolidationArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.FactorValueArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.FilterArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.GeneArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.GeneArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.LimitArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.OffsetArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.PlatformArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.PlatformArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.QuantitationTypeArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.QueryArg
valueOf(String) - Static method in enum class ubic.gemma.rest.util.args.SortArg.Sort.Direction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.rest.util.args.SortArg.Sort.NullMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.SortArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.StringArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.TaxonArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.TaxonArrayArg
valueOf(String) - Static method in enum class ubic.gemma.rest.util.CurationCommitConflictException.Reason: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ubic.gemma.rest.util.LocationType: Returns the enum constant of this class with the specified name.
valueOf(String, String, Function, boolean) - Static method in class ubic.gemma.rest.util.args.AbstractArrayArg: Evaluate an input array argument.
values - Variable in class ubic.gemma.core.loader.util.anndata.NullableArray
values() - Static method in enum class ubic.gemma.cli.completion.CompletionType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.cli.util.CLI.CommandGroup: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.analysis.expression.diff.AnalysisType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter.Mode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat.BlattableGenome: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.analysis.service.ExpressionExperimentDataFileType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl.SingleCellExpressionAggregationMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.job.SubmittedTask.Status: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.entrez.EntrezRetmode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.cellxgene.FileType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.GeoLibrarySource: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.GeoSampleType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoSeriesType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoAmount: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoFormat: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoRecordType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoScope: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.geo.service.GeoSource: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.singleCell.SingleCellDataType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaFieldType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.ontology.GoMetric.Metric: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.ontology.model.OntologyCardinalityRestriction.CardinalityType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.ontology.model.OntologyXref.Strength: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.ontology.providers.OntologyService.InferenceMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.ontology.providers.OntologyService.LanguageLevel: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.ontology.TermViolation.Reason: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.core.visualization.SingleCellSparsityHeatmap.SingleCellHeatmapType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.analysis.expression.diff.Direction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.annotations.WithheldFromApi.Reason: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.association.GOEvidenceCode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.AuditAction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetRole: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSource: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionScope: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions.Disposition: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.ExternalIssueSyncState: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.FindingDisposition: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.ScreeningResult: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketPriority: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketState: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageJudgeKind: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdict: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.description.AnnotationRelationBasis: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.description.AnnotationRelationStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.description.DatabaseType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.description.PublicationAssociationRole: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.description.PublicationAssociationSource: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.description.PublicationAssociationStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.description.RelationInferenceDirection: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.description.RelationTopicality: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.measurement.MeasurementKind: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.measurement.MeasurementType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.quantitationtype.GeneralType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.quantitationtype.PrimitiveType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.quantitationtype.ScaleType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.search.SearchMatchType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.common.search.SearchSettings.SearchMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.expression.experiment.AgentCurationKind: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.expression.experiment.BatchEffectType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.expression.experiment.FactorType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.expression.experiment.GeoScrapeWatermark.Status: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.expression.experiment.WorkflowState: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.genome.biosequence.PolymerType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.genome.biosequence.SequenceType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.pipeline.JobState: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.pipeline.PipelineJobBatch.BatchState: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.pipeline.SchedulerKind: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.model.util.ModelUtils.EqualityOutcome: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao.SummarySort: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.Direction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.util.Cursor.Direction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.util.Filter.Operator: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.util.Sort.Direction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.util.Sort.NullMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.persistence.util.SubqueryMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.rest.AnnotationsWebService.MatchedVia: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.rest.DatasetsWebService.CorrelationMatrixChoice: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.rest.DatasetsWebService.PcLoadingDirection: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.rest.monitoring.health.HealthResult.Status: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.rest.PlatformsWebService.AnnotationFileType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.rest.util.args.SortArg.Sort.Direction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.rest.util.args.SortArg.Sort.NullMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.rest.util.CurationCommitConflictException.Reason: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ubic.gemma.rest.util.LocationType: Returns an array containing the constants of this enum class, in the order they are declared.
Values - Class in ubic.gemma.model.common.description: Commonly used values across Gemma.
Values() - Constructor for class ubic.gemma.model.common.description.Values
valueSpel() - Element in annotation interface ubic.gemma.core.security.audit.Audited: Optional SpEL expression evaluated against the join-point to choose the AuditEventType subclass at runtime.
valueSpel() - Element in annotation interface ubic.gemma.core.security.audit.AuditedConditional: Optional SpEL expression that resolves to a Class<? extends AuditEventType> at runtime.
ValueStringToOntologyMapping - Class in ubic.gemma.core.ontology: Deprecated.
Nothing calls this any more (Paul, 2026-09-04): we do not map submitter text onto preset ontology terms on import. Both callers are gone — GeoConverterImpl and LoadSimpleExpressionDataCli — so a value written by a submitter now survives the load unchanged and grounding is a curation decision rather than something a loader guesses from a 1,386-row lookup table.
🛑 Kept rather than deleted, and the mapping file with it. The table is a reviewed body of value → term decisions built up over years; it is the obvious starting point for a curation-side suggester, and re-deriving it would be expensive. GeoTermReplacementTest still validates that its URIs resolve, which is what stops it rotting while it sits unused.
Do not wire it back into a loader. If a caller wants these terms, the decision to apply one belongs to a curator or to an agent proposing to a curator, not to the import path.
ValueStringToOntologyMapping() - Constructor for class ubic.gemma.core.ontology.ValueStringToOntologyMapping: Deprecated.
valueUri - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.PriorCurationUsage
valueUri - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
variance(DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Provided for convenience!
VARIANCE - Enum constant in enum class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
VectorElementValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
VectorElementValueObject(String, Map) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
VectorElementValueObject(DoubleVectorValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
VectorMergingCli - Class in ubic.gemma.apps: For experiments that used multiple array designs, merge the expression profiles
VectorMergingCli() - Constructor for class ubic.gemma.apps.VectorMergingCli
VectorMergingService - Interface in ubic.gemma.core.analysis.preprocess
VectorMergingServiceImpl - Class in ubic.gemma.core.analysis.preprocess: Tackles the problem of concatenating DesignElementDataVectors for a single experiment.
VectorMergingServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.VectorMergingServiceImpl
VectorsReorderedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Processed expression data vectors were reordered to align with the experimental design layout.
VectorsReorderedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.VectorsReorderedEvent
VelocityConfig - Class in ubic.gemma.core.mail
VelocityConfig() - Constructor for class ubic.gemma.core.mail.VelocityConfig
velocityEngine() - Method in class ubic.gemma.core.mail.VelocityConfig
VerifyPublicationEvidenceCli - Class in ubic.gemma.apps: Check Gemma's GEO-sourced primary publications against what GEO says today, and fill in the ones GEO has a paper for and Gemma does not.
VerifyPublicationEvidenceCli() - Constructor for class ubic.gemma.apps.VerifyPublicationEvidenceCli
version - Variable in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
version(String) - Method in class ubic.gemma.rest.util.BuildInfoValueObject.BuildInfoValueObjectBuilder
Versioned - Interface in ubic.gemma.model.common.description: Interface implemented by entities that are externally versioned.
VersionedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Base class for events relating to a Versioned entity.
VersionedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.VersionedEvent
viewColumn(int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
viewColumn(int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
viewColumn(int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
viewColumn(int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
viewColumn(int) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
viewColumn(int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
viewColumn(int) - Method in class ubic.gemma.core.util.matrix.StringMatrix
viewRow(int) - Method in class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix
viewRow(int) - Method in class ubic.gemma.core.util.matrix.DenseDoubleMatrix
viewRow(int) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix
viewRow(int) - Method in class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix
viewRow(int) - Method in class ubic.gemma.core.util.matrix.ObjectMatrixImpl
viewRow(int) - Method in class ubic.gemma.core.util.matrix.SparseDoubleMatrix
viewRow(int) - Method in class ubic.gemma.core.util.matrix.StringMatrix
VirtualThreadExecutorMetrics - Class in ubic.gemma.core.metrics.binder: Micrometer binder for virtual-thread-per-task executors (JDK 21+).
VirtualThreadExecutorMetrics(String) - Constructor for class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetrics
visit(OpenAPI) - Method in class ubic.gemma.rest.util.OpenAPIVisitor
visitAllStatements(Long, Collection, FactorValueOntologyUtils.StatementVisitor) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Visit every statement, including the ones that say nothing about their subject.
visitBioMaterials(BioMaterial, Consumer) - Static method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialUtils: Visit all the biomaterials in the hierarchy.
visitCharacteristics(Long, Collection, FactorValueOntologyUtils.StatementVisitor) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Visit the characteristics of a FactorValue and generate their annotation IDs.
visitErrorNode(ErrorNode) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
visitStatements(Long, Collection, FactorValueOntologyUtils.StatementVisitor) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Visit the statements of a FactorValue and generate their annotation IDs.
visitTerminal(TerminalNode) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
VLEN - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType
VOCABULARY - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
VOCABULARY - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
VOLUME - Enum constant in enum class ubic.gemma.model.common.measurement.MeasurementKind
vote(Authentication, MethodInvocation, Collection) - Method in class ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter
vote(Authentication, MethodInvocation, Collection) - Method in class ubic.gemma.core.security.acl.voter.AclEntryVoter

W

waitForDownload(Future, long, File) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
waitForInitializationThread() - Method in class ubic.gemma.core.ontology.jena.AbstractOntologyService
waitForInitializationThread() - Method in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService
waitForInitializationThread() - Method in class ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService
waitForInitializationThread() - Method in interface ubic.gemma.core.ontology.providers.OntologyService: Wait for the initialization thread to finish.
warmTopGenes() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExGeneWarmupService: Trigger one warm-up pass.
warning - Variable in class ubic.gemma.rest.AdminWebService.CreateUserResponse
warning - Variable in class ubic.gemma.rest.AdminWebService.ResetPasswordResponse
WCS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
web() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.AllEntitiesUrl
web() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ArrayDesignUrl
web() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl: Generate a URL for Gemma Web.
web() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentUrl
web() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.SomeEntitiesUrl
WEB - Static variable in class ubic.gemma.core.context.EnvironmentProfiles: Independent feature toggles.
WebApplicationExceptionMapper - Class in ubic.gemma.rest.providers: Map WebApplicationException so that it always expose a ResponseErrorObject entity.
WebApplicationExceptionMapper(String, Future, BuildInfo) - Constructor for class ubic.gemma.rest.providers.WebApplicationExceptionMapper
weightedMean(DoubleArrayList, DoubleArrayList) - Static method in class ubic.gemma.core.util.math.DescriptiveWithMissing: Returns the weighted mean of a data sequence.
weightedMean(DoubleArrayList, DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: General formula for weighted mean of effect sizes.
weightedMean(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class ubic.gemma.core.util.math.metaanalysis.MetaAnalysis: General formula for weighted mean of effect sizes including quality index scores for each value.
WellComposedError - Class in ubic.gemma.rest.util
WellComposedError.WellComposedErrorBuilder - Class in ubic.gemma.rest.util
WellComposedErrorBody - Class in ubic.gemma.rest.util: Object acting as a payload for the ResponseErrorObject.
WellComposedErrorBody.WellComposedErrorBodyBuilder - Class in ubic.gemma.rest.util
WellComposedWarning - Class in ubic.gemma.rest.util: A warning, loosely modeled on WellComposedError.
WellComposedWarning.WellComposedWarningBuilder - Class in ubic.gemma.rest.util
WGA - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
WGS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
What is deliberately not checked - Section in class ubic.gemma.rest.providers.UnknownQueryParameterFilter
What is deliberately NOT mapped - Section in class ubic.gemma.core.util.SymbolFontPua
What it is good for - Section in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule
What it will and will not write - Section in class ubic.gemma.apps.VerifyPublicationEvidenceCli
WhatsNew - Class in ubic.gemma.core.analysis.report: A value object to hold onto the 'new' objects.
WhatsNew() - Constructor for class ubic.gemma.core.analysis.report.WhatsNew
WhatsNew(Date) - Constructor for class ubic.gemma.core.analysis.report.WhatsNew
WhatsNewService - Interface in ubic.gemma.core.analysis.report: Creates reports that can be shown on the web pages or in social media feeds.
WhatsNewServiceImpl - Class in ubic.gemma.core.analysis.report: Service to collect data on objects that are new in the system.
WhatsNewServiceImpl() - Constructor for class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
What the damage is - Section in class ubic.gemma.core.util.SymbolFontPua
when() - Element in annotation interface ubic.gemma.core.security.audit.AuditedConditional: SpEL predicate evaluated against the post-invocation context.
Where the table comes from - Section in class ubic.gemma.core.util.SymbolFontPua
WHOLE_CHROMOSOME - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType
WHOLE_GENOME - Enum constant in enum class ubic.gemma.model.genome.biosequence.SequenceType
Why @Lazy(false) - Section in class ubic.gemma.core.security.acl.AclEventListenerConfig
Why @Lazy(false) - Section in class ubic.gemma.persistence.audit.AuditTrailEventListenerConfig
Why acc.cgi and not a batched esummary - Section in class ubic.gemma.apps.VerifyPublicationEvidenceCli
Why an importer needs this - Section in ubic.gemma.core.ontology.OntologyUtils.termIdOrUriToUri(String)
Why a third emitter - Section in ubic.gemma.persistence.util.AclQueryUtils.formAclRestrictionPredicate(Session, CriteriaBuilder, CommonAbstractCriteria, Expression, Class, Permission)
Why Entrez and not acc.cgi - Section in ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder.locatePubMedIds(String)
Why the accepted set cannot go stale - Section in class ubic.gemma.rest.providers.UnknownQueryParameterFilter
Why the fallback needs three exception types, not one - Section in ubic.gemma.core.ontology.search.OntologyQueries.parseSafely(QueryParser, String)
Why the plan is needed to get the count right - Section in ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.previewDesignChange(ExpressionExperiment, ExperimentalDesignValueObject, DesignCommitPlan)
Why the plan is needed to get the count right - Section in ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.previewDesignChange(ExpressionExperiment, ExperimentalDesignValueObject, DesignCommitPlan)
Why the reason is required - Section in annotation interface ubic.gemma.model.annotations.WithheldFromApi
Why these are on the REQUEST type and hidden on the response - Section in ubic.gemma.rest.DatasetsWebService.StatementCommit.getSecondPredicate()
Why these are on the REQUEST type and hidden on the response - Section in ubic.gemma.rest.DatasetsWebService.StatementCommit.setSecondPredicate(DatasetsWebService.OntologyTermRef)
Why the synonyms here are safe to index - Section in class ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService
Why this event carries it - Section in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload
Why this exists (Phase 3 cloud-readiness) - Section in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider
Why this is a subtype rather than a field on TicketSearchHitValueObject - Section in class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject
Why this is not a parameter - Section in class ubic.gemma.core.security.util.ActingIdentity
Why this is on the BioAssay and not the BioMaterial - Section in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule
WikiCompletionGenerator - Class in ubic.gemma.cli.completion: Wraps ConfluenceWikiHtmlGenerator so that we can use it as a CompletionGenerator.
WikiCompletionGenerator(String, SortedMap, String, Path) - Constructor for class ubic.gemma.cli.completion.WikiCompletionGenerator
wikiGenerator - Variable in class ubic.gemma.cli.completion.WikiCompletionGenerator
winnow(double) - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD: Implements method described in Skillicorn et al., "Strategies for winnowing microarray data" (also section 3.5.5 of his book)
wireValue() - Method in enum class ubic.gemma.model.pipeline.SchedulerKind
withAllowedValues(List) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta: A short list of allowed values if that can be determined, or null.
withDatasetConstraint(ExpressionExperiment) - Method in class ubic.gemma.model.common.search.SearchSettings: Constraint results to be related to the given dataset.
withDeprecated(boolean) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta: Indicate if the property is deprecated.
withDescriptions(List) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta: A short description for this parameter if clarifications are needed.
withdraw(AnnotationSet, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService: Withdraw judgedBy's ruling, returning the set to un-triaged if it was the only one.
withdraw(AnnotationSet, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl
withdrawTriage(Long, String) - Method in class ubic.gemma.rest.AnnotationSetsWebService: Withdraw the caller's ruling, returning the set to un-triaged if it was the only one.
withFillResults(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Indicate if result objects (i.e.
withFilterPropertyName(String, String) - Method in class ubic.gemma.persistence.util.Subquery: Create a new subquery with a different property name for the filters.
WithheldFromApi - Annotation Interface in ubic.gemma.model.annotations: Withhold a property from the RESTful API, and say why.
WithheldFromApi.Reason - Enum Class in ubic.gemma.model.annotations
withHighlights(Map) - Method in class ubic.gemma.model.common.search.SearchResult: Copy this search result with the given highlights.
withMatrix(DoubleMatrix) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Create a copy of this matrix with the given data matrix.
withMatrix(DoubleMatrix, Map) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Create a copy of this matrix with the given data matrix and quantitation types.
withMaxResults(int) - Method in class ubic.gemma.model.common.search.SearchSettings: Limit for the number of results per result type.
withMinimumShouldMatch(Query, double) - Static method in class ubic.gemma.core.ontology.search.OntologyQueries: Require a document to carry a share of the query's terms, instead of any one of them.
withMode(SearchSettings.SearchMode) - Method in class ubic.gemma.model.common.search.SearchSettings: Indicate the search mode to use.
withNumberOfCells(int[][]) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
withObjectAlias(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
withoutQuality(MediaType) - Static method in class ubic.gemma.rest.util.MediaTypeUtils: Create a media type without a quality indicator.
withPlatformConstraint(ArrayDesign) - Method in class ubic.gemma.model.common.search.SearchSettings: Constraint results to be related to the given platform.
withPropertyName(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
withPropertyName(String, String) - Method in class ubic.gemma.persistence.util.Filter: Create a copy of this filter with a new property name and original property.
withPropertyType(Class) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
withQuality(MediaType, double) - Static method in class ubic.gemma.rest.util.MediaTypeUtils: Create a media type with a quality indicator.
withQuery(String) - Method in class ubic.gemma.model.common.search.SearchSettings: Processed query for performing a search.
withResultObject(S) - Method in class ubic.gemma.model.common.search.SearchResult: Create a search result from an existing one, replacing the result object with the target one.
withResultTypes(Set) - Method in class ubic.gemma.model.common.search.SearchSettings: Entities to retrieve.
withTaxonConstraint(Taxon) - Method in class ubic.gemma.model.common.search.SearchSettings: Constraint results to to be related to the given taxon.
withUseDatabase(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Use the database for finding results.
withUseFullTextIndex(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Use the full-text index for finding results.
withUseGeneOntology(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Include results from the Gene Ontology (GO).
withUseInferredRelations(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Widen the search into terms Gemma knows are related to the ones matched -- so that ticking "Leigh syndrome" still returns a dataset annotated only as a SURF1 mutant.
withUseOntology(boolean) - Method in class ubic.gemma.model.common.search.SearchSettings: Use the ontology and ontology inference for finding results.
withUsesSubquery(boolean) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta: Indicate if the property uses a subquery for filtering.
WontFix - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdict: There is something here, and we are deliberately not acting on it.
WorkflowHistoryEntry() - Constructor for class ubic.gemma.rest.WorkflowWebService.WorkflowHistoryEntry
WorkflowQueueEntry - Class in ubic.gemma.persistence.service.expression.experiment: Lightweight projection used by GET /workflow/queue.
WorkflowQueueEntry(Long, String, String, Date) - Constructor for class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
WorkflowQueueEntryResponse() - Constructor for class ubic.gemma.rest.WorkflowWebService.WorkflowQueueEntryResponse
WorkflowService - Interface in ubic.gemma.persistence.service.expression.experiment: Service surface for the 8-state workflow lifecycle (HANDOFF_WORKFLOW_STATE_STORAGE.md).
WorkflowServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Default WorkflowService implementation.
WorkflowServiceImpl(AuditEventService, SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.WorkflowServiceImpl
WorkflowState - Enum Class in ubic.gemma.model.expression.experiment: Eight-state workflow lifecycle for experiments (and forthcoming PreboardedExperiments).
WorkflowStateChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Emitted on every successful workflow-state transition of an Investigation (currently: ExpressionExperiment; a forthcoming PreboardedExperiment subclass will join the same stream).
WorkflowStateChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.WorkflowStateChangedEvent
WorkflowStateResponse() - Constructor for class ubic.gemma.rest.WorkflowWebService.WorkflowStateResponse
WorkflowTransition - Class in ubic.gemma.persistence.service.expression.experiment: Return value of WorkflowService.advance(Investigation, WorkflowState, String, Long).
WorkflowTransition(Long, WorkflowState, WorkflowState, Date, Long) - Constructor for class ubic.gemma.persistence.service.expression.experiment.WorkflowTransition
WorkflowTransitionResponse() - Constructor for class ubic.gemma.rest.WorkflowWebService.WorkflowTransitionResponse
WorkflowWebService - Class in ubic.gemma.rest: RESTful interface for the 8-state workflow lifecycle (HANDOFF_WORKFLOW_STATE_STORAGE.md).
WorkflowWebService(WorkflowService, ExpressionExperimentService) - Constructor for class ubic.gemma.rest.WorkflowWebService
WorkflowWebService.AdvanceWorkflowRequest - Class in ubic.gemma.rest: Body of WorkflowWebService.advanceDatasetWorkflow(Long, AdvanceWorkflowRequest).
WorkflowWebService.WorkflowHistoryEntry - Class in ubic.gemma.rest
WorkflowWebService.WorkflowQueueEntryResponse - Class in ubic.gemma.rest: Per-row response of WorkflowWebService.getWorkflowQueue(String, String, String, String, Date, OffsetArg, LimitArg).
WorkflowWebService.WorkflowStateResponse - Class in ubic.gemma.rest: Response of WorkflowWebService.getDatasetWorkflow(Long).
WorkflowWebService.WorkflowTransitionResponse - Class in ubic.gemma.rest: Response of WorkflowWebService.advanceDatasetWorkflow(Long, AdvanceWorkflowRequest).
wrap(Runnable) - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextAsyncTaskExecutor
wrap(Runnable) - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextExecutorService
wrap(Runnable) - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextSchedulingTaskExecutor
wrap(Runnable) - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextTaskExecutor
wrap(Runnable) - Method in class ubic.gemma.cli.batch.BatchTaskExecutorService
wrap(Runnable) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextExecutorService
wrap(Runnable) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextScheduledExecutorService
wrap(Runnable) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutor
wrap(Callable) - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextAsyncTaskExecutor
wrap(Callable) - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextExecutorService
wrap(Callable) - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextSchedulingTaskExecutor
wrap(Callable) - Method in class ubic.gemma.core.security.concurrent.DelegatingSecurityContextTaskExecutor
wrap(Callable) - Method in class ubic.gemma.cli.batch.BatchTaskExecutorService
wrap(Callable) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextExecutorService
wrap(Callable) - Method in class ubic.gemma.core.logging.log4j.DelegatingThreadContextScheduledExecutorService
wrap(Callable) - Method in class ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService
wrap(ExecutorService) - Method in class ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetrics: Wrap a virtual-thread executor so that execute and submit* increment the counters bound by VirtualThreadExecutorMetrics.bindTo(MeterRegistry).
write(Collection, SingleCellDimension, Writer) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.CellLevelCharacteristicsWriter: Write multiple sets of cell-level characteristics to a writer.
write(Collection, Map, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
write(Collection, Map, Writer) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter
write(Stream, int, Map, Map, Path) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter: Writes a stream of vectors to a directory.
write(Stream, Map, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
write(Stream, Map, Writer) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter
write(T, Class, OutputStream) - Method in interface ubic.gemma.core.datastructure.matrix.io.ExpressionDataMatrixWriter: Write the matrix to the given output stream.
write(T, Class, Writer) - Method in interface ubic.gemma.core.datastructure.matrix.io.ExpressionDataMatrixWriter: Write the matrix to the given writer.
write(BatchTaskProcessingResult) - Method in interface ubic.gemma.cli.batch.BatchTaskSummaryWriter: Write the result of a batch task.
write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.CompositeBatchTaskSummaryWriter
write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.LoggingBatchTaskSummaryWriter
write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.SuppressBatchTaskSummaryWriter
write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.TextBatchTaskSummaryWriter
write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.TsvBatchTaskSummaryWriter
write(BulkExpressionDataMatrix, Class, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.JsonMatrixWriter
write(BulkExpressionDataMatrix, Class, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.MatrixWriter
write(BulkExpressionDataMatrix, Class, Map, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.MatrixWriter
write(SingleCellExpressionDataMatrix, OutputStream) - Method in interface ubic.gemma.core.datastructure.matrix.io.SingleCellExpressionDataMatrixWriter
write(SingleCellExpressionDataMatrix, Writer) - Method in interface ubic.gemma.core.datastructure.matrix.io.SingleCellExpressionDataMatrixWriter
write(SingleCellExpressionDataMatrix, Class, OutputStream) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter
write(SingleCellExpressionDataMatrix, Class, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter
write(SingleCellExpressionDataMatrix, Class, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
write(SingleCellExpressionDataMatrix, Class, Writer) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter
write(SingleCellExpressionDataMatrix, Map, OutputStream) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter: Write a MEX matrix as a TAR archive to the given output stream.
write(SingleCellExpressionDataMatrix, Map, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter
write(SingleCellExpressionDataMatrix, Map, Path) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter: Write a matrix to a directory.
write(DifferentialExpressionAnalysis, Map, DifferentialExpressionAnalysisConfig, boolean, OutputStream) - Method in class ubic.gemma.core.analysis.service.DiffExAnalysisResultSetWriter: Write a DifferentialExpressionAnalysis as a ZIP archive containing entries for the analysis and each result set.
write(CellLevelCharacteristics, SingleCellDimension, Writer) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.CellLevelCharacteristicsWriter: Write a single set of cell-level characteristics to a writer.
write(CellTypeAssignment, SingleCellDimension, Writer) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.CellLevelCharacteristicsWriter: Write a single cell type assignment to a writer.
write(SingleCellDimension, Writer) - Method in class ubic.gemma.core.loader.expression.singleCell.metadata.CellLevelCharacteristicsWriter
write(ExpressionExperiment, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriter: Write the experimental design of the given ExpressionExperiment to the given Writer.
write(ExpressionExperiment, QuantitationType, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.MeanVarianceWriter
write(ExpressionExperiment, QuantitationType, Class, Collection, boolean, Writer) - Method in class ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriter: Write the experimental design of the given ExpressionExperiment to the given Writer for a given collection of assays.
write(ExpressionExperiment, SingleCellDimension, Writer) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter
writeBufferedImageAsPNG(OutputStream, BufferedImage, String, BuildInfo) - Static method in class ubic.gemma.core.visualization.ChartUtils
writeCell(BioAssay, String, int, List, Map, SortedMap, SortedMap, List, Writer) - Method in class ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter
writeCellBrowserSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, boolean, int, boolean, Writer, boolean, Console) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeCellBrowserSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, boolean, int, boolean, Writer, boolean, Console) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeChartAsPNG(OutputStream, JFreeChart, int, int, String, BuildInfo) - Static method in class ubic.gemma.core.visualization.ChartUtils
writeCompletions(CompletionSource, PrintStream) - Static method in class ubic.gemma.cli.completion.CompletionUtils
writeDesignMatrix(ExpressionExperiment, boolean, Writer, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Writes out the experimental design for the given experiment.
writeDesignMatrix(ExpressionExperiment, boolean, Writer, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeDesignMatrix(ExpressionExperiment, QuantitationType, Class, Writer, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Writes out the experimental design for the given experiment and quantitation type.
writeDesignMatrix(ExpressionExperiment, QuantitationType, Class, Writer, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis, OutputStream) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write a differential expression analysis archive file for a given analysis to an output stream.
writeDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis, OutputStream) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeDiffExAnalysisArchiveFileById(Long, OutputStream) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeDiffExAnalysisArchiveFileById(Long, OutputStream) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeDiffExAnalysisArchiveFiles(Collection, Path, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeDiffExAnalysisArchiveFiles(Collection, Path, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeDiffExAnalysisArchiveFiles(ExpressionExperiment, Path, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write all the differential expression data files for a given experiment to a particular directory.
writeDiffExAnalysisArchiveFiles(ExpressionExperiment, Path, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeMapping(CellLevelCharacteristics, ExperimentalFactor, Map, Writer) - Static method in class ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils: Create a mapping of cell type assignments to factor values from a file.
writeMatrix(DoubleMatrix1D) - Method in class ubic.gemma.core.util.matrix.MatrixWriter: Write a bare 1D matrix (one value per line)
writeMatrix(DoubleMatrix2D) - Method in class ubic.gemma.core.util.matrix.MatrixWriter: Write a bare matrix without row names or columns
writeMatrix(Matrix2D, boolean) - Method in class ubic.gemma.core.util.matrix.MatrixWriter
writeMexSingleCellExpressionData(ExpressionExperiment, List, QuantitationType, ScaleType, boolean, int, boolean, boolean, Path, boolean, Console) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeMexSingleCellExpressionData(ExpressionExperiment, List, QuantitationType, ScaleType, boolean, int, boolean, boolean, Path, boolean, Console) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeMexSingleCellExpressionData(ExpressionExperiment, List, QuantitationType, ScaleType, boolean, OutputStream) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeMexSingleCellExpressionData(ExpressionExperiment, List, QuantitationType, ScaleType, boolean, OutputStream) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeMexSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, int, boolean, boolean, Path, boolean, Console) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write single-cell expression data to a given output stream for a given quantitation type.
writeMexSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, int, boolean, boolean, Path, boolean, Console) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeMexSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, OutputStream) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write single-cell expression data to a given output stream for a given quantitation type.
writeMexSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, OutputStream) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDesignFile(ExpressionExperiment, boolean, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create an experimental design file for a given experiment.
writeOrLocateDesignFile(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDesignFile(ExpressionExperiment, boolean, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeOrLocateDesignFile(ExpressionExperiment, boolean, boolean, long, TimeUnit) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDifferentialExpressionResultSetTsvFile(Long, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create a cached TSV for a single differential-expression result set.
writeOrLocateDifferentialExpressionResultSetTsvFile(Long, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDifferentialExpressionResultSetTsvFileAsync(Long, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeOrLocateDifferentialExpressionResultSetTsvFileAsync(Long, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create the differential expression archive file for a given analysis.
writeOrLocateDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDiffExAnalysisArchiveFileAsync(DifferentialExpressionAnalysis, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Build the differential expression analysis archive file off the request thread via the expressionDataFileTaskExecutor.
writeOrLocateDiffExAnalysisArchiveFileAsync(DifferentialExpressionAnalysis, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDiffExAnalysisArchiveFileById(Long, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create the differential expression archive file for a given analysis ID.
writeOrLocateDiffExAnalysisArchiveFileById(Long, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDiffExAnalysisArchiveFiles(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create the differential expression archive file(s) for a given experiment.
writeOrLocateDiffExAnalysisArchiveFiles(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment, boolean, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment, QuantitationType, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment, QuantitationType, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateMexSingleCellExpressionData(ExpressionExperiment, QuantitationType, int, boolean, boolean, Console) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write single-cell expression data to a standard location for a given quantitation type.
writeOrLocateMexSingleCellExpressionData(ExpressionExperiment, QuantitationType, int, boolean, boolean, Console) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateMexSingleCellExpressionDataAsync(ExpressionExperiment, QuantitationType, int, boolean, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeOrLocateMexSingleCellExpressionDataAsync(ExpressionExperiment, QuantitationType, int, boolean, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateProcessedDataFile(ExpressionExperiment, boolean, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).
writeOrLocateProcessedDataFile(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateProcessedDataFile(ExpressionExperiment, boolean, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeOrLocateProcessedDataFile(ExpressionExperiment, boolean, boolean, long, TimeUnit) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateProcessedDataFileAsync(ExpressionExperiment, boolean, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Build the processed-expression data file off the request thread via the expressionDataFileTaskExecutor.
writeOrLocateProcessedDataFileAsync(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateRawExpressionDataFile(ExpressionExperiment, QuantitationType, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create a new data file for the given quantitation type.
writeOrLocateRawExpressionDataFile(ExpressionExperiment, QuantitationType, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateRawExpressionDataFile(ExpressionExperiment, QuantitationType, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeOrLocateRawExpressionDataFile(ExpressionExperiment, QuantitationType, boolean, long, TimeUnit) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateRawExpressionDataFileAsync(ExpressionExperiment, QuantitationType, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Build the raw-expression data file off the request thread via the expressionDataFileTaskExecutor.
writeOrLocateRawExpressionDataFileAsync(ExpressionExperiment, QuantitationType, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateTabularSingleCellExpressionData(ExpressionExperiment, QuantitationType, int, boolean, boolean, Console) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write single-cell expression data to a standard location for a given quantitation type in tabular format.
writeOrLocateTabularSingleCellExpressionData(ExpressionExperiment, QuantitationType, int, boolean, boolean, Console) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateTabularSingleCellExpressionDataAsync(ExpressionExperiment, QuantitationType, int, boolean, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeOrLocateTabularSingleCellExpressionDataAsync(ExpressionExperiment, QuantitationType, int, boolean, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeProcessedExpressionData(ExpressionExperiment, boolean, ScaleType, boolean, boolean, boolean, Writer, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write processed expression data to a given writer for a given quantitation type.
writeProcessedExpressionData(ExpressionExperiment, boolean, ScaleType, boolean, boolean, boolean, Writer, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeProcessedExpressionData(ExpressionExperiment, List, boolean, ScaleType, boolean, boolean, boolean, Writer, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeProcessedExpressionData(ExpressionExperiment, List, boolean, ScaleType, boolean, boolean, boolean, Writer, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeRawExpressionData(ExpressionExperiment, List, QuantitationType, ScaleType, boolean, boolean, boolean, Writer, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeRawExpressionData(ExpressionExperiment, List, QuantitationType, ScaleType, boolean, boolean, boolean, Writer, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeRawExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, boolean, boolean, Writer, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write raw expression data to a given writer for a given quantitation type.
writeRawExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, boolean, boolean, Writer, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeSequencesToFile(Collection, File) - Static method in class ubic.gemma.core.analysis.sequence.SequenceWriter: Write a collection of sequences in FASTA format
Write side - Section in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService
writeTabularSingleCellExpressionData(ExpressionExperiment, List, QuantitationType, ScaleType, boolean, boolean, int, boolean, Writer, boolean, Console) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
writeTabularSingleCellExpressionData(ExpressionExperiment, List, QuantitationType, ScaleType, boolean, boolean, int, boolean, Writer, boolean, Console) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeTabularSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, boolean, int, boolean, Writer, boolean, Console) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write single-cell expression data to a given writer for a given quantitation type in tabular format.
writeTabularSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, boolean, int, boolean, Writer, boolean, Console) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeTo(File) - Method in class ubic.gemma.core.ontology.providers.OntologySlimMeta
writeTo(Path, Class, Type, Annotation[], MediaType, MultivaluedMap, OutputStream) - Method in class ubic.gemma.rest.providers.MexBundlerProvider
writeTo(Path, Class, Type, Annotation[], MediaType, MultivaluedMap, OutputStream) - Method in class ubic.gemma.rest.providers.PathProvider
writeTo(Sendfile, Class, Type, Annotation[], MediaType, MultivaluedMap, OutputStream) - Method in class ubic.gemma.rest.providers.SendfileProvider
writeToFile(FileWriter) - Method in class ubic.gemma.core.util.math.distribution.Histogram: Write the histogram to a file.
writeToPng(ColorMatrix, OutputStream, boolean, boolean) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay
writeToRdf(Collection, Writer) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyService: Write multiple individuals represented by the given URIs to RDF.
writeToRdf(Collection, Writer) - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl
writeToRdfIgnoreAcls(Collection, Writer) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyService: Write multiple individuals represented by the given URIs to RDF, ignoring ACLs.
writeToRdfIgnoreAcls(Collection, Writer) - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl
writeTsv(List, Gene, Map, Map, Map, Writer) - Method in interface ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileService: Writes a list of DE results with additional columns for mapping them to source experiments and analyzed experiments (for subsets).
writeTsv(List, Gene, Map, Map, Map, Writer) - Method in class ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileServiceImpl
writeTsv(ExpressionAnalysisResultSet, Baseline, Map, Writer) - Method in interface ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileService: Write the analysis result set with result-to-gene mappings.
writeTsv(ExpressionAnalysisResultSet, Baseline, Map, Writer) - Method in class ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileServiceImpl
writeWithStringifiedGeneAnnotations(Writer, BulkExpressionDataMatrix, Class, Map) - Method in class ubic.gemma.core.datastructure.matrix.io.MatrixWriter: Alternate method that uses annotations in string form (e.g., read from another file).
WS - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
WS - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
WXS - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy

X

X - Enum constant in enum class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
XML - Enum constant in enum class ubic.gemma.core.loader.entrez.EntrezRetmode
XMLUtils - Class in ubic.gemma.core.util: Handy methods for dealing with XML.
XMLUtils() - Constructor for class ubic.gemma.core.util.XMLUtils
XSDEntityResolver - Class in ubic.gemma.persistence.hibernate: Resolves Hibernate XSD schemas from the classpath.
XSDEntityResolver() - Constructor for class ubic.gemma.persistence.hibernate.XSDEntityResolver

Z

ZENODO - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
ZenodoUtils - Class in ubic.gemma.core.loader.expression.zenodo
ZenodoUtils() - Constructor for class ubic.gemma.core.loader.expression.zenodo.ZenodoUtils
ZeroVarianceFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Remove rows that have a variance of zero (within a small constant)
ZeroVarianceFilter() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.ZeroVarianceFilter
Zscore - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
ZSCORE - Enum constant in enum class ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Standard deviations from the mean.

_

_ATN - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
_ATN - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
_decisionToDFA - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
_decisionToDFA - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
_serializedATN - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
_serializedATN - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
_sharedContextCache - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
_sharedContextCache - Static variable in class ubic.gemma.rest.util.args.FilterArgParser

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