Index

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).

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

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

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

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

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

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

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

accept(GeneProductChange) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.GeneProductChangeTsv

Write a row and flush it.

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.

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).

accession - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate

AccessionAlreadyExistsException(String, Long, String) - Constructor for exception class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.AccessionAlreadyExistsException

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

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

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.

ActingIdentityRefusedException - Exception Class in ubic.gemma.core.security.util

An onBehalfOf claim the server refuses to record: an agent naming its own account, or an agent recording a ruling without naming the person who directed it.

ActingIdentityRefusedException(String) - Constructor for exception class ubic.gemma.core.security.util.ActingIdentityRefusedException

activeIngredientIn - Static variable in class ubic.gemma.core.ontology.jena.RO

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

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

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

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

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.

addDataSet(GeoDataset) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries

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

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.

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

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

addGene(DifferentialExpressionGenesConditionsValueObject.DiffExGene) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject

addGene(GeneProductValueObject, GeneValueObject) - Method in class ubic.gemma.model.analysis.sequence.GeneMappingSummary

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

addMatrices(ExpressionDataDoubleMatrix, ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

Add two matrices.

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

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.

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

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

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

🛑 Implemented here rather than as a default on the interface delegating to the six-argument form.

addTarget(Ticket, TicketTargetType, Long, Contact, String, Integer) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService

TicketService.addTarget(Ticket, TicketTargetType, Long, Contact) with the new target's own task attached — see TicketTarget.getPayload().

addTarget(Ticket, TicketTargetType, Long, Contact, String, Integer) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl

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

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.

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

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

AffyPowerToolsProbesetSummarize - Class in ubic.gemma.core.loader.expression

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

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.

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.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

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).

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

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 - 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)}.

allActive() - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService

Every unexpired lock across the whole corpus, for an admin view that needs to see what is locked right now without already holding a list of ids to ask about — CurationLockService.current(Collection)'s sibling for the case where there is no id list to narrow by.

allActive() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl

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

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

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

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

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

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.

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

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

annotationAssociations() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the annotationAssociations record component.

annotationAssociationsDeleted() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

Returns the value of the annotationAssociationsDeleted record component.

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

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

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.

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

AnnotationSetPayloadCounts - Class in ubic.gemma.model.common.auditAndSecurity.curation

How many factors and tags an annotation-set payload proposes.

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

AnnotationSetSource - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation

Source discriminator on AnnotationSet rows.

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.

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

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

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

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}.

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.

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.

applied() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage

Returns the value of the applied record component.

applied() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the applied record component.

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(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

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.

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

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

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

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

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

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

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

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

ArrayDesignPersister - Class in ubic.gemma.persistence.persister

Handles persisting array designs.

ArrayDesignPersister() - Constructor for class ubic.gemma.persistence.persister.ArrayDesignPersister

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

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

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

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 - 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

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

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

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

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

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

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 - 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 - 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

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 interface ubic.gemma.core.security.authentication.ManualAuthenticationService

Perform an anonymous authentication.

authenticateAnonymously() - Method in class ubic.gemma.core.security.authentication.ManualAuthenticationServiceImpl

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

AuthorityConstants - Class in ubic.gemma.core.security

Defines constants used in GrantedAuthories.

AuthorityConstants() - Constructor for class ubic.gemma.core.security.AuthorityConstants

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.

avoidDownload - Variable in class ubic.gemma.core.loader.util.fetcher.FtpFetcher

await(long, TimeUnit) - Method in class ubic.gemma.core.util.StreamDrainer

Wait up to the given time for the end of the stream, then return what was kept.

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.

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

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

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

batchInfoTrigger(JobDetail) - Method in class ubic.gemma.core.config.SchedulerConfig

Every day at 00:30.

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

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

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.

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

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

BioAssayFieldCountValueObject - Class in ubic.gemma.model.expression.bioAssay

One value a dataset's samples carry for a single BioAssay field, and how many carry it.

BioAssayFieldCountValueObject() - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayFieldCountValueObject

BioAssayFieldCountValueObject(String, int) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayFieldCountValueObject

Creates a new BioAssayFieldCountValueObject instance.

BioAssayMapper - Interface in ubic.gemma.core.loader.util.mapper

Strategy used for comparing BioAssay to sample names from the data.

BioAssayMetadataAuditService - Interface in ubic.gemma.core.analysis.service

Records a SampleMetadataChangedEvent.

BioAssayMetadataAuditServiceImpl - Class in ubic.gemma.core.analysis.service

BioAssayMetadataAuditServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.BioAssayMetadataAuditServiceImpl

BioAssayMetadataService - Interface in ubic.gemma.core.analysis.service

Curator edits to the upstream-derived metadata on a sample: libraryStrategy, librarySelection and extractedMolecule.

BioAssayMetadataServiceImpl - Class in ubic.gemma.core.analysis.service

BioAssayMetadataServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.BioAssayMetadataServiceImpl

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.SampleMetadataPayload

Returns the value of the bioAssays record component.

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.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

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

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

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

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

blatAssociations() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the blatAssociations record component.

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

blatAssociationsDeleted() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

Returns the value of the blatAssociationsDeleted record component.

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.

Blocker() - Constructor for class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker

Blocker(String, String) - Constructor for class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker

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

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.

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(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.

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() - Constructor for class ubic.gemma.core.logging.log4j.ProgressUpdateAppender.Builder

Builder() - Constructor for class ubic.gemma.core.logging.log4j.SlackAppender.Builder

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

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.

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

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.ncbi.NcbiGeneResolverImpl

CACHE_NAME - Static variable in class ubic.gemma.core.ontology.ols.OlsTermResolverImpl

Admin-evictable cache of IRI → OlsTerm.

CachedFilteringDao<O> - Interface in ubic.gemma.persistence.service

CachedFilteringVoEnabledDao<O,VO> - Interface in ubic.gemma.persistence.service

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.

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.

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

Deprecated.

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

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

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 - Enum constant in enum class ubic.gemma.core.job.SubmittedTask.Status

CANCELLING - Enum constant in enum class ubic.gemma.model.pipeline.JobState

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.DatasetVersion

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.bioAssay.BioAssayFieldCountValueObject

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.model.pipeline.PipelineJobBatchValueObject

canEqual(Object) - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

canEqual(Object) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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

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.

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

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

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.

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

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, DatabaseEntryService, 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

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

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

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

changes() - Method in record class ubic.gemma.core.loader.genome.gene.ncbi.GeneProductChangeTsv.Report

Returns the value of the changes record component.

ChannelUtils - Class in ubic.gemma.persistence.util

Deprecated.

Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.

ChannelUtils() - Constructor for class ubic.gemma.persistence.util.ChannelUtils

Deprecated.

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(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

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

checkTablesForProbeMapping(ProbeMapperConfig) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis

Check that this database has the tables that GoldenPathSequenceAnalysis.findAssociations(String, Long, Long, String, String, String, ThreePrimeDistanceMethod, ProbeMapperConfig) reads with the given configuration, and that they can be joined.

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

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

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.

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.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

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(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

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

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 - Static variable in class ubic.gemma.core.context.EnvironmentProfiles

Independent feature toggles.

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.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.genome.gene.ncbi.GeneProductChangeTsv

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

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_OF_MATERIAL_URI - Static variable in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl

CollectionMetadata - Class in ubic.gemma.core.loader.expression.cellxgene.model

CollectionMetadata() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata

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.

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

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

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.

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.

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

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

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).

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

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

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

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

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

Deprecated.

computeMissingValues(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl

Deprecated.

computeMissingValues(ExpressionExperiment, double, Collection) - Method in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues

Deprecated.

computeMissingValues(ExpressionExperiment, double, Collection) - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl

Deprecated.

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.

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

🛑 Propagation.NEVER, for the same reason as ProcessedExpressionDataVectorServiceImpl.createProcessedDataVectors(ExpressionExperiment, boolean): the normalization between the read and the assembly is where the 44 minutes go, and nothing in it needs a connection.

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

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

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

ConfigUtils - Class in ubic.gemma.core.config

Shared configuration helpers.

ConfigUtils - Class in ubic.gemma.core.util

Convenience methods for loading configurations.

conjunction(BooleanArrayList, BooleanArrayList) - Static method in class ubic.gemma.core.util.matrix.MatrixUtil

Compute the conjuction (logical 'and') of two boolean vectors

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.

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.

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

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.

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.

ContrastCoding - Enum Class in ubic.gemma.core.util.math.linearmodels

How a categorical factor's levels are turned into columns of a design matrix, which is what decides what each coefficient of that factor means.

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, DatasetVersion, 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

convertAndPersist(Collection, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService

Convert an already-fetched series and persist the resulting experiment(s).

convertAndPersist(Collection, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl

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.

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(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

countBlatResultsBySearchedDatabase(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao

Count the alignments held for this platform's sequences by the genome assembly they were searched against.

countBlatResultsBySearchedDatabase(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl

countBlatResultsBySearchedDatabase(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService

countBlatResultsBySearchedDatabase(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl

countBlatResultsBySearchedDatabase(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService

countBlatResultsBySearchedDatabase(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

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.

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.

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.

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

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().

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

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

🛑 Propagation.NEVER: the quantile normalization in the middle of this takes 44 minutes on a large experiment (GSE260875, measured 2026-09-17) and the connection handling mode is DELAYED_ACQUISITION_AND_HOLD, so a transaction around the whole thing pins a pooled connection for the duration without issuing a statement — against a pool that recycles at 30 minutes.

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.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

See SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.createSubSetsAndAggregateByCellType(ExpressionExperiment, SingleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig) for why this is Propagation.NEVER.

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

Not transactional: SingleCellExpressionExperimentSubSetService.createSubSets(ExpressionExperiment, SingleCellDimension, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellExperimentSubSetsCreationConfig) commits the subset/BioAssay/BioMaterial rows it creates — and with them the ACL rows AclEventListener inserts alongside each — BEFORE SingleCellExpressionExperimentAggregateService.aggregateVectors(ExpressionExperiment, QuantitationType, List, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellAggregationConfig) opens its own, separate, potentially hour-long transaction to stream and aggregate the single-cell data.

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

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

createVectorMatrix(Map, boolean) - Method in interface ubic.gemma.core.ontology.GoMetric

createVectorMatrix(Map, boolean) - Method in class ubic.gemma.core.ontology.GoMetricImpl

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().

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

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

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

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.

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

CurationLockedException(String, String) - Constructor for exception class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService.CurationLockedException

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.

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_VERSION - Static variable in class ubic.gemma.persistence.util.Cursor

Current cursor payload format version.

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

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

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

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 - 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

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

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

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

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.core.loader.expression.geo.service.GeoRecordType

DATASET_TYPE - Enum constant in enum class ubic.gemma.core.loader.expression.geo.service.GeoSearchField

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

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

DatasetMetadata - Class in ubic.gemma.core.loader.expression.cellxgene.model

DatasetMetadata() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata

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

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

DatasetSummary - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser.model

DatasetSummary() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary

DatasetVersion - Class in ubic.gemma.core.loader.expression.cellxgene.model

Identity of a CELLxGENE dataset as reported by the curation API.

DatasetVersion() - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.DatasetVersion

DatasetVersion(String, String, String) - Constructor for class ubic.gemma.core.loader.expression.cellxgene.model.DatasetVersion

dataSource() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload

Returns the value of the dataSource record component.

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[].

dbinom(double, double, double) - Static method in class ubic.gemma.core.util.math.SpecFunc

See dbinom_raw.

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

decode(String) - Static method in class ubic.gemma.persistence.util.Cursor

Decode a base64url-encoded cursor string.

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 - 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_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_CHARS - Static variable in class ubic.gemma.core.util.StreamDrainer

Enough for an error message and its context; the start of a long output is dropped.

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_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

Deprecated.

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.

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

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

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

deleteExistingFiles(ArrayDesign) - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService

deleteExistingFiles(ArrayDesign) - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl

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(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.

deleteUser(String) - Method in interface ubic.gemma.core.security.authentication.UserManager

deleteUser(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl

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.

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

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

describe() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

A short description of the product and its gene, for logs and batch summaries.

describeFilterResult(DifferentialExpressionAnalysisFilterResult) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter

describeFilterResult(ExpressionExperimentFilterResult) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter

describeHalfPair(String, String, String, String, String, String) - Static method in class ubic.gemma.model.expression.experiment.StatementUtils

Name the half of a predicate/object pair that is present without the other.

describeHalfPair(Statement) - Static method in class ubic.gemma.model.expression.experiment.StatementUtils

The first half-present pair on a statement, first pair before second.

describeHalfPair(StatementValueObject) - Static method in class ubic.gemma.model.expression.experiment.StatementUtils

The first half-present pair on a proposed statement, first pair before second.

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(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

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.

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

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(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.

detail() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

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.

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.

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

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

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.

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

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.

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

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.

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.

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

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.core.util.AbstractProgressReporter

doReportProgress(double, long, long, boolean) - Method in class ubic.gemma.core.util.LoggingProgressReporter

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 - 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.

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() - Method in record class ubic.gemma.core.loader.genome.gene.ncbi.GeneProductChangeTsv.Report

Returns the value of the dryRun record component.

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

DUMMY_PRODUCT - Enum constant in enum class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome.SkipReason

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.

🛑 dataSource is how two matrices that disagree explain themselves - Section in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload

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

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

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

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.

enteredCurrentStateAt - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate

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

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

entityPath - Variable in class ubic.gemma.persistence.util.EntityUrlBuilder.WebEntityUrl

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(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<U> - 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() - 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

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

eq - Enum constant in enum class ubic.gemma.persistence.util.Filter.Operator

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.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.DatasetVersion

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 record class ubic.gemma.core.loader.genome.gene.ncbi.GeneProductChangeTsv.Report

Indicates whether some other object is "equal to" this one.

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.SampleMetadataPayload

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.BioAssayFieldCountValueObject

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.PipelineJobBatchValueObject

equals(Object) - Method in class ubic.gemma.model.pipeline.PipelineJobEvent

equals(Object) - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

equals(Object) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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 record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

Indicates whether some other object is "equal to" this one.

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, 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.

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).

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.

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.

exampleExperimentId(Long) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder

exception() - Element in annotation interface ubic.gemma.core.security.audit.AuditedOnError

Optional exception-class filter.

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

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

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(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

EXP - Enum constant in enum class ubic.gemma.model.association.GOEvidenceCode

expander - Variable in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher

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.

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

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.

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

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

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

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

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

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.

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, int) - 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, int) 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.

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

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

ExpressionExperimentMetaFileType - Enum Class in ubic.gemma.persistence.service.expression.experiment

Types of metadata files that can be attached to an ExpressionExperiment.

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

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

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

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

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_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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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 - 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

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.

fetchAllDatasetVersions() - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher

Fetch the permanent and version identifiers of all public CELLxGENE datasets, in a single request.

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

See the 6-arg overload for why this is Propagation.NEVER and routes through GeoServiceImpl.self.

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

🛑 Propagation.NEVER: GeoDomainObjectGenerator.generate(String) downloads and parses the series' SOFT file over the network — 36 MB for one series the size of GSE1024, proportionally more for a bigger one — and hibernate.connection.handling_mode=DELAYED_ACQUISITION_AND_HOLD means a transaction open around that fetch pins a pooled connection for its entire duration without issuing a statement.

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.

fetchDatasetVersionIds(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher

Fetch all the published version IDs of a dataset, most recent first.

fetchDatasetVersions(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher

Fetch the permanent and version identifiers of the datasets in a collection.

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

field() - Method in record class ubic.gemma.core.security.audit.payload.SampleMetadataPayload

Returns the value of the field record component.

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.core.util

FileUtils() - Constructor for class ubic.gemma.core.util.FileUtils

FileUtils.PathWriter<E> - Interface in ubic.gemma.core.util

Writes a file or a directory at a given path, handed to it by FileUtils.writeAtomically(Path, PathWriter).

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(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

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

FilterConfig(boolean, boolean, boolean, boolean, double, double, double, double, double, int, int) - Constructor for record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig

Creates an instance of a FilterConfig record class.

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.

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

findDatasetByVersion(List, String) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher

Find the dataset that a version ID, current or superseded, belongs to.

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.

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

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_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

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.

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

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

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.

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.

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

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

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.

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(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(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(PipelineJob) - Static method in class ubic.gemma.model.pipeline.PipelineJobValueObject

Project a job.

from(PipelineJobBatch) - Static method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

Project a batch without its jobs.

from(PipelineJobEvent) - Static method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

Project an event.

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

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.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

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

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

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_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.

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 - 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.

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_CHANGED - Enum constant in enum class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome.SkipReason

GENE_EXPRESSION_ASSAYS - Static variable in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils

List of all known gene expression assays from CELLxGENE.

GENE_WITHDRAWN - Enum constant in enum class ubic.gemma.core.ontology.TermViolation.Reason

An NCBI gene id that NCBI itself still carries, but as a WITHDRAWN or secondary record: the annotation names a gene NCBI has retired.

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

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

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

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

geneNcbiId() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the geneNcbiId record component.

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

GeneProductChange - Record Class in ubic.gemma.persistence.service.genome.gene

A gene product that GeneWriteService.upsert(ubic.gemma.model.genome.Gene, boolean, java.util.function.Consumer) removed, or would have removed, from a gene, or moved from one gene to another.

GeneProductChange(GeneProductChange.Kind, boolean, String, Integer, String, Integer, String, Long, String, String, long, long, List) - Constructor for record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Creates an instance of a GeneProductChange record class.

GeneProductChange.Kind - Enum Class in ubic.gemma.persistence.service.genome.gene

GeneProductChangeTsv - Class in ubic.gemma.core.loader.genome.gene.ncbi

The TSV report of the gene product changes of a geneUpdate run: one row per GeneProductChange, platforms joined with commas.

GeneProductChangeTsv(Writer, boolean) - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.GeneProductChangeTsv

Write the header of a report.

GeneProductChangeTsv.Report - Record Class in ubic.gemma.core.loader.genome.gene.ncbi

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

GeneProductRemovalOutcome - Record Class in ubic.gemma.persistence.service.genome.gene

What GeneWriteService.replayGeneProductRemoval(GeneProductChange, Collection, boolean) did with one recorded removal, or would have done in a dry run.

GeneProductRemovalOutcome(GeneProductRemovalOutcome.SkipReason, String, boolean, long, long, List) - Constructor for record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

Creates an instance of a GeneProductRemovalOutcome record class.

GeneProductRemovalOutcome.SkipReason - Enum Class in ubic.gemma.persistence.service.genome.gene

Why a recorded removal no longer holds.

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

Write the report summarizing all platforms.

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

Generate the report for one platform, for callers that do so as a side effect of other work.

generateArrayDesignReport(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl

generateArrayDesignReport(ArrayDesignValueObject) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService

Generate the report for one platform.

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.

generatedAt - Variable in class ubic.gemma.core.ontology.providers.OntologySlimMeta

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

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

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

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

geneSymbol() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the geneSymbol record component.

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

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.

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

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.

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

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

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.

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

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.

get() - Static method in class ubic.gemma.core.security.util.ActingIdentity

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

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

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

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

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

getAfterMaxDesignElementsFilter() - 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

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

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

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.

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.

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

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

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.

getAnnotationRelationRowsWritten() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync

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(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

getAnnotationsById(FactorValue) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils

Create a mapping of annotation IDs to annotations for a FactorValue.

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

getAnnotationSetsRebound() - Method in class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PromotionResult

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

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.

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.

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

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

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

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

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

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

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

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

Deprecated.

getBackgroundChannelB() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

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(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.

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.

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

getBasis() - Method in class ubic.gemma.model.common.description.AnnotationRelation

getBasis() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getBatch() - Method in class ubic.gemma.model.pipeline.PipelineJob

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

getBatchEffect() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment

getBatchEffect() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

Batch effect type.

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(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

getBatchId() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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.

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

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

Deprecated.

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

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.

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

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

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

getBioMaterialIds() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan.PendingAssignment

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

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

Deprecated.

getBlackListed() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject

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.

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.

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

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.

getCanonicalLabel() - Method in class ubic.gemma.core.ontology.TermCanonicalization

The term's canonical label, now stored (equals TermCanonicalization.getSubmittedLabel() 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).

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

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(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

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

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

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.

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

For each cell, the id of its label in CellLevelCharacteristicsValueObject.characteristics.

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

The labels cells are grouped under, one entry per distinct label and not one per cell.

getCharacteristics() - Method in class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject

The distinct labels cells are grouped under; see CellLevelCharacteristics.

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

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

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

getClientRef() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.SampleCharacteristicAdd

getClientRef() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.TagAdd

getClosedAt() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch

getClosedAt() - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

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.

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

getColumn() - Method in class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult

Affected column or -1 if all columns are affected.

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.

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.

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

getCommitAnnotationSetId() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitResult

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.

getCompleteness() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset

getComponent() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails.BatchEffectStatistics

A PCA component that is explained by the batch factor.

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

getComponentVarianceProportion() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails.BatchEffectStatistics

The variance explained by the component.

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

getConfig() - Method in exception class ubic.gemma.core.analysis.expression.diff.AnalysisException

getConfigAttribute() - Method in class ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManager

getConsiderUris() - Method in class ubic.gemma.core.ontology.ObsoleteTermUsage

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

getContrastCoding() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig

How each categorical factor's levels are coded in the design matrix, which decides what its coefficients mean.

getContrastCoding(String) - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix

How the given factor's levels are coded into columns; ContrastCoding.TREATMENT unless set.

getContrastCoding(ExperimentalFactor) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig

How the given factor's levels are coded; ContrastCoding.TREATMENT unless set.

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(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

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

getCreatedGeneCount() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

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.

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

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

getCurationDetailsNote() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest

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

getCurationPending() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject

Whether curation of the dataset is under way right now.

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

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.

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

getDatabaseName() - Method in class ubic.gemma.core.goldenpath.GoldenPath

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

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

getDatasetAssets() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata

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

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

getDatasetId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata

getDatasetId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetVersion

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

getDatasetLink() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject

getDatasetMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult

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.

getDatasetMetadata(CollectionMetadata, DatasetVersion) - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils

Select the metadata of a resolved dataset from a collection.

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

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() - 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.

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).

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.

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.

getDatasetVersionId() - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetVersion

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

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).

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

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(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

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.

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

getDerivedLevelColumns() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix

The contrasts a ContrastCoding.SUM_TO_ZERO factor needs but has no column for, as a map from the name such a column would have had to the design columns that determine it.

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.model.pipeline.PipelineJobBatchValueObject

getDescription() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest

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

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

getDesignElementName() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject

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.

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

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

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

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

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

getDisplayRange() - Method in class ubic.gemma.core.util.graphics.MatrixDisplay

getDisposition() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition

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

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.

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(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

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

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

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

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

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

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

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

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.

getError() - Method in interface ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse

getError() - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus

getErrorMessage() - Method in class ubic.gemma.model.expression.experiment.GeoScrapeWatermark

getErrorMessage() - Method in class ubic.gemma.model.pipeline.PipelineJob

getErrorMessage() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

getErrors() - Method in exception class ubic.gemma.core.loader.entrez.EntrezException

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

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

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

getExampleExperimentId() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getException() - Method in class ubic.gemma.core.job.TaskResult

getExcludedExperimentIds() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery

getExcludedSubjectCategoryUris() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery

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.

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".

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(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

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

getExperimentAnalyzed() - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment

The experiment whose cells this assigns, in the EXPERIMENT_ANALYZED_FK column every other analysis in ANALYSIS uses for the same fact (Paul, 2026-09-14).

getExperimentAnalyzedId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject

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

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.model.pipeline.PipelineJobValueObject

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

getExperimentsAffected() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult

getExperimentsAffected() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection

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

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

Deprecated.

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

Deprecated.

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

getExternalDatabaseUri() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

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.

getExtractedMolecules() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

What was extracted from the dataset's samples and assayed, as the distinct extractedMolecule values with a count of the samples carrying each.

getExtractProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel

getExtraMissingValueIndicators() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand

Deprecated.

getFactor() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound

Factor being confounded with the batches.

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

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(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

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(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

getFailedGeneCount() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

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(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

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

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.

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

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.

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

getFilterAttrition() - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.PreparedCoexMatrices

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.

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

getFinishedAt() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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

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.

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.

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

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

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

getGemmaChartTheme(String) - Static method in class ubic.gemma.core.visualization.ChartThemeUtils

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(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

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

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

getGeneGroup() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand

getGeneGroupName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand

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

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

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

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(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

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

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

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

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

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

getGrantedAuthority() - Method in class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid

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(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_

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

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.

getHeldBy() - Method in exception class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService.CurationLockedException

getHgnc_id() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject

getHibernateProperties() - Method in class ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean

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.

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

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

Dataset version identifier; it changes whenever the dataset is revised.

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.model.pipeline.PipelineJobBatchValueObject

getId() - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

getId() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

getId() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers

getId() - Method in enum class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType

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(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(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.

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

getImpliedObject() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getImpliedObjectUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getImpliedPredicate() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getImpliedPredicateUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

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.

getImpliedSubjectUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

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.

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

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.

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

getInfo() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession

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

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

Deprecated.

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

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

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

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

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.

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

getJobId() - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

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.model.pipeline.PipelineJobBatchValueObject

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

getKeptGeneProducts() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

Gene products that would have been removed, but were kept because removing them was off.

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(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

getKillRequestedAt() - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

getKind() - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

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(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

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

getLastEventAt() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

getLastEventKind() - Method in class ubic.gemma.model.pipeline.PipelineJob

getLastEventKind() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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

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

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

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

getLastProgressJson() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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

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

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

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.

getLibrarySelections() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

How the dataset's libraries were selected, as the distinct librarySelection values with a count of the samples carrying each.

getLibrarySize() - Method in class ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator

getLibrarySource() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord

getLibraryStrategies() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

What kind of libraries the dataset's samples were made from, as the distinct libraryStrategy values with a count of the samples carrying each.

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, as the GeoLibraryStrategy constant name (RNA_SEQ, SCRNA_SEQ, RIBO_SEQ, ATAC_SEQ, …) rather than GEO's spelling, or MICROARRAY_ONE_COLOR / MICROARRAY_TWO_COLOR for a microarray sample.

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

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

getLoadedGeneCount() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

getLoading() - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading

getLoadingRank() - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading

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

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.

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.

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(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

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

getMaxDesignElements() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig

Keep at most this many design elements, the most variable ones, or 0 for no cap.

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

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

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

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.

getMeasurementObject() - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject

The measurement associated with this factor value.

getMedianCorrelation() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails

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

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.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

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

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.

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

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

Deprecated.

getMissingValueQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

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.

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

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

getN() - Method in class ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis

getN() - Method in class ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis

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.ncbi.NcbiGeneRecord

NCBI's description field, which is the official full name.

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.model.pipeline.PipelineJobBatchValueObject

getName() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest

getName() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers

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

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.core.ontology.ncbi.NcbiGeneRecord

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

getNcbiTaxonId() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject

getNcbiTaxonId() - Method in class ubic.gemma.core.ontology.model.OntologyTerm.TaxonConstraint

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.

getNetDataSourceUtil() - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher

getNewArrayDesigns() - Method in class ubic.gemma.core.analysis.report.WhatsNew

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

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

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

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

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.

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

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.

getNumberOfBioAssays() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayFieldCountValueObject

How many of the dataset's assays carry BioAssayFieldCountValueObject.value.

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

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

getNumberOfExperimentsAtBioMaterial() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getNumberOfExperimentsAtFactorValue() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getNumberOfExperimentsAtTag() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getNumberOfExperimentsWithSubject() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

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.

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

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".

getNumberOfSamples() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment

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

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.

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

Deprecated.

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

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(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

getObjectCategory() - Method in class ubic.gemma.model.common.description.AnnotationRelation

getObjectCategory() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getObjectCategoryUri() - Method in class ubic.gemma.model.common.description.AnnotationRelation

getObjectCategoryUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

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(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

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

getOccurredAt() - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

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

getOffset() - Method in class ubic.gemma.persistence.util.Slice

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.

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

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

getOperator() - Method in class ubic.gemma.persistence.service.FilteringDao.ConjunctSpec

getOperator() - Method in class ubic.gemma.persistence.util.Filter

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

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

getOrganism() - Method in class ubic.gemma.core.ontology.ncbi.NcbiGeneRecord

Scientific name, e.g.

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.

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.

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.

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

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

getOutputMatrix(M, int, int) - Method in class ubic.gemma.core.util.matrix.datafilter.AbstractFilter

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

getParamsJson() - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

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

getParents() - Method in class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset

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.

getParkedElements() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet

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

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.

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.TicketTarget

getPayload() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

This target's own task — what put THIS experiment on the ticket and what is being asked of the curator.

getPayload() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject

What the screen that produced this ticket asked, verbatim and opaque.

getPayloadJson() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet

getPayloadJson() - Method in class ubic.gemma.model.pipeline.PipelineJobEvent

getPayloadJson() - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

getPayloadSchemaVersion() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket

getPayloadSchemaVersion() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget

getPayloadSchemaVersion() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

Which schema TicketTargetValueObject.payload follows, or null when the writer declared none.

getPayloadSchemaVersion() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject

Which schema TicketValueObject.payload follows; null when the writer declared none.

getPayloadSize() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject

Size of the omitted payloadJson in characters.

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

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

getPipeline() - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

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

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.

getPlatformSampleMap(GeoSeries) - Static method in class ubic.gemma.core.loader.expression.geo.DatasetCombiner

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.

getPostCode() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact

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(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(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.

getPreExistingFactorIds() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan

getPreExistingFactorValueIds() - Method in class ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan

getPreferredAndMissingQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

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

Deprecated.

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.

getPreferredQTypes() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

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

getPreferredQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

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.

getPreflightAtApply() - Method in class ubic.gemma.model.expression.experiment.DesignApplyOutcome

getPrevCursor() - Method in class ubic.gemma.persistence.util.CursorPage

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

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.

getPrimaryTaxon() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign

getPrincipal() - Method in class ubic.gemma.core.security.acl.domain.AclPrincipalSid

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

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

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

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

Deprecated.

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(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

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

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

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

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

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.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

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(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(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

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

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(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

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

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

getRankByMax() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject

getRankByMax() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject

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.ExperimentExpressionLevelsValueObject.VectorElementValueObject

Stored expression-level rank of this vector, by mean and by max, in [0, 1].

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

Deprecated.

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.

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.

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

getReasonCode() - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest

getRecentExperiments() - Method in class ubic.gemma.core.analysis.report.HomeStats

Most-recently curated public experiments, for the scrolling-names widget.

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.

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

getRemovedGeneProducts() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

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

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.

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.

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

getResultObjectUrl() - Method in class ubic.gemma.model.common.search.SearchResultValueObject

A URL for the result.

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

getResultSet() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult

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

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

getResultSetsIncluded() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis

getResultsUsed() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult

getResultType() - Method in class ubic.gemma.model.common.search.SearchResult

Type of search result, immutable.

getResultTypes() - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap

getResultTypes() - Method in class ubic.gemma.model.common.search.SearchSettings

Entities to retrieve.

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

getRSquared() - Method in interface ubic.gemma.core.util.math.linearmodels.LinearModelSummary

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.

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

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

getRuntime() - Static method in class ubic.gemma.core.util.runtime.ExtendedRuntime

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

Deprecated.

getSample() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform

getSample() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject

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

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

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

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

getSchedulerHandle() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

getSchedulerKind() - Method in class ubic.gemma.model.pipeline.PipelineJob

getSchedulerKind() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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.

getScreeningResult() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget

getScreeningResult() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

getScreeningResultReason() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget

getScreeningResultReason() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

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

The database a BLAT result was searched against, named for the assembly (rn8, hg38) so that the result records which assembly its coordinates belong to.

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

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

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

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.

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

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

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

getSeuratDiskFile(ExpressionExperiment) - Method in class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl

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

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

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

Deprecated.

getSignalChannelB() - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

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

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(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

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

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(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

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.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

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.

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(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

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.

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

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

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.

getSpecificityScore() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene

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

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.model.pipeline.PipelineJobValueObject

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

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.model.pipeline.PipelineJobBatchValueObject

getState() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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.

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

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.

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

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(int) - Method in class ubic.gemma.model.expression.experiment.Statement

getSubjectBreadth() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getSubjectCategory() - Method in class ubic.gemma.model.common.description.AnnotationRelation

getSubjectCategory() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

getSubjectCategoryUri() - Method in class ubic.gemma.model.common.description.AnnotationRelation

getSubjectCategoryUri() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

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(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.model.pipeline.PipelineJobBatchValueObject

getSubmittedAt() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

getSubmittedBy() - Method in class ubic.gemma.model.pipeline.PipelineJobBatch

getSubmittedById() - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

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

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

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

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

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

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

getSubsets() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset

getSubSets() - Method in class ubic.gemma.core.visualization.SingleCellSparsityHeatmap

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

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

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.

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

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.

getSwitchedGeneProducts() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

getSymbol() - Method in class ubic.gemma.core.ontology.ncbi.NcbiGeneRecord

NCBI's name field, which is the official symbol.

getSynonyms() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo

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

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

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

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

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

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

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

Deprecated.

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

getTaskName() - Method in class ubic.gemma.core.job.notification.EmailNotificationContext

getTaxa() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject

When genes are included, this field is populated.

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

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(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

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

getTaxonForGemmaRest() - Method in class ubic.gemma.model.genome.gene.GeneValueObject

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.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

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

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.

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

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(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.

getText() - Method in class ubic.gemma.core.util.StreamDrainer

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

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

getTicketCountOpen() - Method in class ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry

getTimeoutSeconds() - Method in class ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskCommand

getTimestamp() - Method in class ubic.gemma.core.util.BuildInfo

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.cellxgene.model.DatasetVersion

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

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

getToLabel() - Method in class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection

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.

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

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

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).

getTripleKey() - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary

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

getTroubleDetails() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject

getTroubleDetails() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject

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

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

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(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.

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.

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.

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.

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

getUpdatedGeneCount() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

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

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(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

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

Deprecated.

getUsefulQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

getUser() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo

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

getUsername() - Method in class ubic.gemma.core.security.authentication.UserDetailsImpl

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(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

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

getValidLibraryStrategies() - Method in interface ubic.gemma.core.analysis.service.BioAssayMetadataService

What BioAssayMetadataService.setLibraryStrategy(ExpressionExperiment, Collection, String) will accept, for the 400 message and for callers that want to offer a menu.

getValidLibraryStrategies() - Method in class ubic.gemma.core.analysis.service.BioAssayMetadataServiceImpl

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.bioAssay.BioAssayFieldCountValueObject

The value itself, spelled exactly as the per-assay field spells it in BioAssayValueObject — so a client can compare the two without a mapping table.

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(int, int) - Method in class ubic.gemma.core.util.graphics.ColorMatrix

getValue(int, int) - Method in class ubic.gemma.core.util.graphics.MatrixDisplay

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.

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(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

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

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

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(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

getVisualizationValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell

getVisualizationValues() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject

getVMatrix() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDResult

Row names: biomaterials; column names: eigengene number (from 0)

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

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

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).

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

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

GI_CHANGED - Enum constant in enum class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome.SkipReason

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

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.

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.

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

GzipUtils - Class in ubic.gemma.core.util

gzip at the deflate level Gemma uses for what it generates: data files, their in-band streams and REST responses.

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.

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

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.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.DatasetVersion

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 record class ubic.gemma.core.loader.genome.gene.ncbi.GeneProductChangeTsv.Report

Returns a hash code value for this object.

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.SampleMetadataPayload

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.BioAssayFieldCountValueObject

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.PipelineJobBatchValueObject

hashCode() - Method in class ubic.gemma.model.pipeline.PipelineJobEvent

hashCode() - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

hashCode() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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 record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns a hash code value for this object.

hashCode() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

Returns a hash code value for this object.

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(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)

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

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.core.analysis.sequence.CompositeSequenceMapSummary

Heatmap - Interface in ubic.gemma.core.visualization

Minimal interface for a labelled heatmap.

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

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

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

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)

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

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() - 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.

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

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.

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.

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

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_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.

incrementOccurrenceCount() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject

incrementWarnings() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig

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

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.

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.

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

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

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(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

InitialDataPopulator - Class in ubic.gemma.persistence.initialization

Populate some initial data for tests.

InitialDataPopulator(boolean) - Constructor for class ubic.gemma.persistence.initialization.InitialDataPopulator

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.

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

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.

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

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

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.

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

Deprecated.

isApplied() - Method in class ubic.gemma.model.expression.experiment.DesignApplyOutcome

isApplyFixes() - Method in class ubic.gemma.core.security.authorization.acl.AclLinterConfig

If true, attempt to fix any issues are found.

isArrayExpress() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand

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

isBackgroundChannelA(String) - Static method in class ubic.gemma.persistence.util.ChannelUtils

Deprecated.

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

Deprecated.

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

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.

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

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.

isDeleteOtherAnalyses() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig

After the new analyses are saved, delete the experiment's other analyses on the same subset factor: without a subset factor, every other analysis that is not a subset analysis; with one, every other analysis of that factor's subsets.

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

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.loader.genome.gene.ncbi.NcbiGeneLoader

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

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

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).

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

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

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

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.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.ncbi.NcbiGeneRecord

Whether NCBI has a record for this id 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

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.

isHasIntercept() - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix

isHasMissing() - Method in class ubic.gemma.core.util.math.linearmodels.LeastSquaresFit

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.

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.

isLive() - Method in class ubic.gemma.core.ontology.ncbi.NcbiGeneRecord

Whether that record is current, as opposed to withdrawn / secondary.

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

isMaxDesignElementsFilterApplied() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult

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

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

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

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(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

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

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.

isRequireSequences() - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig

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).

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

isRunning() - Method in class ubic.gemma.core.config.ServiceBeansConfig.DrainingTaskExecutor

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.

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

Deprecated.

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

Deprecated.

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).

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

isSkipped() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

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

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

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

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

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(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

Deprecated.

Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.

isTwoChannel(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl

Deprecated.

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.

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

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

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.

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.

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 - 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

jCacheCacheManager() - Method in class ubic.gemma.persistence.cache.EhcacheConfig

The single JCache CacheManager shared by Spring's application-cache abstraction.

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.

jiang - Enum constant in enum class ubic.gemma.core.ontology.GoMetric.Metric

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

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

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

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.

kind() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the kind record component.

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) / standardDeviation<sup>4</sup>.

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.

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.

LAST - Enum constant in enum class ubic.gemma.persistence.util.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

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

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 - Class in ubic.gemma.core.context

Mark beans as lazy-init by default.

LazyInitByDefaultPostProcessor() - Constructor for class ubic.gemma.core.context.LazyInitByDefaultPostProcessor

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.

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

LEVEL - Static variable in class ubic.gemma.core.util.GzipUtils

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.

LIBRARY_STRATEGY_MICROARRAY_ONE_COLOR - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssay

libraryStrategy of a microarray sample hybridized in one channel.

LIBRARY_STRATEGY_MICROARRAY_TWO_COLOR - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssay

libraryStrategy of a microarray sample hybridized in two channels.

librarySize() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay

Returns the value of the librarySize record component.

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

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

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

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

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

listDirectoryFiles(File) - Static method in class ubic.gemma.core.util.FileTools

Given a File representing a directory, return the (non-directory) files it contains.

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

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).

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

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 - Enum constant in enum class ubic.gemma.model.expression.experiment.WorkflowState

loadEventValueObjects(Long, Date, int) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService

Project one job's events, newest bound by since and capped at limit.

loadEventValueObjects(Long, Date, int) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl

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

See GeoServiceImpl.fetchAndLoad(String, boolean, boolean, boolean) for why this is Propagation.NEVER and routes through GeoServiceImpl.self.

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

loadPlatforms(String, Collection) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService

Convert already-fetched platform data and persist the resulting array designs.

loadPlatforms(String, Collection) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl

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

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) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService

Project one batch together with its jobs, for the REST surface.

loadValueObject(Long) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl

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

loadValueObjectsByOwner(Long, PipelineJobBatch.BatchState, int) - Method in interface ubic.gemma.persistence.service.pipeline.PipelineJobBatchService

Project a curator's batches, without their jobs.

loadValueObjectsByOwner(Long, PipelineJobBatch.BatchState, int) - Method in class ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl

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

locateMergedDesign(ExpressionExperiment) - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService

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.

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.

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

LockedPath - Interface in ubic.gemma.core.util.locking

A locked path.

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 - 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(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

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

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

logIds(String, Collection) - Method in class ubic.gemma.core.ontology.GoMetricImpl

LoginDetailsValueObject - Class in ubic.gemma.core.security.authentication

LoginDetailsValueObject() - Constructor for class ubic.gemma.core.security.authentication.LoginDetailsValueObject

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

Deprecated.

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

LongComputation - Annotation Interface in ubic.gemma.core.architecture

Marks work that runs long enough that no transaction may be open while it runs.

lookup(String) - Static method in class ubic.gemma.core.ontology.ValueStringToOntologyMapping

Deprecated.

Lookup a value across all categories.

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

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

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.

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

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

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

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

MarkdownUtils - Class in ubic.gemma.core.util

Utilities for handling Markdown text.

MarkdownUtils() - Constructor for class ubic.gemma.core.util.MarkdownUtils

Marker - Class in ubic.gemma.core.loader.expression.ucsc.cellbrowser.model

Marker() - Constructor for class ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker

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.

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_DETAIL_LENGTH - Static variable in class ubic.gemma.model.common.auditAndSecurity.AuditEvent

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_VALUE_LENGTH - Static variable in class ubic.gemma.model.expression.experiment.FactorValue

Maximum length of FactorValue.getValue(), in characters: the VALUE column is VARCHAR(255) and the schema is utf8mb4, so MySQL counts code points, not bytes.

MAX_WARNINGS - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig

maxDesignElements() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig

Returns the value of the maxDesignElements record component.

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.

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.

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.

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.

MBD_SEQ - Enum constant in enum class ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy

GEO's MBD-Seq.

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

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.

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

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

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.

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

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(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.

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.

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

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.

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

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

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

mgiAlleleOntologyService() - Method in class ubic.gemma.core.ontology.OntologyConfig

MgiAlleleOntologyService - Class in ubic.gemma.core.ontology.providers

MGI mouse alleles as a flat lexical source, so an annotation can carry the allele that MGI's disease-model relations are keyed on.

MgiAlleleOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.MgiAlleleOntologyService

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.

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

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

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

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.

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

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)<sup>k</sup> ) / 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

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.

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() - 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_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.

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.

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.

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

Loads gene2go with two threads joined by a bounded queue: the parser and the loader, which persists in batches.

NCBIGene2GOAssociationLoader() - Constructor for class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader

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

NcbiGeneRecord - Class in ubic.gemma.core.ontology.ncbi

What NCBI says about one gene id, as much of it as validation needs.

NcbiGeneRecord(int, String, String, String, boolean, boolean) - Constructor for class ubic.gemma.core.ontology.ncbi.NcbiGeneRecord

NcbiGeneResolver - Interface in ubic.gemma.core.ontology.ncbi

Resolve an NCBI gene id against NCBI itself, for gene URIs Gemma's own gene table does not carry.

NcbiGeneResolverImpl - Class in ubic.gemma.core.ontology.ncbi

NcbiGeneResolver over Entrez esummary db=gene.

NcbiGeneResolverImpl() - Constructor for class ubic.gemma.core.ontology.ncbi.NcbiGeneResolverImpl

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.

NcbiUnavailableException - Exception Class in ubic.gemma.core.ontology.ncbi

Thrown when NCBI cannot be reached or answers in a shape we cannot read — unverified, which is not the same as "no such gene".

NcbiUnavailableException(String) - Constructor for exception class ubic.gemma.core.ontology.ncbi.NcbiUnavailableException

NcbiUnavailableException(String, Throwable) - Constructor for exception class ubic.gemma.core.ontology.ncbi.NcbiUnavailableException

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.

NEITHER - Enum constant in enum class ubic.gemma.model.common.description.RelationInferenceDirection

Neither end implies the other.

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

newGzipOutputStream(OutputStream) - Static method in class ubic.gemma.core.util.GzipUtils

A GZIPOutputStream over the given stream, at GzipUtils.LEVEL.

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

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

newValue() - Method in record class ubic.gemma.core.security.audit.payload.SampleMetadataPayload

Returns the value of the newValue record component.

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

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}.

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

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.

normalizeInPlace(double[][], boolean[]) - Static method in class ubic.gemma.core.analysis.preprocess.normalize.QuantileNormalizer

Normalize rows of data in place, producing exactly the values of QuantileNormalizer.normalize(DoubleMatrix, boolean[]).

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

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(int) - Static method in class ubic.gemma.core.ontology.ncbi.NcbiGeneRecord

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.

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

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.

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

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

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(String) - Static method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCounts

Read the counts off a payload, best-effort.

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(List) - Static method in class ubic.gemma.core.metrics.CompositeMeterRegistryFactory

Build a composite registry that forwards every recording to each backing registry.

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

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.

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

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

ont() - Method in class ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl

Generate a URL for ontologies served by Gemma.

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

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.

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

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.

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

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, GeneService, NcbiGeneResolver) - Constructor for class ubic.gemma.core.ontology.OntologyTermValidatorImpl

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(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

openCompressedFile(Path) - Static method in class ubic.gemma.core.util.FileUtils

Open a GZIP-compressed file safely.

OPENED - Enum constant in enum class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType

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.MgiAlleleOntologyService

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

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.

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

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

OSTTEST - Enum constant in enum class ubic.gemma.core.analysis.expression.diff.AnalysisType

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

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

outranks(PublicationAssociationSource) - Method in enum class ubic.gemma.model.common.description.PublicationAssociationSource

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.

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.

Parent-ACL discovery and the parent stash - Section in class ubic.gemma.core.security.acl.AclEventListener

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.

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.MgiAlleleOntologyService

Parse MGI_PhenotypicAllele.rpt: one allele per line, tab-delimited, accession in column 1, symbol in column 2, name in column 3, allele type and attributes in 4 and 5, the gene's accession and symbol in 7 and 8 (empty for a transgene), and |-separated synonyms in 12.

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

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

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

PCAAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType

PCAAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PCAAnalysisEvent

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

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

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

Deprecated.

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

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

PipelineJobBatchValueObject - Class in ubic.gemma.model.pipeline

Value object projection of PipelineJobBatch for the REST surface.

PipelineJobBatchValueObject() - Constructor for class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

PipelineJobEventValueObject - Class in ubic.gemma.model.pipeline

Value object projection of PipelineJobEvent for the REST surface.

PipelineJobEventValueObject() - Constructor for class ubic.gemma.model.pipeline.PipelineJobEventValueObject

PipelineJobValueObject - Class in ubic.gemma.model.pipeline

Value object projection of PipelineJob for the REST surface.

PipelineJobValueObject() - Constructor for class ubic.gemma.model.pipeline.PipelineJobValueObject

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

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

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

platforms() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the platforms record component.

platforms() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

Returns the value of the platforms record component.

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

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

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

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

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

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

predicate - Variable in class ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample

predicate(String) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder

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

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.

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

🛑 Propagation.NEVER, and it has to be: this is where the time goes.

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

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

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.

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

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.

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

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

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

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

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.

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

PROCESSING_DATE - Static variable in class ubic.gemma.model.expression.bioAssay.BioAssayCategories

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(InputStream, InputStream, InputStream, InputStream) - Method in class ubic.gemma.core.ontology.relation.MgiRelationProducer

Rebuild every MGI relation from the three reports, and also store each asserted relation under the MGI strains whose nomenclature carries its allele.

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] ).

PRODUCT_NOT_FOUND - Enum constant in enum class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome.SkipReason

productDeleted() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

Returns the value of the productDeleted record component.

productGi() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the productGi record component.

productId() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the productId record component.

PRODUCTION - Static variable in class ubic.gemma.core.context.EnvironmentProfiles

Mutually-exclusive environment profiles.

productName() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the productName record component.

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

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

PromotionResult(Long, Long, int) - Constructor for class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PromotionResult

properPartOf - Static variable in class ubic.gemma.core.ontology.jena.RO

Deprecated.

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

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.Factory - Class in ubic.gemma.model.common.protocol

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

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

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

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

publications(boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig.GeoUpdateConfigBuilder

PUBMED - Static variable in class ubic.gemma.model.common.description.ExternalDatabases

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

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

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

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

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.).

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

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

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

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.

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 - 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.

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.

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 - 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

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

RawDataPostprocessingException - Exception Class in ubic.gemma.core.loader.expression

Raised by DataUpdater when new raw data was stored for an experiment, but post-processing it failed.

RawDataPostprocessingException(ExpressionExperiment, String, Throwable) - Constructor for exception class ubic.gemma.core.loader.expression.RawDataPostprocessingException

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

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(Reader) - Static method in class ubic.gemma.core.loader.genome.gene.ncbi.GeneProductChangeTsv

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

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

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.

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.

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.

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

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

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

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.

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

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).

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

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

recordSampleMetadataChange(ExpressionExperiment, String, SampleMetadataPayload) - Method in interface ubic.gemma.core.analysis.service.BioAssayMetadataAuditService

recordSampleMetadataChange(ExpressionExperiment, String, SampleMetadataPayload) - Method in class ubic.gemma.core.analysis.service.BioAssayMetadataAuditServiceImpl

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

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.

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

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

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

refreshCurationDetails(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao

Reload the experiment's curation details from the database, replacing their second-level cache entry.

refreshCurationDetails(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl

refreshDaily() - Method in class ubic.gemma.core.analysis.report.HomeStatsRefresher

Daily refresh.

refreshOnStartup() - Method in class ubic.gemma.core.analysis.report.HomeStatsRefresher

Recompute the snapshot on context startup.

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.

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.

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

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

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

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

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

REMOVE - Enum constant in enum class ubic.gemma.persistence.service.genome.gene.GeneProductChange.Kind

The product is no longer listed by NCBI for the gene, or is an outdated duplicate of one that is.

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

removeAllCellLevelCharacteristics(ExpressionExperiment, SingleCellDimension) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao

Remove all the cell-level characteristics of a single-cell dimension.

removeAllCellLevelCharacteristics(ExpressionExperiment, SingleCellDimension) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl

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

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).

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

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

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

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.

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).

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.

replaceForExperiment(ExpressionExperiment, DoubleMatrix, double[], DoubleMatrix, BioAssayDimension, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService

Remove the experiment's PCA and store the given one, in a single transaction.

replaceForExperiment(ExpressionExperiment, DoubleMatrix, double[], DoubleMatrix, BioAssayDimension, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl

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.

replaceVersionAccession(ExpressionExperiment, String) - Method in interface ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderService

Replace a CELLxGENE accession that holds a dataset version ID by one that holds the permanent dataset ID.

replaceVersionAccession(ExpressionExperiment, String) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderServiceImpl

replayGeneProductRemoval(GeneProductChange, Collection, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneWriteService

Apply a removal that GeneWriteService.upsert(Gene, boolean, Consumer) recorded and did not make, if it still holds.

replayGeneProductRemoval(GeneProductChange, Collection, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl

Report(boolean, List) - Constructor for record class ubic.gemma.core.loader.genome.gene.ncbi.GeneProductChangeTsv.Report

Creates an instance of a Report record class.

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(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

requestCancellation() - Method in interface ubic.gemma.core.job.SubmittedTask

Send cancellation request.

REQUIREMENTS_FILE - Static variable in interface ubic.gemma.core.loader.expression.singleCell.transform.PythonBasedSingleCellDataTransformation

requireOnBehalfOfFromAgent(String) - Static method in class ubic.gemma.core.security.util.SecurityUtil

Refuse a ruling an agent records without naming the person who directed it.

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.

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.

resetMexFileSuffixes() - Method in class ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector

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

resnik - Enum constant in enum class ubic.gemma.core.ontology.GoMetric.Metric

resolve(int) - Method in interface ubic.gemma.core.ontology.ncbi.NcbiGeneResolver

resolve(int) - Method in class ubic.gemma.core.ontology.ncbi.NcbiGeneResolverImpl

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.

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

resolveDataset(String, String) - Method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher

Resolve a dataset in a collection from its permanent ID, its version ID or its title.

resolveDataset(String, List, String) - Static method in class ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils

Resolve a dataset in a collection from a user-supplied identifier.

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().

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).

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

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

Result(Resource, String, double) - Constructor for class ubic.gemma.core.ontology.search.OntologySearchService.Result

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

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

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

RO - Class in ubic.gemma.core.ontology.jena

RO() - Constructor for class ubic.gemma.core.ontology.jena.RO

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

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.

rowMeans(DoubleMatrix) - Static method in class ubic.gemma.core.util.MatrixStats

Return the mean of each row in the matrix.

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

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_.

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

RunMetrics(String, Map) - Constructor for class ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.RunMetrics

Creates a new RunMetrics instance.

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

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

sameSupportingEvidence(String, JsonNode) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils

Whether writing proposed over a row's stored evidence would change nothing.

sameSupportingEvidence(String, String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils

CharacteristicUtils.sameSupportingEvidence(String, JsonNode) for a proposal that is already serialized.

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

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, String) - 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.

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.

SampleMetadataChangedEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType

A curator changed upstream-derived metadata on one or more of an experiment's samples — libraryStrategy, librarySelection or extractedMolecule.

SampleMetadataChangedEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.SampleMetadataChangedEvent

SampleMetadataPayload - Record Class in ubic.gemma.core.security.audit.payload

What a SampleMetadataChangedEvent changed.

SampleMetadataPayload(String, String, List) - Constructor for record class ubic.gemma.core.security.audit.payload.SampleMetadataPayload

Creates an instance of a SampleMetadataPayload record class.

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.

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.

scalarDivideMatrix(ExpressionDataDoubleMatrix, double) - Method in class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

Divide all values by the dividend

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.

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(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(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.

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

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.

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

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)

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

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

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

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

SearchSource - Interface in ubic.gemma.core.search

Search source that provides SearchResult from a search engine.

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

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

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

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.

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

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

serialize(Double, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.core.util.RoundingUtils.SignificantDigitsSerializer

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

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

ServiceBeansConfig.DrainingTaskExecutor - Class in ubic.gemma.core.config

A ConcurrentTaskExecutor that waits for its pending tasks when the context is stopped.

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

sessionFactory(DataSource, Environment) - Method in class ubic.gemma.persistence.hibernate.HibernateConfig

Native Hibernate SessionFactory built from hibernate.cfg.xml.

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.

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.

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.

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(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

setAfterMaxDesignElementsFilter(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

setAgentVersion(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet

setAgentVersion(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject

setAggressiveQtRemoval(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand

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

setAllowArrayExpressDesign(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand

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.

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

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(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

setAnnotationValueObjects(Collection) - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand

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

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

setAssignee(Contact) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket

setAssigneeId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject

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

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

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

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(String, String) - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix

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.

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.

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.

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

setBatchId(Long) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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.

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.

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

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

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.

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(Characteristic) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor

setCategory(CharacteristicValueObject) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry

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

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

setChangeSink(Consumer) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

Receives every gene product removal (made or not) and every move of a gene product between genes, on the loader thread, once the gene's transaction has ended: after its commit, or after its rollback in a dry run.

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

For each cell, the id of its label in CellLevelCharacteristicsValueObject.characteristics.

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

The distinct labels cells are grouped under; see CellLevelCharacteristics.

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

setClosedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch

setClosedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

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

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

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

setColumnsAfterOutliersFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult

setComment(String) - Method in class ubic.gemma.model.genome.GeneOntologyTermValueObject

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

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

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

setContrastCoding(String, ContrastCoding) - Method in class ubic.gemma.core.util.math.linearmodels.DesignMatrix

Choose how one categorical factor's levels are coded, and rebuild the design.

setContrastCoding(ExperimentalFactor, ContrastCoding) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig

Choose how one factor's levels are coded.

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

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

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

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

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(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata

setDatasetId(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetVersion

setDatasetLink(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject

setDatasetName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject

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.

setDatasetType(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset

setDatasetVersionId(String) - Method in class ubic.gemma.core.loader.expression.cellxgene.model.DatasetVersion

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

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.

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

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

setDeleteOtherAnalyses(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig

After the new analyses are saved, delete the experiment's other analyses on the same subset factor: without a subset factor, every other analysis that is not a subset analysis; with one, every other analysis of that factor's subsets.

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.model.pipeline.PipelineJobBatchValueObject

setDescription(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest

setDesign(SraExperimentDesign) - Method in class ubic.gemma.core.loader.expression.sra.model.SraExperiment

setDesign(ExperimentalDesignValueObject) - Method in class ubic.gemma.model.expression.experiment.DesignApplyOutcome

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

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.

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.loader.genome.gene.ncbi.NcbiGeneLoader

Upsert and flush each gene as usual, then roll its transaction back.

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

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.

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

setError(Exception) - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus

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

setErrorMessage(String) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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

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

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(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).

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

setExecutorService(Executor) - Method in class ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter

Executor to use to write MEX files in parallel.

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

setExperimentAnalyzed(ExpressionExperiment) - Method in class ubic.gemma.model.expression.bioAssayData.CellTypeAssignment

The experiment whose cells this assigns, in the EXPERIMENT_ANALYZED_FK column every other analysis in ANALYSIS uses for the same fact (Paul, 2026-09-14).

setExperimentAnalyzedId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject

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.model.pipeline.PipelineJobValueObject

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

Deprecated.

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.

setExtractedMolecule(ExpressionExperiment, Collection, String) - Method in interface ubic.gemma.core.analysis.service.BioAssayMetadataService

Set extractedMolecule on the given samples.

setExtractedMolecule(ExpressionExperiment, Collection, String) - Method in class ubic.gemma.core.analysis.service.BioAssayMetadataServiceImpl

setExtractedMolecules(List) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

What was extracted from the dataset's samples and assayed, as the distinct extractedMolecule values with a count of the samples carrying each.

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

Deprecated.

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

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.

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

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

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

setFailure(AtomicReference) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter

Where the conversion thread records the exception that ended it; the loader waits on this.

setFailure(AtomicReference) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator

Where the gene2accession parsing thread records the exception that ended it; the loader waits on this.

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

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

setFinishedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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(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

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

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.

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

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(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

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

setHasDifferentialExpressionAnalysis(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject

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.model.pipeline.PipelineJobBatchValueObject

setId(Long) - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

setId(Long) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

setId(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers

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

Dataset version identifier; it changes whenever the dataset is revised.

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

setIncludeInteractions(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand

Whether interactions among the factors should be included.

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

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

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

setJob(PipelineJob) - Method in class ubic.gemma.model.pipeline.PipelineJobEvent

setJobId(Long) - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

setJobs(List) - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

setKillRequestedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

setKind(String) - Method in class ubic.gemma.model.pipeline.PipelineJobEvent

setKind(String) - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

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

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

setLastEventAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

setLastEventKind(String) - Method in class ubic.gemma.model.pipeline.PipelineJob

setLastEventKind(String) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

setLastGeneMapping(Date) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject

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

setLastProgressJson(String) - Method in class ubic.gemma.model.pipeline.PipelineJob

setLastProgressJson(String) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

setLastRepeatMask(Date) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject

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

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.

setLibrarySelection(ExpressionExperiment, Collection, String) - Method in interface ubic.gemma.core.analysis.service.BioAssayMetadataService

Set librarySelection on the given samples.

setLibrarySelection(ExpressionExperiment, Collection, String) - Method in class ubic.gemma.core.analysis.service.BioAssayMetadataServiceImpl

setLibrarySelections(List) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

How the dataset's libraries were selected, as the distinct librarySelection values with a count of the samples carrying each.

setLibrarySource(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord

setLibraryStrategies(List) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

What kind of libraries the dataset's samples were made from, as the distinct libraryStrategy values with a count of the samples carrying each.

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, as the GeoLibraryStrategy constant name (RNA_SEQ, SCRNA_SEQ, RIBO_SEQ, ATAC_SEQ, …) rather than GEO's spelling, or MICROARRAY_ONE_COLOR / MICROARRAY_TWO_COLOR for a microarray sample.

setLibraryStrategy(ExpressionExperiment, Collection, String) - Method in interface ubic.gemma.core.analysis.service.BioAssayMetadataService

Set libraryStrategy on the given samples.

setLibraryStrategy(ExpressionExperiment, Collection, String) - Method in class ubic.gemma.core.analysis.service.BioAssayMetadataServiceImpl

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.core.loader.genome.gene.ncbi.NcbiGeneLoader

Stop after this many genes have been upserted.

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

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

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

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

setMaxDesignElements(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig

Keep at most this many design elements, the most variable ones, or 0 for no cap.

setMaxDesignElementsFilterApplied(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult

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

setMeasurementObject(MeasurementValueObject) - Method in class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject

The measurement associated with this factor 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

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(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

setModel(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet

setModel(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject

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.model.pipeline.PipelineJobBatchValueObject

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

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(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.model.common.auditAndSecurity.curation.AbstractCuratableValueObject

setNeedsAttention(Boolean) - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject

Deprecated.

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

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

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

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(int) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayFieldCountValueObject

How many of the dataset's assays carry BioAssayFieldCountValueObject.value.

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

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

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

setOccurredAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

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

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

setOtherRelevantPublications(List) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest

setOtherRelevantPublications(Set) - Method in class ubic.gemma.model.analysis.Investigation

setOutlier(boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject

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

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

setParamsJson(String) - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

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.TicketTarget

setPayload(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

This target's own task — what put THIS experiment on the ticket and what is being asked of the curator.

setPayload(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject

What the screen that produced this ticket asked, verbatim and opaque.

setPayloadJson(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet

setPayloadJson(String) - Method in class ubic.gemma.model.pipeline.PipelineJobEvent

setPayloadJson(String) - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

setPayloadSchemaVersion(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.Ticket

setPayloadSchemaVersion(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget

setPayloadSchemaVersion(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

Which schema TicketTargetValueObject.payload follows, or null when the writer declared none.

setPayloadSchemaVersion(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject

Which schema TicketValueObject.payload follows; null when the writer declared none.

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

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

setPipeline(String) - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

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

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.

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

Blank is stored as null, for the reason spelled out on Characteristic.setValueUri(String): an empty string is a second dialect for ungrounded and no layer reads it that way.

setPredicateUri(String) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject

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.

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

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

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

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

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

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

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

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.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

setQuantitationTypes(Set) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment

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

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(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

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.

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

setReasonCode(String) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest

setRecentExperiments(List) - Method in class ubic.gemma.core.analysis.report.HomeStats

Most-recently curated public experiments, for the scrolling-names widget.

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

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

setRemoveProducts(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

Whether to delete the gene products that NCBI no longer lists for their gene (the default).

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

setRepresentation(String) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject

setRepresentation(String) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject

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

setRequireSequences(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig

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

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

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

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

setS2n(double) - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand

Deprecated.

setSample(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform

setSample(BioMaterialValueObject) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject

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

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

setSchedulerHandle(String) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

setSchedulerKind(SchedulerKind) - Method in class ubic.gemma.model.pipeline.PipelineJob

setSchedulerKind(SchedulerKind) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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(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

setScreeningResultReason(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget

setScreeningResultReason(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

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

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

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

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.

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

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

setSessionFactory(SessionFactory) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

Used to flush in a dry run, and for the summary's counts of created genes and removed gene products, which come from Hibernate's statistics.

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

setShortNameChangeAllowed(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest

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.

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

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(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.

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

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.model.pipeline.PipelineJobValueObject

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(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(JobState) - Method in class ubic.gemma.model.pipeline.PipelineJob

setState(JobState) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

setState(PipelineJobBatch.BatchState) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch

setState(PipelineJobBatch.BatchState) - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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.

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(TicketTargetStatus) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget

setStatus(TicketTargetStatus) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

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

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

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.model.pipeline.PipelineJobBatchValueObject

setSubmittedAt(Date) - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

setSubmittedBy(Contact) - Method in class ubic.gemma.model.pipeline.PipelineJobBatch

setSubmittedById(Long) - Method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

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

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

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

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(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

setSuppressMatching(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand

setSuppressPostProcessing(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand

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

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

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(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition

setTargets(List) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject

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

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

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

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(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

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.

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.cellxgene.model.DatasetVersion

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

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

setTransactionManager(PlatformTransactionManager) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader

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).

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.model.common.auditAndSecurity.curation.AbstractCuratableValueObject

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(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(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(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(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

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

setUseRefGene(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig

setUserFlaggedOutlier(boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject

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)

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.bioAssay.BioAssayFieldCountValueObject

The value itself, spelled exactly as the per-assay field spells it in BioAssayValueObject — so a client can compare the two without a mapping table.

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

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(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

🛑 Blank is stored as null, the way Characteristic.setValue(String) normalises its free text.

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

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.

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

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.

SignificantDigitsSerializer() - Constructor for class ubic.gemma.core.util.RoundingUtils.SignificantDigitsSerializer

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

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

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

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

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

SingleCellDataLoader - Interface in ubic.gemma.core.loader.expression.singleCell

Common interface for all single-cell data loaders.

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

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

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

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

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 - 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

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) / standardDeviation<sup>3</sup>.

skip(long) - Method in class ubic.gemma.core.util.ProgressInputStream

skipReason() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

Returns the value of the skipReason record component.

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.

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

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

sortByColumnAbsoluteValues(int, boolean) - Method in class ubic.gemma.core.util.matrix.DoubleMatrix

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(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.

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

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

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

stages() - Method in record class ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload

Returns the value of the stages record component.

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.

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.

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.

start() - Method in class ubic.gemma.core.config.ServiceBeansConfig.DrainingTaskExecutor

start(InputStream, String) - Static method in class ubic.gemma.core.util.StreamDrainer

Start reading the stream on a new daemon thread, keeping the last StreamDrainer.DEFAULT_MAX_CHARS characters.

start(InputStream, String, int) - Static method in class ubic.gemma.core.util.StreamDrainer

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.

state - Variable in class ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate

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

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

Stats - Class in ubic.gemma.core.util.math

Miscellaneous functions used for statistical analysis.

status(AnnotationRelationStatus) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder

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

stop() - Method in class ubic.gemma.core.config.ServiceBeansConfig.DrainingTaskExecutor

stop() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter

Stop the conversion thread, if it is running.

stop() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator

Stop the gene2accession parsing thread, if it is running.

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

StreamDrainer - Class in ubic.gemma.core.util

Reads a stream to its end on a daemon thread, keeping the last maxChars characters.

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.

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

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.

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

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

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.

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.

SUM_TO_ZERO - Enum constant in enum class ubic.gemma.core.util.math.linearmodels.ContrastCoding

Each level gets a column, the one left over takes -1 in all of them, and a coefficient is that level's deviation from the mean of the level means.

sumArray(int[]) - Static method in class ubic.gemma.core.util.math.MathUtil

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(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

summaryById(String, String, EntrezRetmode, String) - Static method in class ubic.gemma.core.loader.entrez.EntrezUtils

Retrieve a document summary from an Entrez database by ID, without a prior search.

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)<sup>k</sup> ); 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)<sup>k</sup> ) 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]<sup>k</sup> ).

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

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.

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

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

SWITCH - Enum constant in enum class ubic.gemma.persistence.service.genome.gene.GeneProductChange.Kind

The product was moved from one gene to another.

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

switchPlatformAndVectors(ExpressionExperiment, ArrayDesign) - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService

The transactional part of ExpressionExperimentPlatformSwitchService.switchExperimentToArrayDesign(ExpressionExperiment, ArrayDesign): everything except regenerating the processed vectors.

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.

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_WIDE_SALT - Static variable in class ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider

Historical SystemWideSaltSource value from build.properties (commit 66f574e926, 2008-10-02).

T

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

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

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

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

taxon() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the taxon record component.

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.Factory - Class in ubic.gemma.model.genome

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

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(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

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

taxonNcbiId(Integer) - Method in class ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder

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(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

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

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

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

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 response contract, measured 2026-09-12 rather than read from the docs - Section in class ubic.gemma.core.ontology.ncbi.NcbiGeneResolverImpl

The rule - Section in class ubic.gemma.core.loader.expression.geo.GeoCharacteristicKey

The shape that is correct - Section in annotation interface ubic.gemma.core.architecture.LongComputation

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

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

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

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.

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

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

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.

TIMEPOINT - Static variable in class ubic.gemma.model.common.description.Categories

TINY - Static variable in class ubic.gemma.core.util.math.Constants

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

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.

toGeneNcbiId() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the toGeneNcbiId record component.

toGeneSymbol() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns the value of the toGeneSymbol record component.

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

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

topLeft - Variable in class ubic.gemma.core.util.matrix.MatrixWriter

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.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.DatasetVersion

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 record class ubic.gemma.core.loader.genome.gene.ncbi.GeneProductChangeTsv.Report

Returns a string representation of this record class.

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.ncbi.NcbiGeneRecord

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.SampleMetadataPayload

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.BioAssayFieldCountValueObject

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.model.pipeline.PipelineJobBatchValueObject

toString() - Method in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

toString() - Method in class ubic.gemma.model.pipeline.PipelineJobValueObject

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 record class ubic.gemma.persistence.service.genome.gene.GeneProductChange

Returns a string representation of this record class.

toString() - Method in record class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome

Returns a string representation of this record class.

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(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

totalCells() - Method in record class ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay

Returns the value of the totalCells record component.

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.

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 - Enum constant in enum class ubic.gemma.core.util.math.linearmodels.ContrastCoding

Each level gets an indicator column; one level has none and is the baseline.

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

TriageJudgeKind - Enum Class in ubic.gemma.model.common.auditAndSecurity.curation

What kind of judge produced an AnnotationSet triage ruling.

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

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

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

Deprecated.

Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.

TwoChannelExpressionDataMatrixBuilder(Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

TwoChannelExpressionDataMatrixBuilder(Collection, Collection) - Constructor for class ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder

Deprecated.

TwoChannelMissingValueHelperService - Interface in ubic.gemma.core.analysis.preprocess

Deprecated.

Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.

TwoChannelMissingValues - Interface in ubic.gemma.core.analysis.preprocess

Deprecated.

Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.

TwoChannelMissingValuesImpl - Class in ubic.gemma.core.analysis.preprocess

Deprecated.

Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.

TwoChannelMissingValuesImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl

Deprecated.

TwoChannelMissingValueTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression

Deprecated.

Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.

TwoChannelMissingValueTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand

Deprecated.

TwoChannelMissingValueTaskCommand(ExpressionExperiment, double, Collection) - Constructor for class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand

Deprecated.

TwoChannelMissingValueTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression

Deprecated.

Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.

TwoChannelMissingValueTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskImpl

Deprecated.

TWOCOLOR - Enum constant in enum class ubic.gemma.model.expression.arrayDesign.TechnologyType

Indicates this platform uses two channels and expression measurements are ratios.

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.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.ncbi - package ubic.gemma.core.ontology.ncbi

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

UCSC_CELL_BROWSER - Static variable in class ubic.gemma.model.common.description.ExternalDatabases

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.

unifiedOntologyService(boolean, Path, Path) - Method in class ubic.gemma.core.ontology.OntologyConfig

This ontology encompasses all the ontologies declared below.

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() - 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

UnknownDeletedIdsException - Exception Class in ubic.gemma.persistence.service.expression.experiment

Thrown when a curation commit asks to delete a tag or sample characteristic that is not on the experiment.

UnknownDeletedIdsException(String) - Constructor for exception class ubic.gemma.persistence.service.expression.experiment.UnknownDeletedIdsException

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.

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

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.

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

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_NCBI_UNAVAILABLE - Enum constant in enum class ubic.gemma.core.ontology.TermViolation.Reason

A gene id absent from Gemma's gene table that NCBI could not be reached to check — unverified, not proven bad, and retryable.

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 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

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

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

UpdateEEDetailsCommand - Class in ubic.gemma.core.tasks.analysis.expression

UpdateEEDetailsCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand

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.

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

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

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.

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.

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

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(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

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.

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

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

upsert(Gene, boolean, Consumer) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneWriteService

Like GeneWriteService.upsert(Gene), optionally without removing any gene product, and reporting the products it removes or moves between genes.

upsert(Gene, boolean, Consumer) - Method in class ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl

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

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.MgiAlleleOntologyService

Canonical, resolvable MGI allele URI prefix; <prefix>MGI:3794202.

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.

uriToTermId(String) - Static method in class ubic.gemma.core.ontology.OntologyUtils

Converts a URI to an OBO term ID.

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

use10xChemistry(String) - Method in class ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder

Chemistry used for single-cell sequencing.

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

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 - 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.Factory - Class in ubic.gemma.model.common.auditAndSecurity

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.

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

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

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

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

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 - Section in interface ubic.gemma.core.analysis.service.BioAssayMetadataService

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.LongComputation

Optional note on what makes this one long — a measured duration, a complexity, the dataset that showed it.

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 - 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.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.util.math.linearmodels.ContrastCoding

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.service.genome.gene.GeneProductChange.Kind

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class ubic.gemma.persistence.service.genome.gene.GeneProductRemovalOutcome.SkipReason

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.

values - Variable in class ubic.gemma.core.loader.util.anndata.NullableArray

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.util.math.linearmodels.ContrastCoding

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.service.genome.gene.GeneProductChange.Kind

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.genome.gene.GeneProductRemovalOutcome.SkipReason

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 - 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

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

version - Variable in class ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService

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

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.

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.

VLEN - Enum constant in enum class ubic.gemma.core.loader.util.hdf5.H5FundamentalType

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.

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.

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.

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 mapped - Section in class ubic.gemma.core.util.SymbolFontPua

What it is for - Section in annotation interface ubic.gemma.core.architecture.LongComputation

What it is good for - Section in enum class ubic.gemma.model.expression.bioAssay.ExtractedMolecule

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

Where to put it - Section in annotation interface ubic.gemma.core.architecture.LongComputation

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 an importer needs this - Section in ubic.gemma.core.ontology.OntologyUtils.termIdOrUriToUri(String)

Why a separate bean - Section in interface ubic.gemma.core.analysis.service.BioAssayMetadataAuditService

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 live is separate from found - Section in class ubic.gemma.core.ontology.ncbi.NcbiGeneRecord

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 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 - Section in class ubic.gemma.model.common.auditAndSecurity.eventType.SampleMetadataChangedEvent

Why this exists - Section in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

Why this exists - Section in class ubic.gemma.model.pipeline.PipelineJobEventValueObject

Why this exists - Section in class ubic.gemma.model.pipeline.PipelineJobValueObject

Why this exists - Section in interface ubic.gemma.core.analysis.service.BioAssayMetadataService

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

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

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.

withJobs(PipelineJobBatch) - Static method in class ubic.gemma.model.pipeline.PipelineJobBatchValueObject

Project a batch together with its jobs.

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

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

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.

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

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

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

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.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.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(Path) - Method in interface ubic.gemma.core.util.FileUtils.PathWriter

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(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

writeAtomically(Path, FileUtils.PathWriter) - Static method in class ubic.gemma.core.util.FileUtils

Write destination through a temporary sibling that is moved over it only once writer has returned normally.

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

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

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).

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.

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