Index (Gemma 1.31.4 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Z _
All Classes All Packages

A

AbaGene - Class in ubic.gemma.core.image.aba
AbaGene() - Constructor for class ubic.gemma.core.image.aba.AbaGene
AbaGene(Integer, String, String, String, String, Collection<ImageSeries>) - Constructor for class ubic.gemma.core.image.aba.AbaGene
ABALinkOutValueObject - Class in ubic.gemma.core.image: Value Object for transporting details needed from other websites to provide convenient links to them in gemma
ABALinkOutValueObject() - Constructor for class ubic.gemma.core.image.ABALinkOutValueObject
ABALinkOutValueObject(Collection<String>, String, String) - Constructor for class ubic.gemma.core.image.ABALinkOutValueObject
ABORTED - Static variable in class ubic.gemma.core.util.AbstractCLI: Exit code used when a AbstractCLI.doWork() is aborted.
ABSOLUTE - ubic.gemma.model.common.measurement.MeasurementType
AbstractAnalyzer - Class in ubic.gemma.core.analysis.expression.diff: Analyzer base class.
AbstractAnalyzer() - Constructor for class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer
AbstractArg<T> - Class in ubic.gemma.rest.util.args: Base class for non Object-specific functionality argument types, that can be malformed on input (E.g an argument representing a number was a non-numeric string in the request).
AbstractArg(T) - Constructor for class ubic.gemma.rest.util.args.AbstractArg: Constructor for well-formed value.
AbstractArrayArg<T> - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be an array.
AbstractArrayArg(List<T>) - Constructor for class ubic.gemma.rest.util.args.AbstractArrayArg
AbstractAsyncFactoryBean<T> - Class in ubic.gemma.persistence.util: Base implementation of AsyncFactoryBean.
AbstractAsyncFactoryBean() - Constructor for class ubic.gemma.persistence.util.AbstractAsyncFactoryBean
AbstractAsyncFactoryBean(ExecutorService) - Constructor for class ubic.gemma.persistence.util.AbstractAsyncFactoryBean
AbstractAuditable - Class in ubic.gemma.model.common: An entity which can have an audit trail attached to it.
AbstractAuditable() - Constructor for class ubic.gemma.model.common.AbstractAuditable: No-arg constructor added to satisfy javabean contract
AbstractAuthenticatedCLI - Class in ubic.gemma.core.util: Subclass this to create command line interface (CLI) tools that need authentication.
AbstractAuthenticatedCLI() - Constructor for class ubic.gemma.core.util.AbstractAuthenticatedCLI
AbstractCLI - Class in ubic.gemma.core.util: Basic implementation of the CLI interface.
AbstractCLI() - Constructor for class ubic.gemma.core.util.AbstractCLI
AbstractCriteriaFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Class in ubic.gemma.persistence.service: Partial implementation of FilteringVoEnabledDao based on the Hibernate Criteria API.
AbstractCriteriaFilteringVoEnabledDao(Class<? extends O>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
AbstractCuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>> - Class in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Created by tesarst on 07/03/17.
AbstractCuratableDao(String, Class<C>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
AbstractCuratableValueObject<C extends Curatable> - 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(Long) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
AbstractCuratableValueObject(AbstractCuratableValueObject<C>) - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject: Copy constructor.
AbstractDao<T extends Identifiable> - Class in ubic.gemma.persistence.service: AbstractDao can find the generic type at runtime and simplify the code implementation of the BaseDao interface
AbstractDao(Class<? extends T>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractDao
AbstractDao(Class<? extends T>, SessionFactory, ClassMetadata) - Constructor for class ubic.gemma.persistence.service.AbstractDao
AbstractDescribable - Class in ubic.gemma.model.common
AbstractDescribable() - Constructor for class ubic.gemma.model.common.AbstractDescribable: No-arg constructor added to satisfy javabean contract
AbstractDesignElementDataVectorDao<T extends DesignElementDataVector> - Class in ubic.gemma.persistence.service.expression.bioAssayData
AbstractDesignElementDataVectorDao(Class<T>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
AbstractDesignElementDataVectorDao(Class<T>, SessionFactory, ClassMetadata) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
AbstractDesignElementDataVectorService<T extends DesignElementDataVector> - Class in ubic.gemma.persistence.service.expression.bioAssayData
AbstractDesignElementDataVectorService(DesignElementDataVectorDao<T>) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService
AbstractDifferentialExpressionAnalyzer - Class in ubic.gemma.core.analysis.expression.diff: An abstract differential expression analyzer to be extended
AbstractDifferentialExpressionAnalyzer() - Constructor for class ubic.gemma.core.analysis.expression.diff.AbstractDifferentialExpressionAnalyzer
AbstractEntityArg<T,O extends Identifiable,S extends FilteringService<O>> - Class in ubic.gemma.rest.util.args: Interface representing and API call argument that can represent various identifiers of different types.
AbstractEntityArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArg
AbstractEntityArgService<T extends Identifiable,S extends FilteringService<T>> - Class in ubic.gemma.rest.util.args
AbstractEntityArgService(S) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArgService
AbstractEntityArrayArg<O extends Identifiable,S extends FilteringService<O>> - Class in ubic.gemma.rest.util.args
AbstractEntityArrayArg(Class<? extends AbstractEntityArg>, List<String>) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArrayArg
AbstractExceptionMapper<E extends Throwable> - Class in ubic.gemma.rest.providers
AbstractExceptionMapper() - Constructor for class ubic.gemma.rest.providers.AbstractExceptionMapper
AbstractFactorValueValueObjectSerializer<T> - Class in ubic.gemma.rest.serializers: Base serializer for FactorValue VOs.
AbstractFactorValueValueObjectSerializer(Class<T>) - Constructor for class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer
AbstractFetcher - Class in ubic.gemma.core.loader.util.fetcher
AbstractFetcher() - Constructor for class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
AbstractFileService<T> - Class in ubic.gemma.core.analysis.service: Provide base implementation for all sorts of file services that serialize data in tabular format.
AbstractFileService() - Constructor for class ubic.gemma.core.analysis.service.AbstractFileService
AbstractFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Class in ubic.gemma.persistence.service: Base implementation for FilteringVoEnabledDao.
AbstractFilteringVoEnabledDao(String, Class<? extends O>, 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.
AbstractFilteringVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Class in ubic.gemma.persistence.service: Base implementation for FilteringVoEnabledService.
AbstractFilteringVoEnabledService(FilteringVoEnabledDao<O, VO>) - Constructor for class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
AbstractGemmaEndpoint - Class in ubic.gemma.web.services: Abstracts out the security and a few constants.
AbstractGemmaEndpoint() - Constructor for class ubic.gemma.web.services.AbstractGemmaEndpoint
AbstractGeoService - Class in ubic.gemma.core.loader.expression.geo.service
AbstractGeoService() - Constructor for class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
AbstractMatrixRowPairAnalysis - Class in ubic.gemma.core.analysis.expression.coexpression.links
AbstractMatrixRowPairAnalysis() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
AbstractMeterRegistryConfigurer - Class in ubic.gemma.core.metrics
AbstractMeterRegistryConfigurer(MeterRegistry) - Constructor for class ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer
AbstractNoopFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Class in ubic.gemma.persistence.service: Base class to use to pretend to offer filtering, but actually supporting no filterable properties.
AbstractNoopFilteringVoEnabledDao(Class<? extends O>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
AbstractOntologyResourceSimple - Class in ubic.gemma.core.ontology
AbstractOntologyResourceSimple(String, String) - Constructor for class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
AbstractPersister - Class in ubic.gemma.persistence.persister: Base class for Persister implementations.
AbstractPersister() - Constructor for class ubic.gemma.persistence.persister.AbstractPersister
AbstractPersister.Caches - Class in ubic.gemma.persistence.persister: Various caches to refer back to not-yet persisted entities (and thus not easily obtainable from the persistence context).
AbstractQueryFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Class in ubic.gemma.persistence.service: Partial implementation of FilteringVoEnabledDao based on the Hibernate Query API.
AbstractQueryFilteringVoEnabledDao(String, Class<O>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
AbstractService<O extends Identifiable> - Class in ubic.gemma.persistence.service: Base for all services handling DAO access.
AbstractService(BaseDao<O>) - Constructor for class ubic.gemma.persistence.service.AbstractService
AbstractSetListContainer - Class in ubic.gemma.web.persistence
AbstractSetListContainer() - Constructor for class ubic.gemma.web.persistence.AbstractSetListContainer
AbstractTask<C extends TaskCommand> - Class in ubic.gemma.core.tasks
AbstractTask() - Constructor for class ubic.gemma.core.tasks.AbstractTask
AbstractTask(C) - Constructor for class ubic.gemma.core.tasks.AbstractTask
AbstractVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Class in ubic.gemma.persistence.service: Created by tesarst on 01/06/17.
AbstractVoEnabledDao(Class<? extends O>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.AbstractVoEnabledDao
AbstractVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Class in ubic.gemma.persistence.service: Created by tesarst on 01/06/17.
AbstractVoEnabledService(BaseVoEnabledDao<O, VO>) - Constructor for class ubic.gemma.persistence.service.AbstractVoEnabledService
accept(StatementValueObject, U) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyUtils.StatementVisitor
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.HibernateSearchSource
accepts(SearchSettings) - Method in class ubic.gemma.core.search.source.OntologySearchSource
acceptsJson(HttpHeaders) - Static method in class ubic.gemma.rest.util.ExceptionMapperUtils
AccessDeniedExceptionMapper - Class in ubic.gemma.rest.providers: Map Spring Security's AccessDeniedException to a 403 Forbidden response.
AccessDeniedExceptionMapper() - Constructor for class ubic.gemma.rest.providers.AccessDeniedExceptionMapper
ACCURATE - ubic.gemma.model.common.search.SearchSettings.SearchMode: Prefer correctness to speed.
AclAdvice - Class in ubic.gemma.core.security.authorization.acl: For permissions modification to be triggered, the method name must match certain patterns, which include "create", or "remove".
AclAdvice(AclService, SessionFactory, ObjectIdentityRetrievalStrategy) - Constructor for class ubic.gemma.core.security.authorization.acl.AclAdvice
AclAfterCollectionCompSeqByArrayDesignFilter - Class in ubic.gemma.core.security.authorization.acl: For this particular AfterInvocationProvider, composite sequence authorization is determined based on the secured array design acl.
AclAfterCollectionCompSeqByArrayDesignFilter(AclService, List<Permission>) - Constructor for class ubic.gemma.core.security.authorization.acl.AclAfterCollectionCompSeqByArrayDesignFilter
AclAfterCollectionDataVectorByExpressionExperimentFilter - Class in ubic.gemma.core.security.authorization.acl: Filter collections of DesignElementDataVectors or DataVectorValueObjects based on the permissions of the associated ExpressionExperiment(s).
AclAfterCollectionDataVectorByExpressionExperimentFilter(AclService, List<Permission>) - Constructor for class ubic.gemma.core.security.authorization.acl.AclAfterCollectionDataVectorByExpressionExperimentFilter
AclAfterCompSeqByArrayDesignFilter - Class in ubic.gemma.core.security.authorization.acl
AclAfterCompSeqByArrayDesignFilter(AclService, List<Permission>) - Constructor for class ubic.gemma.core.security.authorization.acl.AclAfterCompSeqByArrayDesignFilter
AclCriteriaUtils - Class in ubic.gemma.persistence.util: Utilities for integrating ACLs with Hibernate Criteria API.
AclCriteriaUtils() - Constructor for class ubic.gemma.persistence.util.AclCriteriaUtils
AclQueryUtils - Class in ubic.gemma.persistence.util: Utilities for integrating ACL into Query.
AclQueryUtils() - Constructor for class ubic.gemma.persistence.util.AclQueryUtils
acquireReadLock(Cache, Object) - Static method in class ubic.gemma.persistence.util.CacheUtils
acquireWriteLock(Cache, Object) - Static method in class ubic.gemma.persistence.util.CacheUtils: Acquire an exclusive write lock on the given key in the cache.
add(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
add(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
add(O) - Method in class ubic.gemma.persistence.util.Slice: Deprecated.
add(SearchResult<T>) - Method in class ubic.gemma.core.search.SearchResultSet
add(ArrayDesign) - Method in class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
add(ArrayDesign, Map<CompositeSequence, BioSequence>) - Method in class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
add(ArrayDesign, Set<CompositeSequence>) - Method in class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
addAccession(NCBIGene2Accession) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
addAclParameters(Query, Class<? extends Securable>) - 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<? extends Securable>) - 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.
addAlternateName(Long, String) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
addAlternateName(Long, String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
addAuditEvent(EntityDelegator<? extends Auditable>, String, String, String) - Method in class ubic.gemma.web.remote.AuditController
addAuthority(UserGroup, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao
addAuthority(UserGroup, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
addAutoOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -auto option.
addAutoOption(Options, Class<? extends AuditEventType>) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -auto option for a specific AuditEventType.
addBatchOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -batchFormat and -batchOutputFile options.
addBinToQuery(String, Long, Long) - Static method in class ubic.gemma.persistence.util.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<BioAssayValueObject>) - 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
addCell(Long, String, Double, Double, Integer, Integer, Double) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
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: Will add the characteristic to the expression experiment and persist the changes.
addCoexpCorrelationDistribution(ExpressionExperiment, CoexpCorrelationDistribution) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService: For backfilling of the coexpression distributions from flat files - remove when no longer needed.
addCoexpCorrelationDistribution(ExpressionExperiment, CoexpCorrelationDistribution) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
addColumnName(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
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.
addContrast(Long, Long, Double, Double, Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
addContrast(Long, Long, Double, Double, Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
addContrastsFactorValue(long, String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
addContributer(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<String, String>, DoubleMatrix<String, String>, Integer, Boolean, boolean) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
addCountData(ExpressionExperiment, ArrayDesign, DoubleMatrix<String, String>, DoubleMatrix<String, String>, Integer, Boolean, 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
addDateOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -mdate option.
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 class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
addEmailAlert() - Method in interface ubic.gemma.core.job.SubmittedTask: Add email notification of task completion.
addEmailAlert(String) - Method in interface ubic.gemma.web.job.progress.ProgressStatusService: Set up an email alert for this job; an email will be sent when it has finished (or failed).
addEmailAlert(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl
addEmailNotification(CompletableFuture<? extends TaskResult>, EmailNotificationContext, Executor) - Method in interface ubic.gemma.core.job.executor.common.TaskPostProcessing
addEmailNotification(CompletableFuture<? extends TaskResult>, EmailNotificationContext, Executor) - Method in class ubic.gemma.core.job.executor.common.TaskPostProcessingImpl
addEntities(Collection<Long>) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
addEntity(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
addEntity(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray: Add the data set to the list of those which are in the array.
addErrorObject(Object, Exception) - Method in class ubic.gemma.core.util.AbstractCLI: Add an error object based on an exception.
addErrorObject(Object, String) - Method in class ubic.gemma.core.util.AbstractCLI: Add an error object without a cause stacktrace.
addErrorObject(Object, String, Throwable) - Method in class ubic.gemma.core.util.AbstractCLI: Add an error object with a stacktrace to indicate failure in a batch processing.
addErrorsField(String, String) - Method in class ubic.gemma.rest.util.WellComposedErrorBody: Adds a new field into the errors array property.
addEventsToMap(Map<Long, Collection<AuditEvent>>, Long, AuditEvent) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
addExceptionFields(WellComposedErrorBody, Throwable) - Static method in class ubic.gemma.rest.util.WellComposedErrorBody: Adds descriptive values from the throwable object to the instance of WellComposedErrorBody.
addExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager
addExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
addExperimentSet(SessionBoundExpressionExperimentSetValueObject, boolean) - Method in interface ubic.gemma.web.persistence.SessionListManager
addExperimentSet(SessionBoundExpressionExperimentSetValueObject, boolean) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
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
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
addFactorValues(ExpressionExperiment, Map<BioMaterial, FactorValue>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Intended with the case of a continuous factor being added.
addFactorValues(ExpressionExperiment, Map<BioMaterial, FactorValue>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
addFactorValueTo(Collection<Long>, EntityDelegator<FactorValue>) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController: AJAX
addGene(DifferentialExpressionGenesConditionsValueObject.DiffExGene) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
addGene(GeneProductValueObject, GeneValueObject) - Method in class ubic.gemma.core.analysis.sequence.GeneMappingSummary
addGeneSet(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager
addGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
addGeneSet(SessionBoundGeneSetValueObject, boolean) - Method in interface ubic.gemma.web.persistence.SessionListManager
addGeneSet(SessionBoundGeneSetValueObject, boolean) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
addGroupAndUserNameRestriction(boolean, boolean) - Static method in class ubic.gemma.persistence.util.EntityUtils: Have to add 'and' to start of this if it's a later clause Author: nicolas with fixes to generalize by paul, same code appears in the PhenotypeAssociationDaoImpl
addGroupAuthority(UserGroup, String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
addGroupAuthority(String, GrantedAuthority) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
addImage(Image) - Method in class ubic.gemma.core.image.aba.ImageSeries
addImageSeries(ImageSeries) - Method in class ubic.gemma.core.image.aba.AbaGene
addInteractionToInclude(Collection<ExperimentalFactor>) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
addInteractionToInclude(ExperimentalFactor...) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
ADDITIONAL_PIPELINE_CONFIGURATIONS - ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType
addMatrices(ExpressionDataDoubleMatrix, ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil: Add two matrices.
addMessage(HttpServletRequest, String, Object[]) - Method in class ubic.gemma.web.controller.BaseController
addNewObjects(Collection<? extends Auditable>) - 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 non-administrators
addNumPublications(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
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<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
addProbes(ArrayDesign, Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
addProbes(ArrayDesign, Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
addProbes(ArrayDesign, Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
addProperty(String, Object) - Method in class ubic.gemma.web.util.ConfigurationCookie
addQuantitationType(GeoPlatform, String, Integer) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
addRawVectors(ExpressionExperiment, Collection<RawExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Used when we want to add data for a quantitation type.
addRawVectors(ExpressionExperiment, Collection<RawExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
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.
addRestrictions(Criteria, Gene2GOAssociation) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, Contact) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, Characteristic) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, QuantitationType) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, ArrayDesign) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, BioAssay) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, BioMaterial) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, ExperimentalFactor) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, BioSequence) - Static method in class ubic.gemma.persistence.util.BusinessKey: Note: The finder has to do the additional checking for equality of sequence and/or database entry - we don't know until we get the sequences.
addRestrictions(Criteria, Chromosome) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, Gene, boolean) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(Criteria, Taxon) - Static method in class ubic.gemma.persistence.util.BusinessKey
addRestrictions(DetachedCriteria, DatabaseEntry) - Static method in class ubic.gemma.persistence.util.BusinessKey
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(ArrayDesign) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignParser: Deprecated.
addResult(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
addResult(BlatResult) - Method in class ubic.gemma.core.loader.genome.BlatResultParser
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<GeoSample>) - 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
addSessionGroup(SessionBoundGeneSetValueObject, Boolean) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: * AJAX adds the gene group to the session, used by SessionGeneGroupStore and SessionDatasetGroupStore sets the groups taxon value and reference.
addSessionGroup(SessionBoundExpressionExperimentSetValueObject, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX adds the Expression Experiment group to the session
addSessionGroups(Collection<SessionBoundGeneSetValueObject>, Boolean) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: Deprecated.
addSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: Deprecated.
addSet(GemmaSessionBackedValueObject, boolean) - Method in class ubic.gemma.web.persistence.AbstractSetListContainer: Sets the reference (generates an id and assumes this group was made as a result of a modification for the type value) for the group then adds it to the session-bound list(s) for session-bound groups
addSubSeries(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addSubset(GeoSubset) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
addSuccessObject(Object) - Method in class ubic.gemma.core.util.AbstractCLI
addSuccessObject(Object, String) - Method in class ubic.gemma.core.util.AbstractCLI: Add a success object to indicate success in a batch processing.
addThreadsOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -threads option.
addToCache(Long, Long, Collection<DoubleVectorValueObject>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCache
addToCache(Long, Long, Collection<DoubleVectorValueObject>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
addToCache(Collection<DiffExprGeneSearchResult>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
addToCache(Collection<DiffExprGeneSearchResult>) - 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.util.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
addToScanProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
addToSeriesTypes(GeoSeries.SeriesType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
addToSummary(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<DifferentialExpressionValueObject>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
addToTopHitsCache(ExpressionAnalysisResultSet, List<DifferentialExpressionValueObject>) - 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<? extends Auditable>) - 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<? extends AuditEventType>, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
addUpdateEvent(Auditable, Class<? extends AuditEventType>, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
addUpdateEvent(Auditable, Class<? extends AuditEventType>, String, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
addUpdateEvent(Auditable, Class<? extends AuditEventType>, String, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
addUpdateEvent(Auditable, Class<? extends AuditEventType>, 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<? extends AuditEventType>, String, String, Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
addUpdateEvent(Auditable, Class<? extends AuditEventType>, String, Throwable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService: Add an update audit event with an exception.
addUpdateEvent(Auditable, Class<? extends AuditEventType>, 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
addUserAndGroupParameters(SQLQuery, SessionFactory) - Static method in class ubic.gemma.persistence.util.EntityUtils: Populates parameters in query created using addGroupAndUserNameRestriction(boolean, boolean).
addUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX adds the experiment group to the session
addUserAndSessionGroups(Collection<GeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX adds the gene group to the session
addUserToGroup(UserGroup, User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
addUserToGroup(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
addUserToGroup(String, String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
addUserToGroup(String, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
addValue(GeoSample, Integer, String, Object) - 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
AFFX - ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
AFFY_COLLAPSED - ubic.gemma.model.genome.biosequence.SequenceType: Represents Affymetrix probe sequences that have been "collapsed" or combined into a single sequence.
AFFY_PROBE - ubic.gemma.model.genome.biosequence.SequenceType: Represents a single probe sequence for Affymetrix reporters
AFFY_TARGET - ubic.gemma.model.genome.biosequence.SequenceType: Represents the target sequence provided by the manufacturer.
AffyChipTypeExtractor - Class in ubic.gemma.core.loader.expression.arrayDesign: Extract the chip type from Affymetrix CEL files.
AffyChipTypeExtractor() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractor
AffyDataFromCelCli - Class in ubic.gemma.core.apps: Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.
AffyDataFromCelCli() - Constructor for class ubic.gemma.core.apps.AffyDataFromCelCli
AffyPowerToolsProbesetSummarize - Class in ubic.gemma.core.loader.expression
AffyProbeCollapseCli - Class in ubic.gemma.core.apps: Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
AffyProbeCollapseCli() - Constructor for class ubic.gemma.core.apps.AffyProbeCollapseCli
AffyProbeNameFilter - Class in ubic.gemma.core.analysis.preprocess.filter
AffyProbeNameFilter(AffyProbeNameFilter.Pattern[]) - Constructor for class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter
AffyProbeNameFilter.Pattern - Enum 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
afterCompletion(PrintWriter) - Method in class ubic.gemma.core.util.BashCompletionGenerator
afterCompletion(PrintWriter) - Method in interface ubic.gemma.core.util.CompletionGenerator
afterPropertiesSet() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
afterPropertiesSet() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
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.search.source.HibernateSearchSource
afterPropertiesSet() - Method in class ubic.gemma.core.util.BuildInfo
afterPropertiesSet() - Method in class ubic.gemma.core.util.ConfigurationLinter
afterPropertiesSet() - Method in class ubic.gemma.core.util.DummyMailSender
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
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.coexpression.CoexpressionCacheImpl: Initialize the cache; if it already exists it will not be recreated.
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
afterPropertiesSet() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
afterPropertiesSet() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
afterPropertiesSet() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
afterPropertiesSet() - Method in class ubic.gemma.web.feed.FeedReader
afterPropertiesSet() - Method in class ubic.gemma.web.util.CacheMonitorImpl
age - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
agent - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
AGILENT_DATE_FORMAT - 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
ajaxLoginCheck(HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
ajaxSearch(SearchSettingsValueObject) - Method in interface ubic.gemma.web.controller.GeneralSearchController: AJAX-flavoured search.
ajaxSearch(SearchSettingsValueObject) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl
Alias() - Constructor for class ubic.gemma.persistence.util.Subquery.Alias
ALIGNMENT_METADATA - ubic.gemma.core.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 - ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode
ALL_PHENOCARTA_ANNOTATIONS_FILE_LOCATION - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
AllenBrainAtlasService - Interface in ubic.gemma.core.image.aba
AllenBrainAtlasServiceImpl - Class in ubic.gemma.core.image.aba: Acts as a convenient front end to the Allen Brain Atlas REST (web) services Used the ABAApi.java as the original template for this Service (found in ABA demo code).
AllenBrainAtlasServiceImpl() - Constructor for class ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl
allowPositionalArguments() - Method in class ubic.gemma.core.util.AbstractCLI
allowPositionalArguments() - Method in interface ubic.gemma.core.util.CLI: Indicate if this CLI allows positional arguments.
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.
AlreadyExistsInSystemException - Exception 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 ubic.gemma.core.loader.util.AlreadyExistsInSystemException
AlreadyExistsInSystemException(String, Object) - Constructor for exception ubic.gemma.core.loader.util.AlreadyExistsInSystemException
AlternateName - Class in ubic.gemma.model.expression.arrayDesign
AlternateName() - Constructor for class ubic.gemma.model.expression.arrayDesign.AlternateName: No-arg constructor added to satisfy javabean contract
AlternateName.Factory - Class in ubic.gemma.model.expression.arrayDesign
alternativeToProperAffyPlatform(String) - Static method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
AMOUNT - ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Referring to a measured or derived "amount", indicating the relative or absolute level of something.
Analysis - Class in ubic.gemma.model.analysis: An analysis of one or more Investigations.
Analysis() - Constructor for class ubic.gemma.model.analysis.Analysis: No-arg constructor added to satisfy javabean contract
ANALYSIS - ubic.gemma.core.apps.GemmaCLI.CommandGroup
AnalysisDao<T extends SingleExperimentAnalysis> - Interface in ubic.gemma.persistence.service.analysis
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 extends AnalysisResult> - 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 extends AnalysisResult,O extends AnalysisResultSet<K>> - Interface in ubic.gemma.persistence.service.analysis: Generic DAO for manipulating AnalysisResultSet.
AnalysisResultSetService<K extends AnalysisResult,O extends AnalysisResultSet<K>> - Interface in ubic.gemma.persistence.service.analysis: Interface for services providing AnalysisResultSet.
analysisResultSetsToString(Collection<ExpressionAnalysisResultSet>, Map<Long, String[]>, StringBuilder) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
analysisResultSetsToString(Collection<ExpressionAnalysisResultSet>, Map<Long, String[]>, StringBuilder) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
AnalysisResultSetsWebService - Class in ubic.gemma.rest: Endpoint for AnalysisResultSet
AnalysisResultSetsWebService() - Constructor for class ubic.gemma.rest.AnalysisResultSetsWebService
analysisResultSetToString(ExpressionAnalysisResultSet, Map<Long, String[]>, StringBuilder, Map<Long, StringBuilder>, List<DifferentialExpressionAnalysisResult>) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
analysisResultSetToString(ExpressionAnalysisResultSet, Map<Long, String[]>, StringBuilder, Map<Long, StringBuilder>, List<DifferentialExpressionAnalysisResult>) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
AnalysisResultSetValueObject<K extends AnalysisResult,R extends AnalysisResultSet<K>> - Class in ubic.gemma.model.analysis: Exposes an AnalysisResultSet to the public API.
AnalysisResultSetValueObject() - Constructor for class ubic.gemma.model.analysis.AnalysisResultSetValueObject
AnalysisResultSetValueObject(R) - Constructor for class ubic.gemma.model.analysis.AnalysisResultSetValueObject
AnalysisResultValueObject<A extends AnalysisResult> - 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
AnalysisSelectionAndExecutionService - Interface in ubic.gemma.core.analysis.expression.diff
AnalysisSelectionAndExecutionServiceImpl - Class in ubic.gemma.core.analysis.expression.diff: A differential expression analysis tool that executes the appropriate analysis based on the number of experimental factors and factor values, as well as the block design.
AnalysisSelectionAndExecutionServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
AnalysisService<T extends Analysis> - 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
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 extends Analysis> - Class in ubic.gemma.model.analysis
AnalysisValueObject() - Constructor for class ubic.gemma.model.analysis.AnalysisValueObject
AnalysisValueObject(T) - Constructor for class ubic.gemma.model.analysis.AnalysisValueObject
AnalyticsApplicationEventListener - Class in ubic.gemma.rest.providers: Register AnalyticsRequestEventListener
AnalyticsApplicationEventListener() - Constructor for class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
AnalyticsProvider - Interface in ubic.gemma.rest.analytics: Interface for analytics providers.
AnalyticsRequestEventListener - Class in ubic.gemma.rest.providers: Request event listener that publishes an event when a request is finished.
AnalyticsRequestEventListener(String, Date, AnalyticsProvider) - Constructor for class ubic.gemma.rest.providers.AnalyticsRequestEventListener
analyze() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis: Main entry point.
analyze(Collection<Long>) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService
analyze(Collection<Long>) - Method in class ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceImpl
analyze(ExpressionExperiment, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
analyze(ExpressionExperiment, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
analyze(ExpressionExperimentSubSet, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
analyze(ExpressionExperimentSubSet, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
analyzeResultSets(Collection<Long>) - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
AnchorTagUtil - Class in ubic.gemma.web.util: Used to generate hyperlinks to various things in Gemma.
AnchorTagUtil() - Constructor for class ubic.gemma.web.util.AnchorTagUtil
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<T>, Filter.Operator, Collection<T>) - 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<T>, Filter.Operator, Collection<T>, String) - Method in class ubic.gemma.persistence.util.Filters
and(String, String, Class<T>, 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<T>, Filter.Operator, T, String) - Method in class ubic.gemma.persistence.util.Filters
and(String, String, Class<T>, Filter.Operator, Subquery) - Method in class ubic.gemma.persistence.util.Filters
and(String, String, Class<T>, Filter.Operator, Subquery, String) - Method in class ubic.gemma.persistence.util.Filters
and(IdArray) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
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.
andSet(IdArray) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
andThen(Sort) - Method in class ubic.gemma.persistence.util.Sort: Add a next sort.
annot(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
ANNOT_DATA_DIR - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
Annotation() - Constructor for class ubic.gemma.core.ontology.FactorValueOntologyUtils.Annotation
ANNOTATION_FILE_DIRECTORY_NAME - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
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
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
AnnotationController - Class in ubic.gemma.web.controller.expression.experiment: Controller for methods involving annotation of experiments (and potentially other things); delegates to OntologyService and the CharacteristicService.
AnnotationController() - Constructor for class ubic.gemma.web.controller.expression.experiment.AnnotationController
AnnotationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
AnnotationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationEvent
AnnotationIds() - Constructor for class ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
annotationOf - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Inverse of TGFVO.hasAnnotation.
AnnotationSearchResultValueObject() - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject
AnnotationsWebService - Class in ubic.gemma.rest: RESTful interface for annotations.
AnnotationsWebService() - Constructor for class ubic.gemma.rest.AnnotationsWebService: Required by spring
AnnotationsWebService(OntologyService, SearchService, CharacteristicService, ExpressionExperimentService, DatasetArgService, TaxonArgService) - Constructor for class ubic.gemma.rest.AnnotationsWebService: Constructor for service autowiring
AnnotationsWebService.AnnotationSearchResultValueObject - Class in ubic.gemma.rest
AnnotationValueObject - Class in ubic.gemma.model.common.description
AnnotationValueObject() - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationValueObject(Long) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationValueObject(String, String, String, String, Class<?>) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationValueObject(Characteristic) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationValueObject(Characteristic, Class<?>) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
AnnotationWithUsageStatisticsValueObject(Characteristic, Long, Set<DatasetsWebService.OntologyTermValueObject>) - Constructor for class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject
antibody - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
anyPublicMethod() - Method in class ubic.gemma.core.util.Pointcuts: A public method.
AOI_ALIAS - Static variable in class ubic.gemma.persistence.util.AclQueryUtils: Alias used by AclQueryUtils.formAclRestrictionClause(String, int) and AclQueryUtils.formNativeAclJoinClause(String) for the object identity AclObjectIdentity and the owner identity AclSid.
ApiInfoValueObject(String, OpenAPI, URI, List<ExternalDatabaseValueObject>) - Constructor for class ubic.gemma.rest.RootWebService.ApiInfoValueObject
APP_NAME - Static variable in class ubic.gemma.web.util.Constants
appearsInMultipleSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
append(LoggingEvent) - Method in class ubic.gemma.core.job.executor.common.ProgressUpdateAppender
append(LoggingEvent) - Method in class ubic.gemma.web.logging.SlackAppender
appendBaseHeader(ExpressionExperiment, boolean, StringBuffer) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils: Appends base header information (about the experiment) to a file.
appendBaseHeader(ExpressionExperiment, String, StringBuffer) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils: Appends base header information (about the experiment) to a file.
apply() - Method in class ubic.gemma.core.logging.log4j.Log4jConfigurer
apply() - Method in interface ubic.gemma.core.logging.LoggingConfigurer: Apply pending changes to the configuration from previous LoggingConfigurer.configureAllLoggers(int) and LoggingConfigurer.configureLogger(String, int) invocations.
ArchiveFetcher - Interface in ubic.gemma.core.loader.util.fetcher: Interface defining a class that downloads archives and unpacks them.
Arg<T> - Interface in ubic.gemma.rest.util.args
ArgUtils - Class in ubic.gemma.rest.util: Utilities for working with Arg.
ArgUtils() - Constructor for class ubic.gemma.rest.util.ArgUtils
aroundWriteTo(WriterInterceptorContext) - Method in class ubic.gemma.rest.providers.CacheControlHeaderDecorator
aroundWriteTo(WriterInterceptorContext) - Method in class ubic.gemma.rest.providers.GzipHeaderDecorator
ARRAY_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint: The local name of the expected request.
ARRAY_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ArrayDesignUsedEndpoint: The local name of the expected request.
arrayCGH - 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
ArrayDesignAddCommand - Class in ubic.gemma.web.controller.expression.arrayDesign
ArrayDesignAddCommand() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
ArrayDesignAlternativePopulateCli - Class in ubic.gemma.core.apps: This only needs to be re-run when the mappings change.
ArrayDesignAlternativePopulateCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
ArrayDesignAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: An event involving the analysis of an ArrayDesign
ArrayDesignAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent
ArrayDesignAnnotationFileCli - Class in ubic.gemma.core.apps: Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or merged into another AD.
ArrayDesignAnnotationFileCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
ArrayDesignAnnotationService - Interface in ubic.gemma.core.analysis.service: Methods to generate annotations for array designs, based on information already in the database.
ArrayDesignAnnotationService.OutputType - Enum in ubic.gemma.core.analysis.service
ArrayDesignAnnotationServiceImpl - Class in ubic.gemma.core.analysis.service
ArrayDesignAnnotationServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
ArrayDesignAuditTrailCleanupCli - Class in ubic.gemma.core.apps: work in progress
ArrayDesignAuditTrailCleanupCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
ArrayDesignBioSequenceDetachCli - Class in ubic.gemma.core.apps: Remove all associations that this array design has with BioSequences.
ArrayDesignBioSequenceDetachCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
ArrayDesignBlatCli - Class in ubic.gemma.core.apps: Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
ArrayDesignBlatCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignBlatCli
ArrayDesignController - Interface in ubic.gemma.web.controller.expression.arrayDesign: Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
ArrayDesignControllerImpl - Class in ubic.gemma.web.controller.expression.arrayDesign: Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
ArrayDesignControllerImpl() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
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
ArrayDesignFormController - Class in ubic.gemma.web.controller.expression.arrayDesign: Controller for editing basic information about array designs.
ArrayDesignFormController() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
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
ArrayDesignGroupingTag - Class in ubic.gemma.web.taglib.arrayDesign: For display of information about array designs that subsume or are subsumed.
ArrayDesignGroupingTag() - Constructor for class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
ArrayDesignHtmlUtil - Class in ubic.gemma.web.taglib.arrayDesign: Yes, this is used by the ArrayDesignController, but should be phased out.
ArrayDesignHtmlUtil() - Constructor for class ubic.gemma.web.taglib.arrayDesign.ArrayDesignHtmlUtil
ArrayDesignIdentifierByNameEndpoint - Class in ubic.gemma.web.services: array design short name -> return matching array design identifier
ArrayDesignIdentifierByNameEndpoint() - Constructor for class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint
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(BlatResultService, BlatAssociationService, ArrayDesignService, CompositeSequenceService) - Constructor for class ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl
ArrayDesignMapSummaryCli - Class in ubic.gemma.core.apps: CLI for ArrayDesignMapSummaryService
ArrayDesignMapSummaryCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
ArrayDesignMergeCli - Class in ubic.gemma.core.apps: make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees Separate operations: For an EE, Remap DesignElement references to old array designs to new one, and old BioAssay AD refs to new one.
ArrayDesignMergeCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignMergeCli
ArrayDesignMergeEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
ArrayDesignMergeEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignMergeEvent
ArrayDesignMergeHelperService - Interface in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignMergeHelperServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignMergeHelperServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperServiceImpl
ArrayDesignMergeService - Interface in ubic.gemma.core.loader.expression.arrayDesign: Make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees
ArrayDesignMergeServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignMergeServiceImpl(ArrayDesignService, ArrayDesignReportService, ArrayDesignMergeHelperService) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceImpl
ArrayDesignParser - Class in ubic.gemma.core.loader.expression.arrayDesign: Deprecated.
ArrayDesignParser() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignParser: Deprecated.
ArrayDesignPersister - Class in ubic.gemma.persistence.persister: This class handles persisting array designs.
ArrayDesignPersister() - Constructor for class ubic.gemma.persistence.persister.ArrayDesignPersister
ArrayDesignProbeCleanupCLI - Class in ubic.gemma.core.apps: Delete design elements (probes) that are invalid for one reason or another.
ArrayDesignProbeCleanupCLI() - Constructor for class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
ArrayDesignProbeMapperCli - Class in ubic.gemma.core.apps: Process the blat results for an array design to map them onto genes.
ArrayDesignProbeMapperCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
ArrayDesignProbeMapperController - Class in ubic.gemma.web.controller.expression.arrayDesign: A controller to run array design probe mapper either locally or in a space.
ArrayDesignProbeMapperController() - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignProbeMapperController
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, BlatResultService, CompositeSequenceService, ExpressionDataFileService, GeneProductService, GeneService, Persister, TaskExecutor) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
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
ArrayDesignProbeRenamerCli - Class in ubic.gemma.core.apps: Deprecated.
renaming probes is not a good idea in general
ArrayDesignProbeRenamerCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
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
ArrayDesignPropertyEditor - Class in ubic.gemma.web.propertyeditor: Used to convert ArrayDesigns from and into strings for display in forms.
ArrayDesignPropertyEditor(ArrayDesignService) - Constructor for class ubic.gemma.web.propertyeditor.ArrayDesignPropertyEditor
ArrayDesignRepeatAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
ArrayDesignRepeatAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignRepeatAnalysisEvent
ArrayDesignRepeatScanCli - Class in ubic.gemma.core.apps: Runs repeatmasker on array designs.
ArrayDesignRepeatScanCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
ArrayDesignRepeatScanController - Class in ubic.gemma.web.controller.analysis.sequence: A controller to run array design repeat scan either locally or in a space.
ArrayDesignRepeatScanController() - Constructor for class ubic.gemma.web.controller.analysis.sequence.ArrayDesignRepeatScanController
ArrayDesignRepeatScanTask - Interface in ubic.gemma.web.tasks.analysis.sequence
ArrayDesignRepeatScanTaskCommand - Class in ubic.gemma.web.tasks.analysis.sequence: A command object to be used by spaces.
ArrayDesignRepeatScanTaskCommand(String, ArrayDesign) - Constructor for class ubic.gemma.web.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.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
ArrayDesignRepeatScanTaskImpl - Class in ubic.gemma.web.tasks.analysis.sequence: An array design repeat scan spaces task
ArrayDesignRepeatScanTaskImpl() - Constructor for class ubic.gemma.web.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
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, Persister) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
ArrayDesignSequenceAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: The sequence alignment analysis of an ArrayDesign
ArrayDesignSequenceAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent
ArrayDesignSequenceAssociationCli - Class in ubic.gemma.core.apps: Attach sequences to array design, fetching from BLAST database if requested.
ArrayDesignSequenceAssociationCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
ArrayDesignSequenceManipulatingCli - Class in ubic.gemma.core.apps: Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.
ArrayDesignSequenceManipulatingCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
ArrayDesignSequenceProcessingService - Interface in ubic.gemma.core.loader.expression.arrayDesign
ArrayDesignSequenceProcessingServiceImpl - Class in ubic.gemma.core.loader.expression.arrayDesign: Handles collapsing the sequences, attaching sequences to DesignElements, either from provided input or via a fetch.
ArrayDesignSequenceProcessingServiceImpl(ArrayDesignReportService, ArrayDesignService, BioSequenceService, ExternalDatabaseService, Persister) - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
ArrayDesignSequenceRemoveEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Used to indicate that all associations that this array design has with BioSequences have been removed.
ArrayDesignSequenceRemoveEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent
ArrayDesignSequenceUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: The updating of the sequences associated with an ArrayDesign
ArrayDesignSequenceUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceUpdateEvent
arrayDesignService - Variable in class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
arrayDesignService - Variable in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
ArrayDesignService - Interface in ubic.gemma.persistence.service.expression.arrayDesign
ArrayDesignServiceImpl - Class in ubic.gemma.persistence.service.expression.arrayDesign
ArrayDesignServiceImpl(ArrayDesignDao, AuditEventDao) - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
ArrayDesignsForExperimentCache - Class in ubic.gemma.persistence.util: Used to hold information for matching to a new experiment, during persisting.
ArrayDesignsForExperimentCache() - Constructor for class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
ArrayDesignSubsumeCheckEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
ArrayDesignSubsumeCheckEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent
ArrayDesignSubsumptionTesterCli - Class in ubic.gemma.core.apps: Test two array designs to see if one subsumes the other, and if so update their information.
ArrayDesignSubsumptionTesterCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
ArrayDesignUsedEndpoint - Class in ubic.gemma.web.services: Used for determining which array designs were used in a given expression experiment (EE)
ArrayDesignUsedEndpoint() - Constructor for class ubic.gemma.web.services.ArrayDesignUsedEndpoint
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(ArrayDesignValueObject) - Constructor for class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Copies constructor from other ArrayDesignValueObject
ArrayDesignValueObjectExt - Class in ubic.gemma.web.controller.expression.arrayDesign: Extended value object to carry more data to client.
ArrayDesignValueObjectExt(ArrayDesignValueObject) - Constructor for class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
ArrayDesignWithUsageStatisticsValueObject(ArrayDesignValueObject, Long, Long) - Constructor for class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
ArrayExpressUtil - Class in ubic.gemma.core.loader.expression.arrayExpress.util
ArrayExpressUtil() - Constructor for class ubic.gemma.core.loader.expression.arrayExpress.util.ArrayExpressUtil
ASC - ubic.gemma.persistence.util.Sort.Direction
ASC - ubic.gemma.rest.util.args.SortArg.Sort.Direction
asDoubleArrayNegRanks() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
asDoubleArrayPosRanks() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
asFile() - Method in class ubic.gemma.model.common.description.LocalFile: Attempt to create a java.io.File from the local URI.
asIntArrayNeg() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
asIntArrayPos() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
asRegularGoId(String) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
asRegularGoId(OntologyTerm) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
asRegularGoId(Characteristic) - Static method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
AssayViewTag - Class in ubic.gemma.web.taglib.expression.experiment: Used to display table of biomaterials and bioassays.
AssayViewTag() - Constructor for class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
assemble(Serializable, Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
assignSequencesToDesignElements(Collection<CompositeSequence>, File) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Associate sequences with an array design.
assignSequencesToDesignElements(Collection<CompositeSequence>, File) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
assignSequencesToDesignElements(Collection<CompositeSequence>, InputStream) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
assignSequencesToDesignElements(Collection<CompositeSequence>, InputStream) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl: Associate sequences with an array design.
assignSequencesToDesignElements(Collection<CompositeSequence>, Collection<BioSequence>) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Associate sequences with an array design.
assignSequencesToDesignElements(Collection<CompositeSequence>, Collection<BioSequence>) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
associateBatchFactor(Map<BioMaterial, T>, Map<T, FactorValue>) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Associate dates with bioassays and any new factors with the biomaterials.
associateBatchFactor(Map<BioMaterial, T>, Map<T, FactorValue>) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
asUser() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
AsyncFactoryBean<T> - Interface in ubic.gemma.persistence.util: Async extension of the FactoryBean interface.
AsyncFactoryBeanUtils - Class in ubic.gemma.persistence.util: Utilities for manipulating async factory beans.
AsyncFactoryBeanUtils() - Constructor for class ubic.gemma.persistence.util.AsyncFactoryBeanUtils
attachCriteria(Criteria, Characteristic, String) - Static method in class ubic.gemma.persistence.util.BusinessKey: Restricts the query to the provided OntologyEntry.
attachCriteria(Criteria, DatabaseEntry, String) - Static method in class ubic.gemma.persistence.util.BusinessKey: Restricts query to the given DatabaseEntry association
attachCriteria(Criteria, BioSequence, String) - Static method in class ubic.gemma.persistence.util.BusinessKey: Restricts the query to the provided BioSequence.
attachCriteria(Criteria, Gene, String) - Static method in class ubic.gemma.persistence.util.BusinessKey: Restricts the query to the provided Gene.
attachCriteria(Criteria, PhysicalLocation, String) - Static method in class ubic.gemma.persistence.util.BusinessKey
attachCriteria(Criteria, Taxon, String) - Static method in class ubic.gemma.persistence.util.BusinessKey: Restricts query to the given Taxon.
attachCriteria(DetachedCriteria, DatabaseEntry, String) - Static method in class ubic.gemma.persistence.util.BusinessKey
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.
Auditable - Interface in ubic.gemma.model.common: Created by tesarst on 07/03/17.
AuditableObject - Class in ubic.gemma.core.analysis.report
AuditableObject() - Constructor for class ubic.gemma.core.analysis.report.AuditableObject
AuditAction - Enum in ubic.gemma.model.common.auditAndSecurity
AuditAdvice - Class in ubic.gemma.core.security.audit: Manage audit trails on objects.
AuditAdvice() - Constructor for class ubic.gemma.core.security.audit.AuditAdvice
AuditController - Class in ubic.gemma.web.remote: This is required solely for exposing auditables to remote services would try to marshall the abstract class Auditable.
AuditController() - Constructor for class ubic.gemma.web.remote.AuditController
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
auditEvents2SampleRemovedFlags(Collection<AuditEvent>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
auditEventService - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
AuditEventService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
AuditEventServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
AuditEventServiceImpl(AuditEventDao) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
AuditEventType - Class in ubic.gemma.model.common.auditAndSecurity.eventType
AuditEventType() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType
AuditEventValueObject - Class in ubic.gemma.model.common.auditAndSecurity
AuditEventValueObject() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject: Required when using the class as a spring bean.
AuditEventValueObject(Long) - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
AuditEventValueObject(AuditEvent) - Constructor for class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
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
auditTrailService - Variable in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
auditTrailService - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
AuditTrailService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity: Create and manipulate audit trails.
AuditTrailServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
AuditTrailServiceImpl(AuditTrailDao, AuditEventDao, GenericCuratableDao, UserManager, SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
AUTH_KEY - Static variable in class ubic.gemma.web.listener.UserCounterListener
authenticate() - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
AuthenticationBasedUserIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Strategy for the user ID that uses the authentication object from the SecurityContextHolder.
AuthenticationBasedUserIdRetrievalStrategy(AuthenticationTrustResolver) - Constructor for class ubic.gemma.rest.analytics.ga4.AuthenticationBasedUserIdRetrievalStrategy
AuthenticationExceptionMapper - Class in ubic.gemma.rest.providers: Handles Spring Security AuthenticationException by producing a 403 Forbidden response.
AuthenticationExceptionMapper() - Constructor for class ubic.gemma.rest.providers.AuthenticationExceptionMapper
authorities() - Method in annotation type ubic.gemma.rest.annotations.CacheControl: Authorities to whom this cache directive applies.
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.
AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
avoidDownload - Variable in class ubic.gemma.core.loader.util.fetcher.FtpFetcher

B

BAC - ubic.gemma.model.genome.biosequence.SequenceType
BALANCE - ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.NormalizationMethod
BALANCED - ubic.gemma.model.common.search.SearchSettings.SearchMode: Normal search mode with trade-offs to make it usable.
BASE_GO_URI - Static variable in interface ubic.gemma.core.ontology.providers.GeneOntologyService
BASE_METADATA - ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType
BaseCodeOntologySearchException - Exception in ubic.gemma.core.search: Exception that wraps a baseCode OntologySearchException.
BaseCodeOntologySearchException(OntologySearchException) - Constructor for exception ubic.gemma.core.search.BaseCodeOntologySearchException
BaseController - Class in ubic.gemma.web.controller: Extend this to create a simple Single or MultiActionController; includes configuration for sending email and setting messages in the session.
BaseController() - Constructor for class ubic.gemma.web.controller.BaseController
BaseDao<T> - Interface in ubic.gemma.persistence.service: Interface that supports basic CRUD operations.
BaseExpressionDataMatrix<T> - Class in ubic.gemma.core.datastructure.matrix: Base class for ExpressionDataMatrix implementations.
BaseExpressionDataMatrix() - Constructor for class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
BaseFormController - Class in ubic.gemma.web.controller: Deprecated.
SimpleFormController is deprecated, use annotations-based GET/POST mapping instead.
BaseFormController() - Constructor for class ubic.gemma.web.controller.BaseFormController: Deprecated.
BaseImmutableService<O extends Identifiable> - Interface in ubic.gemma.persistence.service: Base service class for an immutable entity.
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 extends Identifiable> - Interface in ubic.gemma.persistence.service: Interface for read-only services.
BaseScanDateExtractor - Class in ubic.gemma.core.analysis.preprocess.batcheffects
BaseScanDateExtractor() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
BaseService<O extends Identifiable> - Interface in ubic.gemma.persistence.service: Interface that supports basic CRUD operations.
BaseValueObject - Class in ubic.gemma.model
BaseValueObject() - Constructor for class ubic.gemma.model.BaseValueObject
BaseVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Interface in ubic.gemma.persistence.service: Created by tesarst on 01/06/17.
BaseVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Interface in ubic.gemma.persistence.service: Created by tesarst on 01/06/17.
BashCompletionGenerator - Class in ubic.gemma.core.util
BashCompletionGenerator(Set<String>) - Constructor for class ubic.gemma.core.util.BashCompletionGenerator
BasicLineMapParser<K,T> - Class in ubic.gemma.core.loader.util.parser: A line parser that produces a Map instead of a Collection.
BasicLineMapParser() - Constructor for class ubic.gemma.core.loader.util.parser.BasicLineMapParser
BasicLineParser<T> - Class in ubic.gemma.core.loader.util.parser: A simple LineParser implementation that doesn't do anything.
BasicLineParser() - Constructor for class ubic.gemma.core.loader.util.parser.BasicLineParser
batch - ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode
batch(List<T>, 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 - 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 - ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that there is a batch effect.
BATCH_EFFECT_UNDETERMINED_FAILURE - ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that all information necessary is present, but the batch effect could not be determined.
BATCH_FACTOR_CATEGORY_NAME - Static variable in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
BATCH_FACTOR_CATEGORY_NAME - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
BATCH_FACTOR_CATEGORY_URI - Static variable in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
BATCH_FACTOR_CATEGORY_URI - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
BATCH_FACTOR_NAME - Static variable in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
BATCH_FACTOR_NAME - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
BATCH_FACTOR_NAME_PREFIX - Static variable in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
BATCH_FACTOR_NAME_PREFIX - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
BatchConfound - Class in ubic.gemma.core.analysis.preprocess.batcheffects: Represents a summary of a batch effect confound.
BatchConfound() - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
BatchConfound(BioAssaySet, ExperimentalFactor, double, int, double, int) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
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
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(BatchInformationFetchingEvent, boolean, boolean) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
BatchEffectDetails.BatchEffectStatistics - Class in ubic.gemma.core.analysis.preprocess.batcheffects
BatchEffectPopulationCli - Class in ubic.gemma.core.apps: For bulk processing of batch-info-fetching.
BatchEffectPopulationCli() - Constructor for class ubic.gemma.core.apps.BatchEffectPopulationCli
BatchEffectType - Class in ubic.gemma.persistence.hibernate: Workaround to handle existing batch effect value in the database.
BatchEffectType - Enum in ubic.gemma.model.expression.experiment: Represents a batch effect.
BatchEffectType() - Constructor for class ubic.gemma.persistence.hibernate.BatchEffectType
batchIdentifiableParameterList(Collection<T>, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
BatchInfoFetchController - Class in ubic.gemma.web.controller.analysis.preprocess: For populating "batch" information about experiments.
BatchInfoFetchController() - Constructor for class ubic.gemma.web.controller.analysis.preprocess.BatchInfoFetchController
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
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 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 ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException
BatchInfoPopulationException(ExpressionExperiment, Throwable) - Constructor for exception 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
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
batchParameterList(Collection<T>, 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
BeanInitializationTimeMonitor - Class in ubic.gemma.core.util: Hook into the bean post-processing lifecycle and report the worst offenders.
BeanInitializationTimeMonitor() - Constructor for class ubic.gemma.core.util.BeanInitializationTimeMonitor
BeanNameGenerator - Class in ubic.gemma.persistence.util: Our \@Service etc.
BeanNameGenerator() - Constructor for class ubic.gemma.persistence.util.BeanNameGenerator
beforeCompletion(PrintWriter) - Method in class ubic.gemma.core.util.BashCompletionGenerator
beforeCompletion(PrintWriter) - Method in interface ubic.gemma.core.util.CompletionGenerator
BibliographicPhenotypesValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
BibliographicPhenotypesValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
BibliographicPhenotypesValueObject(String, Integer, Set<CharacteristicValueObject>) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
BibliographicPhenotypesValueObject(PhenotypeAssociation) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
BibliographicReference - Class in ubic.gemma.model.common.description
BibliographicReference() - Constructor for class ubic.gemma.model.common.description.BibliographicReference
BibliographicReference.Factory - Class in ubic.gemma.model.common.description
BibliographicReferenceController - Interface in ubic.gemma.web.controller.common.description.bibref: Note: do not use parameterized collections as parameters for ajax methods.
BibliographicReferenceControllerImpl - Class in ubic.gemma.web.controller.common.description.bibref: This controller is responsible for showing a list of all bibliographic references, as well sending the user to the pubMed.Detail.view when they click on a specific link in that list.
BibliographicReferenceControllerImpl() - Constructor for class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
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
bibliographicReferenceSearch(String) - Static method in class ubic.gemma.model.common.search.SearchSettings: Convenience method to get pre-configured settings.
BibliographicReferenceService - Interface in ubic.gemma.core.annotation.reference
BibliographicReferenceServiceImpl - Class in ubic.gemma.core.annotation.reference: Implementation of BibliographicReferenceService.
BibliographicReferenceServiceImpl(BibliographicReferenceDao) - Constructor for class ubic.gemma.core.annotation.reference.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<ExpressionExperimentValueObject>) - 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
BibRefAnnotation() - Constructor for class ubic.gemma.model.common.description.BibRefAnnotation
BibRefUpdaterCli - Class in ubic.gemma.core.apps: Refreshes the information in all the bibliographic references in the system.
BibRefUpdaterCli() - Constructor for class ubic.gemma.core.apps.BibRefUpdaterCli
bindImplementationSpecificMetrics(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics
bindTo(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.database.HikariCPMetrics
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.ThreadPoolTaskExecutorMetrics
binFromRange(int, int) - Method in class ubic.gemma.model.genome.PhysicalLocation
binFromRange(int, int) - Static method in class ubic.gemma.persistence.util.SequenceBinUtils: return bin that this start-end segment is in
BIO_PROCESS_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
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
BioAssayController - Class in ubic.gemma.web.controller.expression.bioAssay
BioAssayController() - Constructor for class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
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
BioAssayOutlierProcessingTask - Interface in ubic.gemma.core.tasks.analysis.expression
BioAssayOutlierProcessingTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
BioAssayOutlierProcessingTaskCommand(Collection<Long>) - Constructor for class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
BioAssayOutlierProcessingTaskCommand(Collection<Long>, 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
BioAssayService - Interface in ubic.gemma.persistence.service.expression.bioAssay
BioAssayServiceImpl - Class in ubic.gemma.persistence.service.expression.bioAssay
BioAssayServiceImpl(BioAssayDao, BioMaterialDao, ArrayDesignDao) - 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
BioAssaySetService - Interface in ubic.gemma.persistence.service.expression.experiment: Generic service for dealing with all subclasses of BioAssaySet.
BioAssaySetServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
BioAssaySetServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
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, 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<Long, ArrayDesignValueObject>, boolean) - Constructor for class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
BIOLOGICAL_PROCESS - ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect
biologicalReplicate - 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
BioMaterialController - Class in ubic.gemma.web.controller.expression.biomaterial
BioMaterialController() - Constructor for class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
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
BioMaterialMappingUpdate - Class in ubic.gemma.model.common.auditAndSecurity.eventType: To indicate that the biomaterial to bioassay mapping of the expression experiment was modified.
BioMaterialMappingUpdate() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate
BioMaterialService - Interface in ubic.gemma.persistence.service.expression.biomaterial
BioMaterialServiceImpl - Class in ubic.gemma.persistence.service.expression.biomaterial
BioMaterialServiceImpl(BioMaterialDao, FactorValueDao, BioAssayDao, ExperimentalFactorDao) - Constructor for class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
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) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
BioMaterialValueObject(BioMaterial, BioAssay) - Constructor for class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
BIOPROCESS - ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType
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: No-arg constructor added to satisfy javabean contract
BioSequence.Factory - Class in ubic.gemma.model.genome.biosequence
BioSequence2GeneProduct - Class in ubic.gemma.model.association: An association between a BioSequence and a Gene Product.
BioSequence2GeneProduct() - Constructor for class ubic.gemma.model.association.BioSequence2GeneProduct
BioSequenceCleanupCli - Class in ubic.gemma.core.apps: Goes through the biosequences for array designs in the database and removes duplicates.
BioSequenceCleanupCli() - Constructor for class ubic.gemma.core.apps.BioSequenceCleanupCli
BioSequenceDao - Interface in ubic.gemma.persistence.service.genome.biosequence
BioSequenceDaoImpl - Class in ubic.gemma.persistence.service.genome.biosequence
BioSequenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
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.
BlacklistCli - Class in ubic.gemma.core.apps: Add entries to the blacklist
BlacklistCli() - Constructor for class ubic.gemma.core.apps.BlacklistCli
BlacklistedEntity - Class in ubic.gemma.model.expression
BlacklistedEntity() - Constructor for class ubic.gemma.model.expression.BlacklistedEntity
BlacklistedEntityDao - Interface in ubic.gemma.persistence.service.expression.experiment
BlacklistedEntityDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
BlacklistedEntityDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl
BlacklistedEntityService - Interface in ubic.gemma.persistence.service.expression.experiment
BlacklistedEntityServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
BlacklistedEntityServiceImpl(BlacklistedEntityDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceImpl
BlacklistedExperiment - Class in ubic.gemma.model.expression.experiment: TODO Document Me
BlacklistedExperiment() - Constructor for class ubic.gemma.model.expression.experiment.BlacklistedExperiment
BlacklistedPlatform - Class in ubic.gemma.model.expression.arrayDesign
BlacklistedPlatform() - Constructor for class ubic.gemma.model.expression.arrayDesign.BlacklistedPlatform
BlacklistedValueObject - Class in ubic.gemma.model.expression
BlacklistedValueObject() - Constructor for class ubic.gemma.model.expression.BlacklistedValueObject: Required when using the class as a spring bean.
blacklistExpressionExperiment(ExpressionExperiment, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityService: Blacklist a given dataset.
blacklistExpressionExperiment(ExpressionExperiment, String) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceImpl
blacklistPlatform(ArrayDesign, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityService: Blacklist a given platform.
blacklistPlatform(ArrayDesign, String) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceImpl
Blat - Interface in ubic.gemma.core.apps
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
BlatAssociationScorer - Class in ubic.gemma.core.analysis.sequence: Given a set of BlatAssociations that might be redundant, clean them up and score them.
BlatAssociationScorer() - Constructor for class ubic.gemma.core.analysis.sequence.BlatAssociationScorer
BlatAssociationService - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
BlatAssociationServiceImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis: Spring Service base class for BlatAssociationService, provides access to all services and entities referenced by this service.
BlatAssociationServiceImpl(BlatAssociationDao) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl
blatFormatChromosomeName(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Puts "chr" prefix on the chromosome name, if need be.
blatLocationsToIntArray(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Convert a psl-formatted list (comma-delimited) to an int[].
blatQuery(Collection<BioSequence>, boolean, Taxon) - Method in interface ubic.gemma.core.apps.Blat
blatQuery(Collection<BioSequence>, boolean, Taxon) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
blatQuery(Collection<BioSequence>, Taxon) - Method in interface ubic.gemma.core.apps.Blat
blatQuery(Collection<BioSequence>, Taxon) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
blatQuery(BioSequence) - Method in interface ubic.gemma.core.apps.Blat: Run a BLAT search using the gfClient.
blatQuery(BioSequence) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
blatQuery(BioSequence, Taxon, boolean) - Method in interface ubic.gemma.core.apps.Blat: Run a BLAT search using the gfClient.
blatQuery(BioSequence, Taxon, boolean) - Method in class ubic.gemma.core.apps.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) - 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
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
BlatResultTrackController - Class in ubic.gemma.web.controller.genome: See goldenPath help on custom track.
BlatResultTrackController() - Constructor for class ubic.gemma.web.controller.genome.BlatResultTrackController
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) - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
blockComplete(BioAssaySet, Collection<ExperimentalFactor>) - 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.
BOOLEAN - ubic.gemma.model.common.quantitationtype.PrimitiveType
BOOLEANARRAY - ubic.gemma.model.common.quantitationtype.PrimitiveType
BooleanVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData: This is used to represent missing value data.
BooleanVectorValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
BooleanVectorValueObject(DesignElementDataVector, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
browse(int, int) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
browse(int, int) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
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.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.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.ExpressionExperimentService
browse(int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
browse(int, int, String) - Method in class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController: AJAX
browse(int, int, String, boolean) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
browse(int, int, String, boolean) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
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.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.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
browse(ListBatchCommand) - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController
browse(ListBatchCommand) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
browse(ListBatchCommand) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
browse(ListBatchCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX call for remote paging store security isn't incorporated in db query, so paging needs to occur at higher level.
browse(ListBatchCommand, Long[], boolean, boolean) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController: AJAX call for remote paging store security isn't incorporated in db query, so paging needs to occur at higher level? Is there security for ArrayDesigns? ids can be null
browse(ListBatchCommand, Long[], boolean, boolean) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
browseByTaxon(ListBatchCommand, Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
browseSpecificIds(ListBatchCommand, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX call for remote paging store
BrowsingDao<T> - Interface in ubic.gemma.persistence.service: Support for paging through the data.
build() - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder
buildBadResponse(Document, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
buildDesignMatrix(List<ExperimentalFactor>, List<BioMaterial>, Map<ExperimentalFactor, FactorValue>) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils: Convert factors to a matrix usable in R.
buildFeedItems(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.rss.CustomRssViewer
buildFeedMetadata(Map<String, Object>, Channel, HttpServletRequest) - Method in class ubic.gemma.web.controller.common.rss.CustomRssViewer
BuildInfo - Class in ubic.gemma.core.util
BuildInfo() - Constructor for class ubic.gemma.core.util.BuildInfo
buildOptions(Options) - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.BlacklistCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.GeeqCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
buildOptions(Options) - Method in class ubic.gemma.core.apps.GeoGrabberCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.IndexGemmaCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.LinkAnalysisCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.apps.MultifunctionalityCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.PubMedLoaderCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ReplaceDataCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.SplitExperimentCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.SVDCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.TaxonLoaderCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.UpdateEE2CCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.UpdatePubMedCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.VectorMergingCli
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
buildOptions(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Build option implementation.
buildStandardOptions(Options) - Method in class ubic.gemma.core.util.AbstractCLI
buildWrapper(Document, Collection<String>, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint: Function to handle the constructing of output in xml format for returning the response to the client.
BUNDLE_KEY - Static variable in class ubic.gemma.web.util.Constants: The name of the ResourceBundle used in this application
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<T>, Filter.Operator, Collection<T>) - 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<T>, Filter.Operator, Collection<T>) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Class<T>, Filter.Operator, Collection<T>, String) - Static method in class ubic.gemma.persistence.util.Filter: Create a new filter with a collection right hand side.
by(String, String, Class<T>, Filter.Operator, Collection<T>, String) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Class<T>, Filter.Operator, T) - Static method in class ubic.gemma.persistence.util.Filter: Create a new filter without an original property.
by(String, String, Class<T>, Filter.Operator, T) - Static method in class ubic.gemma.persistence.util.Filters: Create a singleton Filters from an explicit clause.
by(String, String, Class<T>, Filter.Operator, T, String) - Static method in class ubic.gemma.persistence.util.Filter: Create a new filter.
by(String, String, Class<T>, Filter.Operator, T, String) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Class<T>, Filter.Operator, Subquery) - Static method in class ubic.gemma.persistence.util.Filter
by(String, String, Class<T>, Filter.Operator, Subquery) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Class<T>, Filter.Operator, Subquery, String) - Static method in class ubic.gemma.persistence.util.Filter
by(String, String, Class<T>, Filter.Operator, Subquery, String) - Static method in class ubic.gemma.persistence.util.Filters
by(String, String, Sort.Direction) - Static method in class ubic.gemma.persistence.util.Sort: Create a sort without an original property.
by(String, String, Sort.Direction, 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.
byteArrayConverter - Static variable in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
bytesRead(int) - Method in interface ubic.gemma.web.util.upload.OutputStreamListener
bytesRead(int) - Method in class ubic.gemma.web.util.upload.UploadListener

C

C - ubic.gemma.model.common.auditAndSecurity.AuditAction: Create
cache(Map<Long, GeneCoexpressionTestedIn>) - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
cache(Map<Long, GeneCoexpressionTestedIn>) - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
CACHE_QUERY_STRINGENCY - Static variable in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache: The stringency used to query when populating the cache.
cacheCoexpression(Long, Collection<CoexpressionValueObject>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
cacheCoexpression(Long, Collection<CoexpressionValueObject>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
cacheCoexpression(Map<Long, List<CoexpressionValueObject>>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
cacheCoexpression(Map<Long, List<CoexpressionValueObject>>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
CacheControl - Annotation Type in ubic.gemma.rest.annotations
CacheControlHeaderDecorator - Class in ubic.gemma.rest.providers
CacheControlHeaderDecorator() - Constructor for class ubic.gemma.rest.providers.CacheControlHeaderDecorator
CacheControls - Annotation Type in ubic.gemma.rest.annotations
CachedFilteringDao<O extends Identifiable> - Interface in ubic.gemma.persistence.service
CachedFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Interface in ubic.gemma.persistence.service
CacheMonitor - Interface in ubic.gemma.web.util
CacheMonitorImpl - Class in ubic.gemma.web.util: Get statistics about and manage caches.
CacheMonitorImpl() - Constructor for class ubic.gemma.web.util.CacheMonitorImpl
Caches() - Constructor for class ubic.gemma.persistence.persister.AbstractPersister.Caches
cacheTestedIn(GeneCoexpressionTestedIn) - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
cacheTestedIn(GeneCoexpressionTestedIn) - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
CacheUtils - Class in ubic.gemma.persistence.util: Created by tesarst on 04/04/17.
CacheUtils() - Constructor for class ubic.gemma.persistence.util.CacheUtils
CacheUtils.Lock - Interface in ubic.gemma.persistence.util
calculateExternalDatabasesStatistics() - Method in class ubic.gemma.web.controller.PhenotypeController
calculateGoTermOverlap(Long, Collection<Long>) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
calculateGoTermOverlap(Long, Collection<Long>) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
calculateGoTermOverlap(Gene, Collection<Long>) - 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<Long>) - 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
calculateMetrics() - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
calculateMetrics() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics: Calculate the linear correlation matrix of a matrix, allowing missing values.
calculateMetrics() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics: Compute correlations.
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
call() - Method in class ubic.gemma.core.job.executor.common.ExecutingTask
call() - Method in class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskImpl
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.PreprocessTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskImpl
call() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapperTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskImpl
call() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskImpl
call() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskImpl
call() - Method in class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskImpl
cancelJob(String) - Method in interface ubic.gemma.web.job.progress.ProgressStatusService: Attempt to cancel the job.
cancelJob(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl
CANCELLING - ubic.gemma.core.job.SubmittedTask.Status
canConvertFromId(Class<? extends IdentifiableValueObject<?>>) - Method in class ubic.gemma.core.search.SearchServiceImpl
canCurrentUserEditExperiment(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX returns a JSON string encoding whether the current user owns the experiment and whether they can edit it
canCurrentUserEditGroup(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed
canCurrentUserEditGroup(GeneSetValueObject) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed
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
canRead() - Method in class ubic.gemma.model.common.description.LocalFile
canSkipAclCheck(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
canSkipAssociationCheck(Object, String) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
canWrite() - Method in class ubic.gemma.model.common.description.LocalFile
CASE_INSENSITIVE_ORDER - Static variable in class ubic.gemma.web.util.LabelValue: Comparator that can be used for a case insensitive sort of LabelValue objects.
categorical - ubic.gemma.model.expression.experiment.FactorType
CATEGORICAL - ubic.gemma.model.common.quantitationtype.GeneralType
CATEGORICAL - Static variable in enum ubic.gemma.model.expression.experiment.FactorType: Aliases for consistency.
CategoryWithUsageStatisticsValueObject() - Constructor for class ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject
cdfcut - ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.SingularThreshold
Cell() - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
cellLine - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
cellType - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
CELLULAR_COMPONENT - ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect
CHANGE - 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.UserManager
changePasswordForUser(String, String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
channelNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
ChannelUtils - Class in ubic.gemma.persistence.util: Determine if a quantitation type (by name) represents background or signal.
ChannelUtils() - Constructor for class ubic.gemma.persistence.util.ChannelUtils
CHAR - 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<? extends Characteristic>) - Static method in class ubic.gemma.model.common.description.CharacteristicValueObject
CharacteristicBrowserController - Class in ubic.gemma.web.controller.common: NOTE: Logging messages from this service are important for tracking changes to annotations.
CharacteristicBrowserController() - Constructor for class ubic.gemma.web.controller.common.CharacteristicBrowserController
CharacteristicConverter - Class in ubic.gemma.web.remote
CharacteristicConverter() - Constructor for class ubic.gemma.web.remote.CharacteristicConverter
CharacteristicDao - Interface in ubic.gemma.persistence.service.common.description
CharacteristicDao.CharacteristicUsageFrequency - Class in ubic.gemma.persistence.service.common.description: Represents a set of characteristics grouped by Characteristic.getValueUri() or Characteristic.getValue().
CharacteristicDaoImpl - Class in ubic.gemma.persistence.service.common.description
CharacteristicDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
CharacteristicService - Interface in ubic.gemma.persistence.service.common.description
CharacteristicServiceImpl - Class in ubic.gemma.persistence.service.common.description
CharacteristicServiceImpl(CharacteristicDao, StatementDao) - 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
CharacteristicUsageFrequency() - Constructor for class ubic.gemma.persistence.service.common.description.CharacteristicDao.CharacteristicUsageFrequency
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
characteristicValueObject2Characteristic(CharacteristicValueObject) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper: Deprecated.

CharacteristicValueObject to Characteristic with no valueUri given
characteristicValueObject2Characteristic(CharacteristicValueObject) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl: Deprecated.
CharacteristicWithUsageStatisticsAndOntologyTerm() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm
CHARARRAY - ubic.gemma.model.common.quantitationtype.PrimitiveType
checkBatchFetchStatus(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
checkBatchFetchStatus(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
checkCorrectability(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService: Is there a Batch factor provided? Is there a confound problem? Do we have at least two samples per batch? This will return true even if there is evidence the data has been batch-corrected before; we assume the caller wants to redo it based on the raw data
checkCorrectability(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
checkEntity(AbstractEntityArg<?, T, S>, T) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService: Checks whether the given object is null, and throws an appropriate exception if necessary.
checkForFile(String) - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
checkHasBatchInfo(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
checkHasBatchInfo(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
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(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
checkResult(String) - Method in class ubic.gemma.web.controller.TaskCompletionController
checkResult(String) - Method in interface ubic.gemma.web.job.progress.ProgressStatusService
checkResult(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl
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(LocalFile) - 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
ChIPChip - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
Chromosome - Class in ubic.gemma.model.genome: Immutable representation of a chromosome
Chromosome() - Constructor for class ubic.gemma.model.genome.Chromosome: No-arg constructor added to satisfy javabean contract
Chromosome(String, ExternalDatabase, BioSequence, Taxon) - Constructor for class ubic.gemma.model.genome.Chromosome
Chromosome(String, Taxon) - Constructor for class ubic.gemma.model.genome.Chromosome
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: No-arg constructor added to satisfy javabean contract
ChromosomeLocation - Class in ubic.gemma.model.genome
ChromosomeLocation() - Constructor for class ubic.gemma.model.genome.ChromosomeLocation: No-arg constructor added to satisfy javabean contract
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
ChromosomeUtil - Class in ubic.gemma.persistence.util: A utility class for Chromosome
ChromosomeUtil() - Constructor for class ubic.gemma.persistence.util.ChromosomeUtil
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
ClassConverter - Class in ubic.gemma.web.remote
ClassConverter() - Constructor for class ubic.gemma.web.remote.ClassConverter
CLASSIC_HOME_PAGE - Static variable in class ubic.gemma.web.controller.WebConstants
clause() - Method in class ubic.gemma.rest.util.args.FilterArgParser
clause() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
clause(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
ClauseContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
clazz - Variable in class ubic.gemma.web.taglib.ConstantsTag: The class to expose the variables from.
cleanUp(File) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
cleanupMultipart(MultipartHttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver
cleanUpQueryName(String) - Static method in class ubic.gemma.core.loader.genome.BlatResultParser
clear() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis: Clear/null data so this object can be reused.
clear() - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter: Remove old results.
clear() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
clear() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject: Used during recomputation only.
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<GeoSample>, Integer) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: If possible, null out the data for a quantitation type on a given platform.
clearAllCaches() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController: Flush (clear) all caches.
clearAllCaches() - Method in interface ubic.gemma.web.util.CacheMonitor: Remove all items from all caches.
clearAllCaches() - Method in class ubic.gemma.web.util.CacheMonitorImpl
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() - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache: Remove all elements from the cache.
clearCache() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
clearCache() - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
clearCache() - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
clearCache() - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCache
clearCache() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
clearCache() - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
clearCache() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
clearCache() - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
clearCache() - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
clearCache(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache: Remove all elements from the cache for the given result set, if the cache exists.
clearCache(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
clearCache(Long) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCache
clearCache(Long) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
clearCache(String) - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController: Flush (clear) a cache.
clearCache(String) - Method in interface ubic.gemma.web.util.CacheMonitor: Remove all items from the cache with the given name.
clearCache(String) - Method in class ubic.gemma.web.util.CacheMonitorImpl
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
clearCaches(Long) - Method in interface ubic.gemma.core.visualization.ExperimentalDesignVisualizationService: removed the cached layouts and cached BioAssayDimensions for this experiment (could be a subset?).
clearCaches(Long) - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl
clearFactorValuesNeedsAttention(Long[], String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
clearFromCaches(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX clear entries in caches relevant to experimental design for the experiment passed in.
clearNeedsAttentionFlag(FactorValue, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Clear a needs attention flag on a given factor value.
clearNeedsAttentionFlag(FactorValue, String) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
clearResultObject() - Method in class ubic.gemma.core.search.SearchResult: Clear the result object.
clearTopHitCache(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache: Remove all elements from the top hits cache for the given result set, if the cache exists.
clearTopHitCache(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
CLI - Interface in ubic.gemma.core.util: Interface for CLI tools.
ClientIdRetrievalStrategy - Interface in ubic.gemma.rest.analytics.ga4: Strategy for retrieving a client ID.
close() - Method in class ubic.gemma.core.job.executor.common.ProgressUpdateAppender
close() - Method in class ubic.gemma.core.job.executor.common.ProgressUpdateAppender.ProgressUpdateContext
close() - Method in class ubic.gemma.core.metrics.binder.jpa.Hibernate4QueryMetrics
close() - Method in class ubic.gemma.core.util.StopWatchUtils.StopWatchRegion
close() - Method in interface ubic.gemma.persistence.util.CacheUtils.Lock
close() - Method in class ubic.gemma.web.logging.SlackAppender
close() - Method in class ubic.gemma.web.util.upload.MonitoredOutputStream
close(RetryContext, RetryCallback<T>, Throwable) - Method in class ubic.gemma.persistence.retry.RetryLogger
CoexpCorrelationDistribution - Class in ubic.gemma.model.analysis.expression.coexpression
CoexpCorrelationDistribution() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution
CoexpCorrelationDistribution.Factory - Class in ubic.gemma.model.analysis.expression.coexpression
CoexpressionAnalysis - Class in ubic.gemma.model.analysis.expression.coexpression: A coexpression analysis of one experiment.
CoexpressionAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis
CoexpressionAnalysis.Factory - Class in ubic.gemma.model.analysis.expression.coexpression
CoexpressionAnalysisDao - Interface in ubic.gemma.persistence.service.analysis.expression.coexpression
CoexpressionAnalysisDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression.coexpression: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.
CoexpressionAnalysisDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDaoImpl
CoexpressionAnalysisService - Interface in ubic.gemma.persistence.service.analysis.expression.coexpression: Deals with the Analysis objects for Coexpression - not the coexpression results themselves.
CoexpressionAnalysisServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.coexpression
CoexpressionAnalysisServiceImpl(CoexpressionAnalysisDao, CoexpressionService) - Constructor for class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
CoexpressionCache - Interface in ubic.gemma.persistence.service.association.coexpression: Cache for coexpression results.
CoexpressionCacheImpl - Class in ubic.gemma.persistence.service.association.coexpression: Configures the cache for gene2gene coexpression.
CoexpressionCacheImpl() - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
CoexpressionCacheValueObject - Class in ubic.gemma.persistence.service.association.coexpression: Used to cache results; these objects are unmodifiable, and contains the coexpression data for one query gene and one result gene, in all experiments.
CoexpressionCacheValueObject() - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject
CoexpressionCacheValueObject(CoexpressionValueObject) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject
CoexpressionDao - Interface in ubic.gemma.persistence.service.association.coexpression
CoexpressionDaoImpl - Class in ubic.gemma.persistence.service.association.coexpression: Manages and queries coexpression 'links' between genes.
CoexpressionDaoImpl() - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
CoexpressionMetaValueObject - Class in ubic.gemma.core.analysis.expression.coexpression
CoexpressionMetaValueObject() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
CoexpressionNodeDegreeDao - Interface in ubic.gemma.persistence.service.association.coexpression
CoexpressionNodeDegreeDaoImpl - Class in ubic.gemma.persistence.service.association.coexpression
CoexpressionNodeDegreeDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionNodeDegreeDaoImpl
coexpressionSearch(Collection<Long>, Collection<Long>, int, int, boolean) - Method in interface ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService
coexpressionSearch(Collection<Long>, Collection<Long>, int, int, boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchServiceImpl
CoexpressionSearchCommand - Class in ubic.gemma.core.analysis.expression.coexpression
CoexpressionSearchCommand() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
CoexpressionSearchController - Class in ubic.gemma.web.controller.coexpressionSearch
CoexpressionSearchController() - Constructor for class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController
coexpressionSearchQuick(Collection<Long>, Collection<Long>, int, int, boolean) - Method in interface ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService: Skips some of the postprocessing steps, use in situations where raw speed is more important than details.
coexpressionSearchQuick(Collection<Long>, Collection<Long>, int, int, boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchServiceImpl
CoexpressionService - Interface in ubic.gemma.persistence.service.association.coexpression: A key service for working with coexpression at a fairly low level.
CoexpressionServiceImpl - Class in ubic.gemma.persistence.service.association.coexpression
CoexpressionServiceImpl() - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
CoexpressionSummaryValueObject - Class in ubic.gemma.core.analysis.expression.coexpression
CoexpressionSummaryValueObject() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
CoexpressionSummaryValueObject(Long) - Constructor for class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
CoexpressionValueObject - Class in ubic.gemma.persistence.service.association.coexpression: Lightweight/convenient object for manipulating coexpression for a pair of genes.
CoexpressionValueObject() - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
CoexpressionValueObject(Long, Long, Boolean, Integer, Long, Set<Long>) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
CoexpressionValueObject(Long, String, boolean, Long, String, Integer, Long, Collection<Long>, Collection<Long>) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
CoexpressionValueObject(Long, String, boolean, Long, String, Integer, Long, Set<Long>, Set<Long>) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
CoexpressionValueObject(Gene2GeneCoexpression) - Constructor for class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject: Construct a value object.
CoexpressionValueObjectExt - Class in ubic.gemma.core.analysis.expression.coexpression: A more heavyweight version of CoexpressionValueObject; has a bit more information about the genes.
CoexpressionValueObjectExt() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
CoexSearchTaskCommand - Class in ubic.gemma.web.controller.coexpressionSearch
CoexSearchTaskCommand(CoexpressionSearchCommand) - Constructor for class ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand
collapse(Collection<Reporter>) - 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.
collection() - Method in class ubic.gemma.rest.util.args.FilterArgParser
collection() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
COLLECTION_OF_MATERIAL_URI - Static variable in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
CollectionContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
collectionOperator() - Method in class ubic.gemma.rest.util.args.FilterArgParser
collectionOperator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
collectionOperator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
CollectionOperatorContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
columns() - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
columns() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
columns() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
columns() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
columns() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Total number of columns.
columns() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
columns(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
columns(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Number of columns that use the given design element.
comBat(ExpressionDataDoubleMatrix) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService: Run ComBat using default settings (parametric)
comBat(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
comBat(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService
comBat(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
ComBat<R,C> - Class in ubic.gemma.core.analysis.preprocess.batcheffects: An implementation of the ComBat algorithm described by Johson et al as described in:
ComBat(DoubleMatrix<R, C>, ObjectMatrix<C, String, ?>) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.ComBat
ComBat(ObjectMatrix<C, String, ?>) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.ComBat: Constructor that can be used just for testing correctability (data is not provided) - FIXME refactor so it's not a constructor.
commence(HttpServletRequest, HttpServletResponse, AuthenticationException) - Method in class ubic.gemma.rest.security.RestAuthEntryPoint
COMMENT_MARK - Static variable in class ubic.gemma.core.loader.util.parser.BasicLineMapParser: Lines starting with this will be ignored.
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
CommonPersister - Class in ubic.gemma.persistence.persister: Persister for ubic.gemma.model.common package classes.
CommonPersister() - Constructor for class ubic.gemma.persistence.persister.CommonPersister
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
CommonsMultipartFile - Class in ubic.gemma.web.util.upload: Deprecated.
CommonsMultipartFile(FileItem) - Constructor for class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.

Create an instance wrapping the given FileItem.
CommonsMultipartMonitoredResolver - Class in ubic.gemma.web.util.upload: An adaptation of the standard Spring CommonsMultipartResolver that uses a MonitoredOutputStream.
CommonsMultipartMonitoredResolver() - Constructor for class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver
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
compare(Gene, Gene) - Method in class ubic.gemma.web.util.GeneSymbolComparator
compareTerm(String, String, String, String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Compare a pair of ontology terms.
compareTo(Object) - Method in class ubic.gemma.model.genome.ChromosomeLocation
compareTo(Object) - Method in class ubic.gemma.model.genome.PhysicalLocation
compareTo(OntologyResource) - Method in class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
compareTo(CoexpressionValueObjectExt) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
compareTo(CompositeSequenceMapValueObject) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
compareTo(ExpressionDataMatrixRowElement) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
compareTo(GeoData) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
compareTo(SearchResult<?>) - Method in class ubic.gemma.core.search.SearchResult
compareTo(SearchResultDisplayObject) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
compareTo(Gene2GeneCoexpression) - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
compareTo(PhenotypeMappingType) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
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(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
compareTo(StatementValueObject) - Method in class ubic.gemma.model.expression.experiment.StatementValueObject
compareTo(BibliographicPhenotypesValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
compareTo(EvidenceValueObject<E>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
compareTo(ExternalDatabaseStatisticsValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
compareTo(PhenotypeAssPubValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
compareTo(SimpleTreeValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
compareTo(CoexpressionValueObject) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
compareTo(NonPersistentNonOrderedCoexpLink) - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
compareTo(SidValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
compareTo(LabelValue) - Method in class ubic.gemma.web.util.LabelValue
COMPLETED - ubic.gemma.core.job.SubmittedTask.Status
CompletionGenerator - Interface in ubic.gemma.core.util
CompositeClientIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Composite strategy for retrieving client ID.
CompositeClientIdRetrievalStrategy(List<ClientIdRetrievalStrategy>) - Constructor for class ubic.gemma.rest.analytics.ga4.CompositeClientIdRetrievalStrategy
CompositeSearchSource - Class in ubic.gemma.core.search.source: A search source constituted of multiple other sources.
CompositeSearchSource(List<SearchSource>) - 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: No-arg constructor added to satisfy javabean contract
CompositeSequence.Factory - Class in ubic.gemma.model.expression.designElement
CompositeSequenceArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for Composite Sequence arguments.
CompositeSequenceArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.CompositeSequenceArg
CompositeSequenceArgService - Class in ubic.gemma.rest.util.args
CompositeSequenceArgService(CompositeSequenceService) - Constructor for class ubic.gemma.rest.util.args.CompositeSequenceArgService
CompositeSequenceArrayArg - Class in ubic.gemma.rest.util.args
CompositeSequenceController - Class in ubic.gemma.web.controller.expression.designElement
CompositeSequenceController() - Constructor for class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
CompositeSequenceDao - Interface in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceDaoImpl - Class in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
CompositeSequenceGeneMapperService - Class in ubic.gemma.core.analysis.service
CompositeSequenceGeneMapperService() - Constructor for class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService
CompositeSequenceIdArg - Class in ubic.gemma.rest.util.args: Composite Sequence argument for CS ID.
CompositeSequenceMapSummary - Class in ubic.gemma.core.analysis.sequence: This is a convenience object to hold the results of CompositeSequence mapping results.
CompositeSequenceMapSummary(CompositeSequence) - Constructor for class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
CompositeSequenceMapValueObject - Class in ubic.gemma.core.analysis.sequence
CompositeSequenceMapValueObject() - Constructor for class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
CompositeSequenceNameArg - Class in ubic.gemma.rest.util.args: Composite Sequence argument for CS name.
CompositeSequenceParser - Class in ubic.gemma.core.loader.expression.arrayDesign: Parse the "old" array description format.
CompositeSequenceParser() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
compositeSequenceSearch(String, ArrayDesign) - Static method in class ubic.gemma.model.common.search.SearchSettings: Convenience method to get pre-configured settings.
compositeSequenceService - Variable in class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer
CompositeSequenceService - Interface in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceServiceImpl - Class in ubic.gemma.persistence.service.expression.designElement
CompositeSequenceServiceImpl(CompositeSequenceDao, BioSequenceService, GeneProductService, BlatResultService, ArrayDesignService) - 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
Compound - Class in ubic.gemma.model.expression.biomaterial
Compound() - Constructor for class ubic.gemma.model.expression.biomaterial.Compound: No-arg constructor added to satisfy javabean contract
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
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.
computeHitListSizes(Collection<DifferentialExpressionAnalysisResult>, Map<CompositeSequence, Collection<Gene>>) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer: Generate HitListSize entities that will be stored to count the number of diff.
computeHitListSizes(Collection<DifferentialExpressionAnalysisResult>, Map<CompositeSequence, Collection<Gene>>) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
computeMatrixSimilarity(Gene, Gene, DoubleMatrix<Long, String>, GoMetric.Metric) - Method in interface ubic.gemma.core.ontology.GoMetric
computeMatrixSimilarity(Gene, Gene, DoubleMatrix<Long, String>, GoMetric.Metric) - Method in class ubic.gemma.core.ontology.GoMetricImpl
computeMaxSimilarity(Gene, Gene, Map<String, Double>, GoMetric.Metric) - Method in interface ubic.gemma.core.ontology.GoMetric
computeMaxSimilarity(Gene, Gene, Map<String, Double>, GoMetric.Metric) - Method in class ubic.gemma.core.ontology.GoMetricImpl
computeMergedOverlap(List<Gene>, List<Gene>, Map<Long, Collection<String>>) - Method in interface ubic.gemma.core.ontology.GoMetric
computeMergedOverlap(List<Gene>, List<Gene>, Map<Long, Collection<String>>) - Method in class ubic.gemma.core.ontology.GoMetricImpl: Tailored to handle computing overlap between two gene lists which may contain duplicate genes of the same name but different IDs.
computeMissingValues(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
computeMissingValues(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl
computeMissingValues(ExpressionExperiment, double, Collection<Double>) - Method in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
computeMissingValues(ExpressionExperiment, double, Collection<Double>) - Method in class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl
computeOverlap(long, long, long, long) - Static method in class ubic.gemma.model.genome.PhysicalLocation
computeOverlap(Collection<OntologyTerm>, Collection<OntologyTerm>) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
computeOverlap(Collection<OntologyTerm>, Collection<OntologyTerm>) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
computeOverlap(PhysicalLocation) - Method in class ubic.gemma.model.genome.PhysicalLocation
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.
computeProcessedExpressionData(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Compute processed expression data, ignoring mismatched with the inferred scale.
computeProcessedExpressionData(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
computeProcessedExpressionData(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: This method should not be called on its own, if possible.
computeProcessedExpressionData(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
computeSimilarity(Gene, Gene, Map<String, Double>, GoMetric.Metric) - Method in interface ubic.gemma.core.ontology.GoMetric
computeSimilarity(Gene, Gene, Map<String, Double>, GoMetric.Metric) - Method in class ubic.gemma.core.ontology.GoMetricImpl
computeSimpleOverlap(Gene, Gene, Map<Long, Collection<String>>) - Method in interface ubic.gemma.core.ontology.GoMetric
computeSimpleOverlap(Gene, Gene, Map<Long, Collection<String>>) - Method in class ubic.gemma.core.ontology.GoMetricImpl
CONC - ubic.gemma.model.common.measurement.MeasurementKind: Concentration
CONCENTRATION - Static variable in enum ubic.gemma.model.common.measurement.MeasurementKind: Alias for readability.
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 - ubic.gemma.model.common.quantitationtype.StandardQuantitationType
CONFIG - Static variable in class ubic.gemma.web.util.Constants: The name of the configuration hashmap stored in application scope.
configExperimentalFactorValueObject(ExperimentalFactor) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService
configExperimentalFactorValueObject(ExperimentalFactor) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
configExpressionExperimentValueObject(ExpressionExperimentValueObject) - Method in interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService
configExpressionExperimentValueObject(ExpressionExperimentValueObject) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
ConfigurationCookie - Class in ubic.gemma.web.util: Cookie class that also presents a commons configuration interface.
ConfigurationCookie(String) - Constructor for class ubic.gemma.web.util.ConfigurationCookie: Create a cookie with the given name.
ConfigurationCookie(Cookie) - Constructor for class ubic.gemma.web.util.ConfigurationCookie: Used when loading cookies from the user.
ConfigurationLinter - Class in ubic.gemma.core.util: Lint various aspects of the configuration for the CLI profile.
ConfigurationLinter() - Constructor for class ubic.gemma.core.util.ConfigurationLinter
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.MeterRegistryCliConfigurer
configure(MeterRegistry) - Method in class ubic.gemma.core.metrics.MeterRegistryEhcacheConfigurer
configure(MeterRegistry) - Method in class ubic.gemma.web.metrics.MeterRegistryWebConfigurer
configureAllLoggers(int) - Method in class ubic.gemma.core.logging.log4j.Log4jConfigurer
configureAllLoggers(int) - Method in interface ubic.gemma.core.logging.LoggingConfigurer: Set the logging level of all loggers.
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
configureLogger(String, int) - Method in class ubic.gemma.core.logging.log4j.Log4jConfigurer: Set up logging according to the user-selected (or default) verbosity level.
configureLogger(String, int) - Method in interface ubic.gemma.core.logging.LoggingConfigurer: Set the logging level of a specific logger.
confirmRegistration(String, String, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
CONJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
CONJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
CONJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
CONJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
CONJUNCTION(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
connect(int) - Method in class ubic.gemma.core.util.NetDatasourceUtil
Constants - Class in ubic.gemma.web.util: Constant values used throughout the application.
Constants() - Constructor for class ubic.gemma.web.util.Constants
ConstantsTag - Class in ubic.gemma.web.taglib: This class is designed to put all the public variables in a class to a specified scope - designed for exposing a Constants class to Tag Libraries.
ConstantsTag() - Constructor for class ubic.gemma.web.taglib.ConstantsTag
ConstantsTei - Class in ubic.gemma.web.taglib: Implementation of TagExtraInfo for the constants tag, identifying the scripting object(s) to be made visible.
ConstantsTei() - Constructor for class ubic.gemma.web.taglib.ConstantsTei
constructBioAssayName(ExpressionDataMatrix<?>, int) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils: Constructs a bioassay name.
constructBioAssayName(BioMaterial, Collection<BioAssay>) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
constructCitation(BibliographicReference) - Static method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
constructCitations(Collection<BibliographicReference>) - Static method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
constructConditionId(long, long) - Static method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
constructFactorValueName(FactorValue) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils: Produce a value for representing a factor value.
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: No-arg constructor added to satisfy javabean contract
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
ContactService - Interface in ubic.gemma.persistence.service.common.auditAndSecurity
ContactServiceImpl - Class in ubic.gemma.persistence.service.common.auditAndSecurity
ContactServiceImpl(ContactDao) - Constructor for class ubic.gemma.persistence.service.common.auditAndSecurity.ContactServiceImpl
contains(Long) - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
contains(Long) - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
containsAnyAlias(Filters, Sort, String...) - Static method in class ubic.gemma.persistence.util.FiltersUtils: Check if an alias is mentioned in a set of Filter.
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.util.CacheUtils: Check if a cache contains a given key.
containsKey(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
contextDestroyed(ServletContextEvent) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolverRegistrationListener
contextDestroyed(ServletContextEvent) - Method in class ubic.gemma.web.listener.UserCounterListener
contextInitialized(ServletContextEvent) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolverRegistrationListener
contextInitialized(ServletContextEvent) - Method in class ubic.gemma.web.listener.StartupListener
contextInitialized(ServletContextEvent) - Method in class ubic.gemma.web.listener.UserCounterListener
continuous - ubic.gemma.model.expression.experiment.FactorType
CONTINUOUS - Static variable in enum ubic.gemma.model.expression.experiment.FactorType: Aliases for consistency.
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) - 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
ContrastVO - Class in ubic.gemma.model.analysis.expression.diff: Helper object, not for general use.
ContrastVO(Long, Long, Double, Double, Long) - Constructor for class ubic.gemma.model.analysis.expression.diff.ContrastVO
ControllerUtils - Class in ubic.gemma.web.controller: Created by tesarst on 09/03/17.
ControllerUtils() - Constructor for class ubic.gemma.web.controller.ControllerUtils
conversionService() - Method in class ubic.gemma.persistence.util.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<? extends S>) - Method in interface ubic.gemma.core.loader.util.converter.Converter
convert(Collection<? extends GeoData>) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convert(Collection<? extends GeoData>) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(Collection<? extends GeoData>, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convert(Collection<? extends GeoData>, boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(BlockingQueue<NcbiGeneData>, BlockingQueue<Gene>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
convert(S) - Method in interface ubic.gemma.core.loader.util.converter.Converter
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(GeoData, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convert(GeoData, boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
convert(SimpleExpressionExperimentMetaData, DoubleMatrix<String, String>) - Method in interface ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService
convert(SimpleExpressionExperimentMetaData, DoubleMatrix<String, String>) - 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
convert2CitationValueObject(BibliographicReference) - Static method in class ubic.gemma.model.common.description.CitationValueObject
convert2CitationValueObjects(Collection<BibliographicReference>) - 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<SubmittedTask>) - Static method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
convert2ValueObjects(Collection<BibliographicReference>) - Static method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject: does not set related experiments field
convert2ValueObjects(Collection<BioAssay>) - Static method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
convertData(List<Object>, QuantitationType) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
convertData(List<Object>, QuantitationType) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl: Convert a vector of strings into a byte[] for saving in the database.
converter - Variable in class ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService
Converter<S,T> - Interface in ubic.gemma.core.loader.util.converter: Defines a class that can convert objects from one type to another.
convertFromBytes(List<Object>, PrimitiveType, DesignElementDataVector) - Method in class ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService
convertFromGeneSetValueObject(GeneSetValueObject, String) - Static method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
convertibleTypes - Variable in class ubic.gemma.persistence.util.ServiceBasedEntityConverter
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.CharacteristicConverter
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.DirectionConverter
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.GOEvidenceCodeConverter
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.ScaleTypeConverter
convertInbound(Class, InboundVariable, InboundContext) - Method in class ubic.gemma.web.remote.StandardQuantitationTypeConverter
convertMembers2GeneValueObjects(Collection<GeneSetMember>) - Static method in class ubic.gemma.model.genome.gene.GeneValueObject: A static method for easily converting GeneSetMembers into GeneValueObjects
convertOutbound(Object, OutboundContext) - Method in class ubic.gemma.web.remote.ClassConverter
convertOutbound(Object, OutboundContext) - Method in class ubic.gemma.web.remote.DoublePointConverter
convertSearchResults2SearchResultDisplayObjects(List<SearchResult<T>>) - Static method in class ubic.gemma.core.search.SearchResultDisplayObject: Creates a collection of SearchResultDisplayObjects from a collection of objects.
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 Complete list of possibilities according to Nathaniel (6/2018) Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Expression profiling by array Non-coding RNA profiling by array Genome variation profiling by genome tiling array Genome variation profiling by high throughput sequencing Other Non-coding RNA profiling by high throughput sequencing Genome variation profiling by SNP array SNP genotyping by SNP array Expression profiling by genome tiling array Genome variation profiling by array Expression profiling by RT-PCR Methylation profiling by high throughput sequencing Genome binding/occupancy profiling by genome tiling array Methylation profiling by genome tiling array Methylation profiling by array Genome binding/occupancy profiling by array Expression profiling by SAGE Protein profiling by protein array Genome binding/occupancy profiling by SNP array Non-coding RNA profiling by genome tiling array Third-party reanalysis Expression profiling by MPSS Expression profiling by SNP array Methylation profiling by SNP array Protein profiling by Mass Spec
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.model.GeoSeries: 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.core.expression.experiment.ExpressionExperimentSetValueObjectHelper: 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.
convertToEntity(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.core.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
convertToGOValueObject(GeneSet, String, String) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper: Method to create a GO group object from an ad hoc entity
convertToGOValueObject(GeneSet, String, String) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
convertToLightValueObject(GeneSet) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper: Constructor to build value object from GeneSet.
convertToLightValueObject(GeneSet) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
convertToLightValueObjects(Collection<GeneSet>, boolean) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper: results will be sorted by size
convertToLightValueObjects(Collection<GeneSet>, boolean) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
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.core.genome.gene.GeneSetValueObjectHelper: Constructor to build value object from GeneSet.
convertToValueObject(GeneSet) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
convertToValueObjects(Collection<GeneSet>) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper
convertToValueObjects(Collection<GeneSet>) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
convertToValueObjects(Collection<GeneSet>, boolean) - Method in interface ubic.gemma.core.genome.gene.GeneSetValueObjectHelper
convertToValueObjects(Collection<GeneSet>, boolean) - Method in class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
COORDINATE - 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(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.BioMaterialService: Copies a bioMaterial.
copy(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
copyUploadedFile(HttpServletRequest, String) - Static method in class ubic.gemma.web.util.upload.FileUploadUtil
copyUploadedFile(MultipartFile, HttpServletRequest) - Static method in class ubic.gemma.web.util.upload.FileUploadUtil
copyUploadedInputStream(InputStream) - Static method in class ubic.gemma.web.util.upload.FileUploadUtil
correctedPvalue(int, int, double, int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
CORRELATION - ubic.gemma.model.common.quantitationtype.StandardQuantitationType
correlFast(double[], double[], int, int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics
CorsFilter - Class in ubic.gemma.rest.servlet: Filter for adding CORS headers to the RESTful API responses.
CorsFilter() - Constructor for class ubic.gemma.rest.servlet.CorsFilter
cosine - ubic.gemma.core.ontology.GoMetric.Metric
count - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
count() - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController
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 - ubic.gemma.model.common.measurement.MeasurementKind
COUNT - ubic.gemma.model.common.quantitationtype.ScaleType: Indicates value was (originally) an integer count of something, such as RNAseq reads.
COUNT - ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Indicates value is a count, such as the number of sequencing reads.
COUNT_KEY - Static variable in class ubic.gemma.web.listener.UserCounterListener
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 instances of specific class in the persitent storage.
countAll() - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
countAll() - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
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.ExpressionExperimentService
countBioMaterials(Filters) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
countCharacteristicsByValueUri(Collection<String>) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
countCharacteristicsByValueUri(Collection<String>) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
countCharacteristicsByValueUriGroupedByNormalizedValue(Collection<String>) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Count characteristics matching the provided value URIs.
countCharacteristicsByValueUriGroupedByNormalizedValue(Collection<String>) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
countDownregulated(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
countDownregulated(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
countDownregulated(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: counts the evidence that from neurocarta that came from a specific MetaAnalysis
countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
countLinks(BioAssaySet, Gene) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
countLinks(BioAssaySet, Gene) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
countLinks(Gene, BioAssaySet) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
countLinks(Gene, BioAssaySet) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
countOldLinks(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
countOldLinks(Collection<Gene>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
countOldLinks(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
countOldLinks(Collection<Gene>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
countProbesMeetingThreshold(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
countProbesMeetingThreshold(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
countProbesMeetingThreshold(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
countUpregulated(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
countUpregulated(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
countUpregulated(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
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.ArrayDesignService
countWithCache(Filters) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
countWithCache(Filters, Set<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
countWithCache(Filters, Set<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
create(double, Long, Long) - Method in class ubic.gemma.persistence.service.association.coexpression.LinkCreator
create(C) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
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.UserService
create(UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
create(Collection<C>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
create(Collection<O>) - Method in class ubic.gemma.persistence.service.AbstractService
create(Collection<O>) - Method in interface ubic.gemma.persistence.service.BaseImmutableService: Creates all the given entities in a persistent storage
create(Collection<T>) - Method in class ubic.gemma.persistence.service.AbstractDao
create(Collection<T>) - Method in interface ubic.gemma.persistence.service.BaseDao: Crates all the given entities in the persistent storage.
create(Collection<DifferentialExpressionAnalysisResult>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
create(Collection<ExternalDatabase>) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
create(Collection<ArrayDesign>) - Static method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
create(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
create(Collection<GeneSet>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
create(Collection<GeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX create an entities in the database based on the value objects passed in
create(O) - Method in class ubic.gemma.persistence.service.AbstractService
create(O) - Method in interface ubic.gemma.persistence.service.BaseImmutableService: Creates the given entity in the persistent storage.
create(T) - Method in class ubic.gemma.persistence.service.AbstractDao
create(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Create an object.
create(SimpleExpressionExperimentMetaData, InputStream) - Method in interface ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService: Parses, converts (into Gemma objects), and loads data into the database.
create(SimpleExpressionExperimentMetaData, InputStream) - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl
create(CoexpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
create(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
create(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
create(GeneDifferentialExpressionMetaAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
create(ExpressionExperimentSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
create(GeneCoexpressionNodeDegree) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionNodeDegreeDaoImpl: The coexpression node degree model has its ID assigned from its associated Gene and thus cannot be persisted with Session.persist(Object).
create(Gene2GOAssociation) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
create(GenericExperiment) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
create(GenericExperiment) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
create(PhenotypeAssociation) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
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.core.annotation.reference.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 interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
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(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
create(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
create(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
create(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
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<CompositeSequence, Integer>, double[], DoubleMatrix<Integer, BioMaterial>, BioAssayDimension, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
create(ExpressionExperiment, DoubleMatrix<CompositeSequence, Integer>, double[], DoubleMatrix<Integer, BioMaterial>, BioAssayDimension, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl
create(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
create(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
create(Gene) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
create(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
create(GeneSet) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
create(AnnotationAssociation) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
create(BlatAssociation) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
create(Taxon) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
CREATE - Static variable in enum ubic.gemma.model.common.auditAndSecurity.AuditAction: Aliases, for readability.
createBADMap(List<BioMaterial>) - Static method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer: This bioAssayDimension shouldn't get persisted; it is only for dealing with subset diff ex.
createBatchFactor(ExpressionExperiment, Map<BioMaterial, Date>) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService
createBatchFactor(ExpressionExperiment, Map<BioMaterial, Date>) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl
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.
createBiomaterialTag(Characteristic, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
createDatabaseEntity(GeneSetValueObject) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService: create an entity in the database based on the value object parameter
createDatabaseEntity(GeneSetValueObject) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
createDesignFromFile(Long, String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
createEELink(BioAssaySet, Long, Long, Long) - Method in class ubic.gemma.persistence.service.association.coexpression.LinkCreator
createExperimentalFactor(EntityDelegator<ExperimentalDesign>, ExperimentalFactorValueWebUIObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
createExperimentTag(Characteristic, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController: Ajax
createFactorValue(EntityDelegator<ExperimentalFactor>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
createFactorValueCharacteristic(EntityDelegator<FactorValue>, CharacteristicValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
createFile(File) - Static method in class ubic.gemma.persistence.util.EntityUtils
createFromValueObject(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
createFromValueObject(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
createGroup(String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
createGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
createGroup(String, List<GrantedAuthority>) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
createInstance() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory
createItem(String, String, boolean, String) - Method in class ubic.gemma.web.util.upload.MonitoredDiskFileItemFactory
createMeanVariance(ExpressionExperiment, MeanVarianceRelation) - Method in interface ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper
createObject() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceFactory
createObject() - Method in class ubic.gemma.persistence.util.AbstractAsyncFactoryBean: Create a new bean as per AbstractAsyncFactoryBean.getObject().
createOrUpdate(BioAssaySet, List<NonPersistentNonOrderedCoexpLink>, LinkCreator, Set<Gene>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
createOrUpdate(BioAssaySet, List<NonPersistentNonOrderedCoexpLink>, LinkCreator, Set<Gene>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
createOrUpdate(BioAssaySet, List<NonPersistentNonOrderedCoexpLink>, LinkCreator, Set<Gene>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService: Maintenance method.
createOrUpdate(BioAssaySet, List<NonPersistentNonOrderedCoexpLink>, LinkCreator, Set<Gene>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
createOrUpdateAclSpecialCases(MutableAcl, Acl, Sid, Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
createPrimaryPublication(String) - Static method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
createProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
createProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
createProcessedDataVectors(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao: Populate the processed data for the given experiment.
createProcessedDataVectors(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
createProcessedDataVectors(ExpressionExperiment, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Populate the processed data for the given experiment.
createProcessedDataVectors(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
createQueryObject(Criteria, ExpressionExperimentSubSet) - Static method in class ubic.gemma.persistence.util.BusinessKey
createQueryObject(Criteria, FactorValue) - Static method in class ubic.gemma.persistence.util.BusinessKey
createQueryObject(Criteria, Gene) - Static method in class ubic.gemma.persistence.util.BusinessKey
createQueryObject(Criteria, GeneProduct) - Static method in class ubic.gemma.persistence.util.BusinessKey
createQueryObject(Session, Characteristic) - Static method in class ubic.gemma.persistence.util.BusinessKey
createQueryObject(Session, Unit) - Static method in class ubic.gemma.persistence.util.BusinessKey
createQueryObject(Session, ArrayDesign) - Static method in class ubic.gemma.persistence.util.BusinessKey
createQueryObject(Session, BioAssay) - Static method in class ubic.gemma.persistence.util.BusinessKey
createQueryObject(Session, BioSequence) - Static method in class ubic.gemma.persistence.util.BusinessKey
createQueryStringFromMap(Map<String, String[]>, String) - Static method in class ubic.gemma.web.util.RequestUtil: Builds a query string from a given map of parameters
createRelevantPublication(String) - Static method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
createRnaSeqBatchFactor(ExpressionExperiment, Map<BioMaterial, String>) - 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<BioMaterial, String>) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl
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
createSupportDetails(Long, Long, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.LinkCreator
createSupportDetails(Gene, Gene, Boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.LinkCreator
createUser(UserDetails) - Method in interface ubic.gemma.core.security.authentication.UserManager
createUser(UserDetails) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
createValueObject() - Method in class ubic.gemma.model.expression.experiment.BioAssaySet: Special use case.
createValueObject() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
createValueObject() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
createVectorMatrix(Map<Long, Collection<String>>, boolean) - Method in interface ubic.gemma.core.ontology.GoMetric
createVectorMatrix(Map<Long, Collection<String>>, boolean) - Method in class ubic.gemma.core.ontology.GoMetricImpl
createWebApplicationContext(ServletContext) - Method in class ubic.gemma.web.listener.StartupListener
createWriteFolder() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
creator() - Method in class ubic.gemma.core.util.Pointcuts: Methods that create new objects in the persistent store
CtdDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
CtdDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
Curatable - Interface in ubic.gemma.model.common.auditAndSecurity.curation: Created by tesarst on 06/03/17.
CuratableDao<C extends Curatable> - Interface in ubic.gemma.persistence.service.common.auditAndSecurity.curation: Created by tesarst on 13/03/17.
CuratableService<C extends Curatable,VO extends AbstractCuratableValueObject<C>> - Interface in ubic.gemma.persistence.service.expression.arrayDesign: Interface for curatable services.
CURATED - Static variable in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
CURATION_DETAILS_ALIAS - Static variable in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: HQL alias for Curatable.getCurationDetails().
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: Event types that can change CurationDetails of Curatable objects.
CurationDetailsEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent
CurationNoteUpdateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that previous validation is being invalidated
CurationNoteUpdateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent
currentContext() - Static method in class ubic.gemma.core.job.executor.common.ProgressUpdateAppender.ProgressUpdateContext
CustomModelResolver - Class in ubic.gemma.rest.swagger.resolver: Resolve Arg parameters' schema.
CustomModelResolver(ObjectMapper, SearchService) - Constructor for class ubic.gemma.rest.swagger.resolver.CustomModelResolver
CustomModelResolverRegistrationListener - Class in ubic.gemma.rest.swagger.resolver: Registers our customized ModelResolver.
CustomModelResolverRegistrationListener() - Constructor for class ubic.gemma.rest.swagger.resolver.CustomModelResolverRegistrationListener
CustomRssViewer - Class in ubic.gemma.web.controller.common.rss
CustomRssViewer() - Constructor for class ubic.gemma.web.controller.common.rss.CustomRssViewer
CV - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
cvs2tsv(String) - Static method in class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser: Deprecated.
cytoplasmicRNA - ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule

D

D - ubic.gemma.model.analysis.expression.diff.Direction: Down
D - ubic.gemma.model.common.auditAndSecurity.AuditAction: Delete
daily(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController
daoMethod() - Method in class ubic.gemma.core.util.Pointcuts: A DAO method, public and within a class annotated with Repository.
data - Variable in class ubic.gemma.model.analysis.expression.coexpression.IdArray
DATA_ARCHIVE_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
DATA_DIR - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
DATA_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
DATA_FILE_SUFFIX_COMPRESSED - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
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
DataAnalysisEvidence - Class in ubic.gemma.model.association.phenotype: Deprecated.
DataAnalysisEvidence() - Constructor for class ubic.gemma.model.association.phenotype.DataAnalysisEvidence: Deprecated.
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: No-arg constructor added to satisfy javabean contract
DatabaseEntry.Factory - Class in ubic.gemma.model.common.description
DatabaseEntryArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for DatabaseEntry API.
DatabaseEntryArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.DatabaseEntryArg
DatabaseEntryArgService - Class in ubic.gemma.rest.util.args
DatabaseEntryArgService(DatabaseEntryService) - Constructor for class ubic.gemma.rest.util.args.DatabaseEntryArgService
DatabaseEntryArrayArg - Class in ubic.gemma.rest.util.args
DatabaseEntryDao - Interface in ubic.gemma.persistence.service.common.description
DatabaseEntryDaoImpl - Class in ubic.gemma.persistence.service.common.description: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type DatabaseEntry.
DatabaseEntryDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImpl
DatabaseEntryIdArg - Class in ubic.gemma.rest.util.args: Long argument type for DatabaseEntry API, referencing the Taxon ID.
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) - Constructor for class ubic.gemma.persistence.service.common.description.DatabaseEntryServiceImpl
DatabaseEntryStringArg - Class in ubic.gemma.rest.util.args: String argument type for DatabaseEntry API, Can also be null.
DatabaseEntryTag - Class in ubic.gemma.web.taglib
DatabaseEntryTag() - Constructor for class ubic.gemma.web.taglib.DatabaseEntryTag
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
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 in ubic.gemma.model.common.description
DatabaseViewGenerator - Interface in ubic.gemma.core.analysis.report
DatabaseViewGeneratorCLI - Class in ubic.gemma.core.apps: Simple driver of DatabaseViewGenerator.
DatabaseViewGeneratorCLI() - Constructor for class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
DatabaseViewGeneratorImpl - Class in ubic.gemma.core.analysis.report: Generates textual views of the database so other people can use the data.
DatabaseViewGeneratorImpl() - Constructor for class ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl
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
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_FOLDER_NAME - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
DatasetArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for dataset (ExpressionExperiment) API.
DatasetArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.DatasetArg
DatasetArgService - Class in ubic.gemma.rest.util.args
DatasetArgService(ExpressionExperimentService, SearchService, ArrayDesignService, BioAssayService, OutlierDetectionService) - Constructor for class ubic.gemma.rest.util.args.DatasetArgService
DatasetArrayArg - Class in ubic.gemma.rest.util.args
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
datasetFetcher - Variable in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
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
DatasetIdArg - Class in ubic.gemma.rest.util.args: Long argument type for dataset API, referencing the Dataset ID.
DatasetIdArg(long) - Constructor for class ubic.gemma.rest.util.args.DatasetIdArg
DatasetStringArg - Class in ubic.gemma.rest.util.args: String argument type for dataset API, referencing the Dataset short name.
DatasetsWebService - Class in ubic.gemma.rest: RESTful interface for datasets.
DatasetsWebService() - Constructor for class ubic.gemma.rest.DatasetsWebService
DatasetsWebService.AnnotationWithUsageStatisticsValueObject - Class in ubic.gemma.rest: This is an aggregated entity across value URI and value, thus the id and objectClass are omitted.
DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.CategoryWithUsageStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.ExpressionExperimentWithSearchResultValueObject - Class in ubic.gemma.rest
DatasetsWebService.OntologyTermValueObject - Class in ubic.gemma.rest
DatasetsWebService.TaxonWithUsageStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.UsageStatistics - Interface in ubic.gemma.rest
DataUpdater - Interface in ubic.gemma.core.loader.expression
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 experiment.
DataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVector
DataVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData
DataVectorValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject: Required when using the class as a spring bean.
DataVectorValueObject(Long) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
DataVectorValueObject(DesignElementDataVector, Collection<Long>, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
DataVectorValueObject(DesignElementDataVector, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
date - Variable in class ubic.gemma.core.analysis.report.AuditableObject
DE_EXCLUDE_URI - Static variable in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
DE_INCLUDE_URI - Static variable in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
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.
decodeCompressedArg(String) - Static method in class ubic.gemma.rest.util.ArgUtils: Decode a base64-encoded gzip-compressed argument.
decrementSessions() - Static method in class ubic.gemma.web.listener.UserTracker
DEDVController - Class in ubic.gemma.web.controller.expression.experiment: Exposes methods for accessing underlying Design Element Data Vectors.
DEDVController() - Constructor for class ubic.gemma.web.controller.expression.experiment.DEDVController
DEDVfromEEIDGeneIDEndpoint - Class in ubic.gemma.web.services: Given a list Experiment IDs and a list gene IDs will return design element data vectors (DEDV), all the genes that could have been responsible for that DEDV (only needs to contain 1 of the given genes) and the Expression Experiment that the data came from.
DEDVfromEEIDGeneIDEndpoint() - Constructor for class ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint
DEDVRankEndpoint - Class in ubic.gemma.web.services: Given a collection of gene IDs, a collection of experiment IDs, and the method, the service will return a list of genes mapped to a list of space delimited ranks.
DEDVRankEndpoint() - Constructor for class ubic.gemma.web.services.DEDVRankEndpoint
deepCopy(Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
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_BLAT_SCORE_THRESHOLD - Static variable in interface ubic.gemma.core.apps.Blat: This value is basically a threshold fraction of aligned bases in the query.
DEFAULT_DISTINCTVALUE_FRACTION - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
DEFAULT_EBAYES - Static variable in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig: Default value for whether empirical Bayes moderation of test statistics should be used.
DEFAULT_HIGHEXPRESSION_CUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
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_LOWEXPRESSIONCUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
DEFAULT_LOWVARIANCECUT - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
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_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_MINPRESENT_FRACTION - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
DEFAULT_PA_LIMIT - Static variable in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
DEFAULT_PROBE_DEGREE_THRESHOLD - Static variable in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig: probes with more links than this are ignored.
DEFAULT_QC_IMAGE_SIZE_PX - Static variable in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
DEFAULT_REQUEST_HEADER - Static variable in class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy
DEFAULT_SCORE_THRESHOLD - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig: BLAT score threshold below which we do not consider hits.
DEFAULT_SIGNAL_TO_NOISE_THRESHOLD - Static variable in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
DEFAULT_THRESHOLD - Static variable in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
DEFAULT_TOOSMALLTOKEEP - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
DEFAULT_TRIM_NONCANONICAL_CHROMOSOMES - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
DefaultHighlighter - Class in ubic.gemma.core.search
DefaultHighlighter() - Constructor for class ubic.gemma.core.search.DefaultHighlighter
DefaultHighlighter(Formatter) - Constructor for class ubic.gemma.core.search.DefaultHighlighter
defineTask(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
defineTask(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
delete(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
delete(UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
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.web.controller.expression.arrayDesign.ArrayDesignController: Delete an arrayDesign.
delete(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
delete(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
delete(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
DELETE - Static variable in enum ubic.gemma.model.common.auditAndSecurity.AuditAction: Aliases, for readability.
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
deleteAllFiles(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Delete any existing coexpression, data, or differential expression data files.
deleteAllFiles(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
deleteAnalyses(BioAssaySet) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersister: Remove any links and coexpression analyses for the given experiment.
deleteAnalyses(BioAssaySet) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersisterImpl
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
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
deleteById(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Exposed for AJAX calls.
deleteCookie(HttpServletResponse, Cookie, String) - Static method in class ubic.gemma.web.util.RequestUtil: Convenience method for deleting a cookie by name
deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService: Security is handled within method
deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject>) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
deleteDatabaseEntity(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: Security is handled within method, when the set is loaded
deleteDatabaseEntity(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
deleteDatabaseEntity(DatabaseBackedGeneSetValueObject) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService: Security is handled within method, when the set is loaded
deleteDatabaseEntity(DatabaseBackedGeneSetValueObject) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
deleteDiffExArchiveFile(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
deleteDiffExArchiveFile(DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
DeleteDiffExCli - Class in ubic.gemma.core.apps: Delete differential expression analsyes on a per-experiment basis.
DeleteDiffExCli() - Constructor for class ubic.gemma.core.apps.DeleteDiffExCli
DeleteEvidenceCLI - Class in ubic.gemma.core.loader.association.phenotype: When we need to remove all evidence from an external database, usually to reimport them after
DeleteEvidenceCLI() - Constructor for class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
deleteExistingFiles(ArrayDesign) - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
deleteExistingFiles(ArrayDesign) - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
deleteExperimentalFactors(EntityDelegator<ExperimentalDesign>, Long[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
DeleteExperimentsCli - Class in ubic.gemma.core.apps: Delete one or more experiments from the system.
DeleteExperimentsCli() - Constructor for class ubic.gemma.core.apps.DeleteExperimentsCli
deleteFactorValueCharacteristics(FactorValueValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
deleteFactorValues(Collection<Long>) - Method in interface ubic.gemma.core.expression.experiment.FactorValueDeletion
deleteFactorValues(Collection<Long>) - Method in class ubic.gemma.core.expression.experiment.FactorValueDeletionImpl
deleteFactorValues(EntityDelegator<ExperimentalFactor>, Long[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
deleteFile(File) - Static method in class ubic.gemma.persistence.util.EntityUtils
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
deleteGroup(String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController: AJAX
deleteGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
deleteLinks(BioAssaySet) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService: Maintenance method.
deleteLinks(BioAssaySet) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
deleteLinks(Taxon, BioAssaySet) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
deleteLinks(Taxon, BioAssaySet) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
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
deleter() - Method in class ubic.gemma.core.util.Pointcuts: Methods that remove items in the persistent store
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
DELIMITER - Static variable in class ubic.gemma.web.services.AbstractGemmaEndpoint
DELIMITER_BETWEEN_BIOMATERIAL_AND_BIOASSAYS - Static variable in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
DEPRECATED - ubic.gemma.core.apps.GemmaCLI.CommandGroup
DESC - ubic.gemma.persistence.util.Sort.Direction
DESC - ubic.gemma.rest.util.args.SortArg.Sort.Direction
Describable - Interface in ubic.gemma.model.common
DescribableComparator - Class in ubic.gemma.persistence.util
DescribableComparator() - Constructor for class ubic.gemma.persistence.util.DescribableComparator
description - Variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
DesignElementDataVector - Class in ubic.gemma.model.expression.bioAssayData
DesignElementDataVector() - Constructor for class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
DesignElementDataVectorDao<T extends DesignElementDataVector> - Interface in ubic.gemma.persistence.service.expression.bioAssayData
DesignMatrixRowValueObject - Class in ubic.gemma.web.controller.expression.experiment: For the display of a summary table about experimental design.
DesignMatrixRowValueObject(FactorValueVector, int) - Constructor for class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
DesignMatrixRowValueObject.Factory - Class in ubic.gemma.web.controller.expression.experiment
destroy() - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
destroy() - Method in class ubic.gemma.core.job.executor.webapp.TaskRunningServiceImpl
destroy() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
destroy() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
destroy() - Method in class ubic.gemma.persistence.util.AbstractAsyncFactoryBean
destroy() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
destroyInstance(T) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory
detailedFactorAnalysis(Long, OutputStream) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
detectSuspiciousValues(ExpressionDataDoubleMatrix, QuantitationType) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil: Detect suspicious values for a given quantitation type.
determineAnalysis(BioAssaySet, Collection<ExperimentalFactor>, ExperimentalFactor, boolean) - Method in interface ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService: Determines the analysis to execute based on the experimental factors, factor values, and block design.
determineAnalysis(BioAssaySet, Collection<ExperimentalFactor>, ExperimentalFactor, boolean) - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl: FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
determineAnalysis(BioAssaySet, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
determineAnalysis(BioAssaySet, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl: FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
determineAnalysisType(Long) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController: Ajax method.
determineEncoding(HttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver: Determine the encoding for the given request.
determineInterceptFactor(Collection<ExperimentalFactor>, QuantitationType) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer
determineInterceptFactor(Collection<ExperimentalFactor>, QuantitationType) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer: Determine if any factor should be treated as the intercept term.
DEV - Static variable in class ubic.gemma.persistence.util.EnvironmentProfiles
developmentStage - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
DgaDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
DgaDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
diagnostics(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.PreprocessController: Only update the daignostics
diagnosticsOnly() - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
DifferentialExpressionAnalysis - Class in ubic.gemma.model.analysis.expression.diff: An analysis of changes in expression levels across experimental conditions
DifferentialExpressionAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
DifferentialExpressionAnalysis.Factory - Class in ubic.gemma.model.analysis.expression.diff
DifferentialExpressionAnalysisCli - Class in ubic.gemma.core.apps: A command line interface to the DifferentialExpressionAnalysis.
DifferentialExpressionAnalysisCli() - Constructor for class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
DifferentialExpressionAnalysisConfig - Class in ubic.gemma.core.analysis.expression.diff: Holds the settings used for differential expression analysis, and defines some defaults.
DifferentialExpressionAnalysisConfig() - Constructor for class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
DifferentialExpressionAnalysisController - Class in ubic.gemma.web.controller.diff: A controller to run differential expression analysis either locally or in a space.
DifferentialExpressionAnalysisController() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController
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
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
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: No-arg constructor added to satisfy javabean contract
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
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(ExpressionAnalysisResultSet) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject: Create a simple analysis results set VO with limited data.
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet, Map<Long, List<Gene>>) - 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, List<Gene>) - Constructor for class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
DifferentialExpressionAnalysisService - Interface in ubic.gemma.persistence.service.analysis.expression.diff
DifferentialExpressionAnalysisServiceImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
DifferentialExpressionAnalysisServiceImpl(DifferentialExpressionAnalysisDao) - 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(String, 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.
DifferentialExpressionAnalyzerInfo - Class in ubic.gemma.web.controller.diff: Used to carry information about the experimental design analysis settings to clients.
DifferentialExpressionAnalyzerInfo() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo
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
DifferentialExpressionAnalyzerServiceImpl.AnalysisType - Enum 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
DifferentialExpressionEvidence - Class in ubic.gemma.model.association.phenotype: Deprecated.
DifferentialExpressionEvidence() - Constructor for class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence: Deprecated.
DifferentialExpressionEvidence.Factory - Class in ubic.gemma.model.association.phenotype: Deprecated.
DifferentialExpressionEvidenceDao - Interface in ubic.gemma.persistence.service.association.phenotype
DifferentialExpressionEvidenceDaoImpl - Class in ubic.gemma.persistence.service.association.phenotype
DifferentialExpressionEvidenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.phenotype.DifferentialExpressionEvidenceDaoImpl
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
DifferentialExpressionProbeResultEndpoint - Class in ubic.gemma.web.services: Allows access to the differential expression analysis.
DifferentialExpressionProbeResultEndpoint() - Constructor for class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint
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
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
DifferentialExpressionResultServiceImpl(DifferentialExpressionResultDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
DifferentialExpressionSearchController - Class in ubic.gemma.web.controller.diff: A controller used to get differential expression analysis and meta analysis results.
DifferentialExpressionSearchController() - Constructor for class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController
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<GeneValueObject>, Collection<ExpressionExperimentDetailsValueObject>, 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
DiffExAnalyzer - Interface in ubic.gemma.core.analysis.expression.diff
DiffExGene(long, String, String) - Constructor for class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
DiffExMetaAnalyzerController - Class in ubic.gemma.web.controller.diff: A controller to analyze result sets either locally or in a space.
DiffExMetaAnalyzerController() - Constructor for class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
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<Long>) - Constructor for class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
DiffExMetaAnalyzerTaskCommand(Collection<Long>, 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
DiffExpressionEvidenceValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
DiffExpressionEvidenceValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject: Required when using the class as a spring bean.
DiffExpressionEvidenceValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
DiffExpressionEvidenceValueObject(Long, GeneDifferentialExpressionMetaAnalysis, GeneDifferentialExpressionMetaAnalysisResult, SortedSet<CharacteristicValueObject>, String, Double) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
DiffExpressionEvidenceValueObject(DifferentialExpressionEvidence, GeneDifferentialExpressionMetaAnalysisSummaryValueObject) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
DiffExpressionSearchCommand - Class in ubic.gemma.web.controller.diff
DiffExpressionSearchCommand() - Constructor for class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
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
DIRECT - Static variable in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
Direction - Enum in ubic.gemma.model.analysis.expression.diff: Represents the direction of a change e.g.
DirectionConverter - Class in ubic.gemma.web.remote: DWR converter for Direction type.
DirectionConverter() - Constructor for class ubic.gemma.web.remote.DirectionConverter
disableEmail() - Method in interface ubic.gemma.persistence.service.TableMaintenanceUtil
disableEmail() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilImpl: For use in tests.
disableStatistics() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController: Exposed to AJAX
disableStatistics() - Method in interface ubic.gemma.web.util.CacheMonitor: Disable collection of statistics on the caches.
disableStatistics() - Method in class ubic.gemma.web.util.CacheMonitorImpl
disassemble(Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
DISCLAIMER - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
disconnect(FTPClient) - Method in class ubic.gemma.core.util.NetDatasourceUtil
discontinuedIdForSymbol(String, Integer) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
DISEASE_ONTOLOGY_ROOT - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
diseaseState - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
disjunction() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
disjunction() - Method in class ubic.gemma.rest.util.args.FilterArgParser
disjunction(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
DISJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
DISJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
DISJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
DISJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
DisjunctionContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
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 - ubic.gemma.model.common.measurement.MeasurementKind
distinctIfNecessary() - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: If the filters or sort refer to one of the one-to-many relations, multiple rows will be returned per datasets, so the query has to use a "distinct" clause make pagination work properly.
DISTINCTVALUES - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
DNA - ubic.gemma.model.genome.biosequence.PolymerType
DNA - ubic.gemma.model.genome.biosequence.SequenceType: Generic DNA sequence of any other type not representable by another value
doAll() - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
doBackgroundCoexSearch(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController: Used by CoexpressionSearchData.js - the main home page coexpression search.
doCreateAdvice(JoinPoint) - Method in class ubic.gemma.core.security.audit.AuditAdvice: Perform the audit advice on when entities are created.
doDelete - Variable in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
doDeleteAdvice(JoinPoint) - Method in class ubic.gemma.core.security.audit.AuditAdvice: Perform auditing when entities are deleted.
doEndTag() - Method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
doEndTag() - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
doEndTag() - Method in class ubic.gemma.web.taglib.DatabaseEntryTag
doEndTag() - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
doEndTag() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
doEndTag() - Method in class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
doesCurrentUserOwnExperiment(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX returns a JSON string encoding whether the current user owns the experiment and whether they can edit it
DoesNotNeedAttentionEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: An event that occurs when a curator has validated the entity and indicated that it is "approved".
DoesNotNeedAttentionEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent: No-arg constructor added to satisfy javabean contract
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.rest.servlet.CorsFilter
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilter
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.web.metrics.binder.servlet.ServletMetricsFilter
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(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(BlacklistedEntity) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl
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<O>) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao: Load all the value objects for the given entities.
doLoadValueObjects(Collection<ExpressionExperimentSet>) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
done() - Method in interface ubic.gemma.web.util.upload.OutputStreamListener
done() - Method in class ubic.gemma.web.util.upload.UploadListener
doNothingFilter(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
doPersist(Object, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.AbstractPersister
doPersist(Object, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.ArrayDesignPersister
doPersist(Object, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.CommonPersister
doPersist(Object, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.ExpressionPersister
doPersist(Object, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.GenomePersister
doPersist(Object, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.PersisterHelperImpl
doPersist(Object, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.RelationshipPersister
doPersist(Collection<?>, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.AbstractPersister
doPersistOrUpdate(Object, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.AbstractPersister
doPersistOrUpdate(Object, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.GenomePersister
doSaveAdvice(JoinPoint) - Method in class ubic.gemma.core.security.audit.AuditAdvice: Perform auditing when entities are saved.
dose - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
doSearch(HttpServletRequest, HttpServletResponse, SearchSettings, BindException) - Method in interface ubic.gemma.web.controller.GeneralSearchController
doSearch(HttpServletRequest, HttpServletResponse, SearchSettings, BindException) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl
doSearch(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController: Important entry point - called by the CoexpressionSearchTask
doSearchQuickComplete(CoexpressionSearchCommand, Collection<Long>) - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController: Do a search that fills in the edges among the genes already found.
doStartTag() - Method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
doStartTag() - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
doStartTag() - Method in class ubic.gemma.web.taglib.ConstantsTag
doStartTag() - Method in class ubic.gemma.web.taglib.DatabaseEntryTag
doStartTag() - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
doStartTag() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
doStartTag() - Method in class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
doSubmittedTasksMaintenance() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTasksMaintenance: Check if a task has been running or queued for too long, and cancel it if necessary.
doTask(FutureTask<Boolean>, long, String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
doTask(FutureTask<Boolean>, long, String, String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
doTask(FutureTask<Boolean>, String, String) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
DOUBLE - ubic.gemma.model.common.quantitationtype.PrimitiveType
DOUBLEARRAY - ubic.gemma.model.common.quantitationtype.PrimitiveType
DoublePointConverter - Class in ubic.gemma.web.remote: The 8 decimal precision of a double is just a waste of bandwidth in most cases.
DoublePointConverter() - Constructor for class ubic.gemma.web.remote.DoublePointConverter
DoubleVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData: Simple wrapper for a double[] that is derived from a DesignElementDataVector.
DoubleVectorValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: Required when using the class as a spring bean.
DoubleVectorValueObject(DesignElementDataVector, Collection<Long>, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
DoubleVectorValueObject(DesignElementDataVector, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
DoubleVectorValueObject(DesignElementDataVector, BioAssayDimensionValueObject, Collection<Long>, BioAssayDimension) - 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(ExpressionExperimentSubSet, DoubleVectorValueObject, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject: Create a vector that is a slice of another one.
doUpdateAdvice(JoinPoint) - Method in class ubic.gemma.core.security.audit.AuditAdvice: Perform auditing when entities are updated.
DOWN - Static variable in enum ubic.gemma.model.analysis.expression.diff.Direction: Aliases for readability.
downloadAnnotationFile(Long, String, HttpServletResponse) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
downloadAnnotationFile(Long, String, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
downloadFile(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController: Regular spring MVC request to fetch a file that already has been generated.
downloadMetaFile(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
doWork() - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
doWork() - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
doWork() - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
doWork() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
doWork() - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
doWork() - Method in class ubic.gemma.core.apps.BlacklistCli
doWork() - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
doWork() - Method in class ubic.gemma.core.apps.DeleteDiffExCli
doWork() - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
doWork() - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
doWork() - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
doWork() - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
doWork() - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
doWork() - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
doWork() - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
doWork() - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
doWork() - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
doWork() - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
doWork() - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
doWork() - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
doWork() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
doWork() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
doWork() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
doWork() - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
doWork() - Method in class ubic.gemma.core.apps.GeeqCli
doWork() - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
doWork() - Method in class ubic.gemma.core.apps.GeoGrabberCli
doWork() - Method in class ubic.gemma.core.apps.IndexGemmaCLI
doWork() - Method in class ubic.gemma.core.apps.LinkAnalysisCli
doWork() - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
doWork() - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
doWork() - Method in class ubic.gemma.core.apps.MakeExperimentPrivateCli
doWork() - Method in class ubic.gemma.core.apps.MakeExperimentsPublicCli
doWork() - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
doWork() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
doWork() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
doWork() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
doWork() - Method in class ubic.gemma.core.apps.OrderVectorsByDesignCli
doWork() - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
doWork() - Method in class ubic.gemma.core.apps.PubMedLoaderCli
doWork() - Method in class ubic.gemma.core.apps.ReplaceDataCli
doWork() - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
doWork() - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
doWork() - Method in class ubic.gemma.core.apps.SplitExperimentCli
doWork() - Method in class ubic.gemma.core.apps.SVDCli
doWork() - Method in class ubic.gemma.core.apps.TaxonLoaderCli
doWork() - Method in class ubic.gemma.core.apps.UpdateEE2CCli
doWork() - Method in class ubic.gemma.core.apps.UpdatePubMedCli
doWork() - Method in class ubic.gemma.core.apps.VectorMergingCli
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
doWork() - Method in class ubic.gemma.core.util.AbstractCLI: Command line implementation.
dualChannel - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
dualChannelGenomic - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
DUALMODE - ubic.gemma.model.expression.arrayDesign.TechnologyType: Indicates this platform can be used in either a one- or two- channel mode.
DUMMY - ubic.gemma.model.genome.biosequence.SequenceType: A placeholder element used for annotation associations for RNA-seq
DummyMailSender - Class in ubic.gemma.core.util: Mock mail sender for testing.
DummyMailSender() - Constructor for class ubic.gemma.core.util.DummyMailSender
DumpsValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
DumpsValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
DumpsValueObject(String, String, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
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.

E

E - ubic.gemma.model.analysis.expression.diff.Direction: Either direction (up or down).
editUser(String, String, String, String, String, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController: Entry point for updates.
EE2AD_QUERY_SPACE - Static variable in interface ubic.gemma.persistence.service.TableMaintenanceUtil: Query space used by the EXPRESSION_EXPERIMENT2ARRAY_DESIGN table.
EE2C_QUERY_SPACE - Static variable in interface ubic.gemma.persistence.service.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
eeService - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
ehcache(String) - Method in class ubic.gemma.persistence.util.EhcacheConfig: The ehcache.xml assume that -Dehcache.disk.store.dir is set.
EhCache24Metrics - Class in ubic.gemma.core.metrics.binder.cache: Metrics for Ehcache 2.4 series.
EhCache24Metrics(Ehcache, Iterable<Tag>) - Constructor for class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics
EhcacheConfig - Class in ubic.gemma.persistence.util
EhcacheConfig() - Constructor for class ubic.gemma.persistence.util.EhcacheConfig
Eigenvalue - Class in ubic.gemma.model.analysis.expression.pca
Eigenvalue() - Constructor for class ubic.gemma.model.analysis.expression.pca.Eigenvalue: No-arg constructor added to satisfy javabean contract
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 ubic.gemma.model.analysis.expression.diff.Direction: Aliases for readability.
elementClass - Variable in class ubic.gemma.persistence.service.AbstractDao
EmailNotificationContext - Class in ubic.gemma.core.job: author: anton date: 10/02/13
EmailNotificationContext(String, String, String) - Constructor for class ubic.gemma.core.job.EmailNotificationContext
empty() - Static method in class ubic.gemma.persistence.util.Filters: Create an empty filter.
EmptyController - Class in ubic.gemma.web.controller: This exists just to have an easy way to trick web pages into importing DWR-defined classes that are not in dwrServices.js.
EmptyController() - Constructor for class ubic.gemma.web.controller.EmptyController
EmptyExpressionMatrix - Class in ubic.gemma.core.datastructure.matrix: Used to make a 'dummy matrix' that has the column information populated.
EmptyExpressionMatrix(Collection<BioAssayDimension>) - Constructor for class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
EmptyExpressionMatrix(BioAssayDimension) - Constructor for class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
enableStatistics() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController: Exposed to AJAX
enableStatistics() - Method in interface ubic.gemma.web.util.CacheMonitor: Enable collection of statistics on the caches.
enableStatistics() - Method in class ubic.gemma.web.util.CacheMonitorImpl
encode(Object[]) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
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
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.
ensureInSession(Collection<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
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.datastructure.matrix.ExpressionDataDoubleMatrixUtil
ensureLog2Scale(ExpressionDataDoubleMatrix, boolean) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil: Ensures that the given matrix is on a Log2 scale.
enterClause(FilterArgParser.ClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.clause().
enterClause(FilterArgParser.ClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.clause().
enterCollection(FilterArgParser.CollectionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.collection().
enterCollection(FilterArgParser.CollectionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.collection().
enterCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.collectionOperator().
enterCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.collectionOperator().
enterDisjunction(FilterArgParser.DisjunctionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.disjunction().
enterDisjunction(FilterArgParser.DisjunctionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.disjunction().
enterEveryRule(ParserRuleContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
enterFilter(FilterArgParser.FilterContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.filter().
enterFilter(FilterArgParser.FilterContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.filter().
enterOperator(FilterArgParser.OperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.operator().
enterOperator(FilterArgParser.OperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.operator().
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
enterScalar(FilterArgParser.ScalarContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.scalar().
enterScalar(FilterArgParser.ScalarContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.scalar().
enterSubClause(FilterArgParser.SubClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.subClause().
enterSubClause(FilterArgParser.SubClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.subClause().
EntityArgService<T extends Identifiable,S extends FilteringService<T>> - Interface in ubic.gemma.rest.util.args: Bridges Arg operating on entities with their corresponding FilteringService.
entityArgValueOf(Class<? extends AbstractEntityArg<?, T, S>>, String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService: Invoke either a static valueOf method or a suitable constructor to instantiate the argument.
EntityDelegator<T extends Identifiable> - Class in ubic.gemma.web.remote: Bean to expose for remote access via AJAX, when all that is needed is the ID and a way to know what the class is.
EntityDelegator() - Constructor for class ubic.gemma.web.remote.EntityDelegator
EntityDelegator(T) - Constructor for class ubic.gemma.web.remote.EntityDelegator
EntityNotFoundException - Exception in ubic.gemma.core.association.phenotype: Deprecated.
EntityNotFoundException - Exception in ubic.gemma.rest.util
EntityNotFoundException - Exception in ubic.gemma.web.util: Signals that an entity was not found in the system.
EntityNotFoundException(String) - Constructor for exception ubic.gemma.core.association.phenotype.EntityNotFoundException: Deprecated.
EntityNotFoundException(String) - Constructor for exception ubic.gemma.rest.util.EntityNotFoundException
EntityNotFoundException(String) - Constructor for exception ubic.gemma.web.util.EntityNotFoundException
EntityNotFoundExceptionMapper - Class in ubic.gemma.rest.providers: Deprecated.
EntityNotFoundExceptionMapper() - Constructor for class ubic.gemma.rest.providers.EntityNotFoundExceptionMapper: Deprecated.
EntityUtils - Class in ubic.gemma.persistence.util
EntityUtils() - Constructor for class ubic.gemma.persistence.util.EntityUtils
environmentalHistory - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
EnvironmentProfiles - Class in ubic.gemma.persistence.util: Environment profiles used in the Spring context.
EnvironmentProfiles() - Constructor for class ubic.gemma.persistence.util.EnvironmentProfiles
EOF() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
eq - ubic.gemma.persistence.util.Filter.Operator
EQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
EQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
EQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
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(Object) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
equals(Object) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
equals(Object) - Method in class ubic.gemma.core.analysis.report.AuditableObject
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.genome.gene.GOGroupValueObject
equals(Object) - Method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
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.genome.gene.ncbi.model.NcbiGeneHistory
equals(Object) - Method in class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
equals(Object) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
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.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.expression.coexpression.CoexpCorrelationDistribution: Returns true if the argument is an PvalueDistribution instance and all identifiers for this entity equal the identifiers of the argument entity.
equals(Object) - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressedGenes
equals(Object) - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
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.coexpression.SupportDetails
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
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.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.HitListSize
equals(Object) - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
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.ProbeLoading
equals(Object) - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
equals(Object) - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
equals(Object) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
equals(Object) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
equals(Object) - Method in class ubic.gemma.model.association.Gene2GeneAssociation
equals(Object) - Method in class ubic.gemma.model.association.Gene2GeneIdAssociation
equals(Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
equals(Object) - Method in class ubic.gemma.model.common.AbstractDescribable: Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity.
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.curation.CurationDetails: Compares the objects type and IDs.
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.UserQuery
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.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.ExternalDatabase
equals(Object) - Method in class ubic.gemma.model.common.description.LocalFile
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.quantitationtype.QuantitationType
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.bioAssay.BioAssay
equals(Object) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector: Returns true if the argument is an DataVector instance and all identifiers for this entity equal the identifiers of the argument entity.
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.MeanVarianceRelation
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
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.ExperimentalFactor
equals(Object) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
equals(Object) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
equals(Object) - Method in class ubic.gemma.model.expression.experiment.FactorValue
equals(Object) - Method in class ubic.gemma.model.expression.experiment.Geeq
equals(Object) - Method in class ubic.gemma.model.expression.experiment.Statement
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.ChromosomeLocation: Returns true if the argument is an ChromosomeLocation instance and all identifiers for this entity equal the identifiers of the argument entity.
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.GeneSetMember
equals(Object) - Method in class ubic.gemma.model.genome.gene.Multifunctionality
equals(Object) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
equals(Object) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
equals(Object) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
equals(Object) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject: Deprecated.
equals(Object) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
equals(Object) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
equals(Object) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
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.BioSequenceValueObject
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: Returns true if the argument is a Taxon instance and all identifiers for this entity equal the identifiers of the argument entity.
equals(Object) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
equals(Object) - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
equals(Object) - Method in class ubic.gemma.persistence.util.FactorValueVector
equals(Object) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
equals(Object) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
equals(Object) - Method in class ubic.gemma.web.util.LabelValue
equals(Object, Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
equals(String, String, String, String) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Compare a pair of ontology terms.
ERMINEJ_FOLDER_NAME - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
error(String) - Method in interface ubic.gemma.web.util.upload.OutputStreamListener
error(String) - Method in class ubic.gemma.web.util.upload.UploadListener
ERROR_MSG - Static variable in class ubic.gemma.rest.util.args.AbstractArrayArg
escapeLike(String) - Static method in class ubic.gemma.persistence.util.QueryUtils
escapeTsv(String) - Method in class ubic.gemma.core.analysis.service.AbstractFileService
ESearchException - Exception in ubic.gemma.core.loader.entrez.pubmed
ESearchException(String) - Constructor for exception ubic.gemma.core.loader.entrez.pubmed.ESearchException
ESearchXMLParser - Class in ubic.gemma.core.loader.entrez.pubmed
ESearchXMLParser() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParser
EST - ubic.gemma.model.genome.biosequence.SequenceType
EutilFetch - Class in ubic.gemma.core.loader.entrez
EutilFetch() - Constructor for class ubic.gemma.core.loader.entrez.EutilFetch
EutilFetch.Mode - Enum in ubic.gemma.core.loader.entrez
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
evictIf(Cache, Predicate<Object>) - Static method in class ubic.gemma.persistence.util.CacheUtils: Evict entries from the cache where the key is matching a given predicate.
evictionCount() - Method in class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics
EvidenceFilter - Class in ubic.gemma.model.genome.gene.phenotype: Used to filter values received depending on taxon and privacy chosen
EvidenceFilter() - Constructor for class ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
EvidenceFilter(Long, boolean) - Constructor for class ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
EvidenceFilter(Long, boolean, Collection<Long>) - Constructor for class ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
EvidenceImporterAbstractCLI - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
EvidenceImporterAbstractCLI() - Constructor for class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
EvidenceImporterCLI - Class in ubic.gemma.core.loader.association.phenotype: Class used to load evidence into Phenocarta.
EvidenceImporterCLI() - Constructor for class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
EvidenceSecurityValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
EvidenceSecurityValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
EvidenceSecurityValueObject(boolean, boolean, boolean, boolean, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
EvidenceSourceValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
EvidenceSourceValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSourceValueObject
EvidenceSourceValueObject(String, ExternalDatabaseValueObject) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSourceValueObject
EvidenceSourceValueObject(DatabaseEntry) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSourceValueObject
EvidenceValueObject<E extends PhenotypeAssociation> - Class in ubic.gemma.model.genome.gene.phenotype.valueObject: Parent class of all evidence value objects
EvidenceValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject: Required when using the class as a spring bean.
EvidenceValueObject(E) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject: set fields common to all evidence.
EvidenceValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
EvidenceValueObject(Long, Integer, Set<CharacteristicValueObject>, String, String, boolean, EvidenceSourceValueObject) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
ExceptionMapperUtils - Class in ubic.gemma.rest.util
ExceptionMapperUtils() - Constructor for class ubic.gemma.rest.util.ExceptionMapperUtils
ExceptionTag - Class in ubic.gemma.web.taglib.common.auditAndSecurity
ExceptionTag() - Constructor for class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
ExcludeArg<T> - Class in ubic.gemma.rest.util.args
executeBatchTasks(Collection<? extends Runnable>) - Method in class ubic.gemma.core.util.AbstractAuthenticatedCLI: Execute the given batch tasks.
executeBatchTasks(Collection<? extends Runnable>) - Method in class ubic.gemma.core.util.AbstractCLI: Execute the given batch tasks.
executeCommand(String[]) - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
executeCommand(String...) - Method in class ubic.gemma.core.util.AbstractCLI: Execute the given command given CLI arguments.
executeCommand(String...) - Method in interface ubic.gemma.core.util.CLI: Execute the given command given CLI arguments.
ExecutingTask - Class in ubic.gemma.core.job.executor.common: Task Lifecycle Hooks ProgressUpdateAppender -
ExecutingTask(Task<?>, String) - Constructor for class ubic.gemma.core.job.executor.common.ExecutingTask
ExecutingTask.TaskLifecycleHandler - Interface in ubic.gemma.core.job.executor.common
existsByExperiment(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.AnalysisDao: Indicate if there is an analysis (or at least one) for the given experiment.
existsByExperiment(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDaoBase
existsByExpressionExperimentAndVectorType(QuantitationType, ExpressionExperiment, Class<? extends DesignElementDataVector>) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: Test if a given quantitation type is used by a given experiment for a given vector type.
existsByExpressionExperimentAndVectorType(QuantitationType, ExpressionExperiment, Class<? extends DesignElementDataVector>) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
existsByExpressionExperimentAndVectorType(QuantitationType, ExpressionExperiment, Class<? extends DesignElementDataVector>) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService: Find a quantitation type by ID and vector type.
existsByExpressionExperimentAndVectorType(QuantitationType, ExpressionExperiment, Class<? extends DesignElementDataVector>) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
exitClause(FilterArgParser.ClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.clause().
exitClause(FilterArgParser.ClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.clause().
exitCollection(FilterArgParser.CollectionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.collection().
exitCollection(FilterArgParser.CollectionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.collection().
exitCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.collectionOperator().
exitCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.collectionOperator().
exitDisjunction(FilterArgParser.DisjunctionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.disjunction().
exitDisjunction(FilterArgParser.DisjunctionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.disjunction().
exitEveryRule(ParserRuleContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
exitFilter(FilterArgParser.FilterContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.filter().
exitFilter(FilterArgParser.FilterContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.filter().
exitOperator(FilterArgParser.OperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.operator().
exitOperator(FilterArgParser.OperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.operator().
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
exitScalar(FilterArgParser.ScalarContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.scalar().
exitScalar(FilterArgParser.ScalarContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.scalar().
exitSubClause(FilterArgParser.SubClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.subClause().
exitSubClause(FilterArgParser.SubClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.subClause().
EXP - ubic.gemma.model.association.GOEvidenceCode
expander - Variable in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
EXPERIMENT - ubic.gemma.core.apps.GemmaCLI.CommandGroup
EXPERIMENT_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExperimentIdEndpoint: The local name of the request/response.
EXPERIMENT_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExperimentNameEndpoint: The local name of the expected request/response.
EXPERIMENT_LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExperimentNumSamplesEndpoint: The local name of the expected request.
EXPERIMENTAL_FACTOR_DESCRIPTION_LINE_INDICATOR - Static variable in class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl
ExperimentalDesign - Class in ubic.gemma.model.expression.experiment
ExperimentalDesign() - Constructor for class ubic.gemma.model.expression.experiment.ExperimentalDesign
ExperimentalDesign.Factory - Class in ubic.gemma.model.expression.experiment
ExperimentalDesignController - Class in ubic.gemma.web.controller.expression.experiment: Main entry point to editing and viewing experimental designs.
ExperimentalDesignController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
ExperimentalDesignDao - Interface in ubic.gemma.persistence.service.expression.experiment
ExperimentalDesignDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExperimentalDesignDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl
ExperimentalDesignImportCli - Class in ubic.gemma.core.apps
ExperimentalDesignImportCli() - Constructor for class ubic.gemma.core.apps.ExperimentalDesignImportCli
ExperimentalDesignImporter - Interface in ubic.gemma.core.loader.expression.simple: Parse a description of ExperimentalFactors from a file, and associate it with a given ExpressionExperiment.
ExperimentalDesignImporterImpl - Class in ubic.gemma.core.loader.expression.simple: See interface for docs.
ExperimentalDesignImporterImpl() - Constructor for class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl
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.core.analysis.util
ExperimentalDesignUtils() - Constructor for class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
ExperimentalDesignViewCli - Class in ubic.gemma.core.apps
ExperimentalDesignViewCli() - Constructor for class ubic.gemma.core.apps.ExperimentalDesignViewCli
ExperimentalDesignVisualizationService - Interface in ubic.gemma.core.visualization
ExperimentalDesignVisualizationServiceImpl - Class in ubic.gemma.core.visualization: Tools for visualizing experimental designs.
ExperimentalDesignVisualizationServiceImpl(ExpressionExperimentService) - Constructor for class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl
ExperimentalDesignWriter - Class in ubic.gemma.core.datastructure.matrix: Output compatible with ExperimentalDesignImporterImpl.
ExperimentalDesignWriter() - Constructor for class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriter
ExperimentalDesignWriterCLI - Class in ubic.gemma.core.apps: Writes out the experimental design for a given experiment.
ExperimentalDesignWriterCLI() - Constructor for class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
ExperimentalEvidence - Class in ubic.gemma.model.association.phenotype: Deprecated.
ExperimentalEvidence() - Constructor for class ubic.gemma.model.association.phenotype.ExperimentalEvidence: Deprecated.

No-arg constructor added to satisfy javabean contract
ExperimentalEvidence.Factory - Class in ubic.gemma.model.association.phenotype: Deprecated.
ExperimentalEvidenceDao - Interface in ubic.gemma.persistence.service.association.phenotype
ExperimentalEvidenceDaoImpl - Class in ubic.gemma.persistence.service.association.phenotype
ExperimentalEvidenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.phenotype.ExperimentalEvidenceDaoImpl
ExperimentalEvidenceValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject: Deprecated.
ExperimentalEvidenceValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject: Deprecated.

Required when using the class as a spring bean.
ExperimentalEvidenceValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject: Deprecated.
ExperimentalEvidenceValueObject(ExperimentalEvidence) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject: Deprecated.
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
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
ExperimentalFactorValueWebUIObject - Class in ubic.gemma.web.controller.expression.experiment
ExperimentalFactorValueWebUIObject() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject
ExperimentalFactorValueWebUIObject(Long) - Constructor for class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject
ExperimentAnnotationEndpoint - Class in ubic.gemma.web.services: Expression Experiments in Gemma contain annotations.
ExperimentAnnotationEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentAnnotationEndpoint
ExperimentCoexpressionLink - Class in ubic.gemma.model.association.coexpression: Represents coexpression at the level of experiment, referinng to links stored as Gene2GeneCoexpression.
ExperimentCoexpressionLink(BioAssaySet, Long, Long, Long) - Constructor for class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
ExperimentDEDVEndpoint - Class in ubic.gemma.web.services: Allows access to all the Design Element Data Vectors (DEDV's) for a given Expression Experiment.
ExperimentDEDVEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentDEDVEndpoint
ExperimentExpressionLevelsValueObject - Class in ubic.gemma.model.expression.bioAssayData
ExperimentExpressionLevelsValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject
ExperimentExpressionLevelsValueObject(long, Map<Gene, List<DoubleVectorValueObject>>, boolean, String) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject
ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject - Class in ubic.gemma.model.expression.bioAssayData
ExperimentExpressionLevelsValueObject.VectorElementValueObject - Class in ubic.gemma.model.expression.bioAssayData
ExperimentIDbyTaxonEndpoint - Class in ubic.gemma.web.services: Given a Taxon (eg.
ExperimentIDbyTaxonEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint
ExperimentIdEndpoint - Class in ubic.gemma.web.services: Given the short name of an Expression Experiment, will return the matching Expression Experiment ID
ExperimentIdEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentIdEndpoint
ExperimentNameEndpoint - Class in ubic.gemma.web.services: Used for getting the Short Name given an Expression Experiment ID eg: 793 --> GSE10470
ExperimentNameEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentNameEndpoint
ExperimentNumSamplesEndpoint - Class in ubic.gemma.web.services: Used for determining the number of samples (biomaterials) associated with a given expression experiment
ExperimentNumSamplesEndpoint() - Constructor for class ubic.gemma.web.services.ExperimentNumSamplesEndpoint
ExperimentPlatformSwitchHelperService - Interface in ubic.gemma.core.loader.expression: Use to finish final transactional step in updating platform
ExperimentQCTag - Class in ubic.gemma.web.taglib.expression.experiment
ExperimentQCTag() - Constructor for class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
ExperimentSetListContainer - Class in ubic.gemma.web.persistence
ExperimentSetListContainer() - Constructor for class ubic.gemma.web.persistence.ExperimentSetListContainer
experimentType - Variable in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
ExpLevelConsolidationArg - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be one of the expression level consolidation options.
EXPRESSION - ubic.gemma.model.common.description.DatabaseType
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: No-arg constructor added to satisfy javabean contract
ExpressionAnalysisResultSet - Class in ubic.gemma.model.analysis.expression.diff: A group of results for an ExpressionExperiment.
ExpressionAnalysisResultSet() - Constructor for class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
ExpressionAnalysisResultSet.Factory - Class in ubic.gemma.model.analysis.expression.diff
ExpressionAnalysisResultSetArg - Class in ubic.gemma.rest.util.args: Represents an expression analysis result set identifier.
ExpressionAnalysisResultSetArgService - Class in ubic.gemma.rest.util.args
ExpressionAnalysisResultSetArgService(ExpressionAnalysisResultSetService) - Constructor for class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgService
ExpressionAnalysisResultSetDao - Interface in ubic.gemma.persistence.service.analysis.expression.diff
ExpressionAnalysisResultSetDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression.diff
ExpressionAnalysisResultSetDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
ExpressionAnalysisResultSetFileService - Interface in ubic.gemma.core.analysis.service
ExpressionAnalysisResultSetFileServiceImpl - Class in ubic.gemma.core.analysis.service
ExpressionAnalysisResultSetFileServiceImpl() - Constructor for class ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileServiceImpl
ExpressionAnalysisResultSetService - Interface in ubic.gemma.persistence.service.analysis.expression.diff
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(Collection<? extends DesignElementDataVector>) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
ExpressionDataBooleanMatrix(Collection<? extends DesignElementDataVector>, List<QuantitationType>) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
ExpressionDataCorrMatCli - Class in ubic.gemma.core.apps: Create correlation visualizations for expression experiments
ExpressionDataCorrMatCli() - Constructor for class ubic.gemma.core.apps.ExpressionDataCorrMatCli
ExpressionDataDoubleMatrix - Class in ubic.gemma.core.datastructure.matrix: A data structure that holds a reference to the data for a given expression experiment.
ExpressionDataDoubleMatrix() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: To comply with bean specifications.
ExpressionDataDoubleMatrix(Collection<? extends DesignElementDataVector>) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
ExpressionDataDoubleMatrix(Collection<? extends DesignElementDataVector>, Collection<QuantitationType>) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
ExpressionDataDoubleMatrix(Collection<? extends DesignElementDataVector>, QuantitationType) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix, List<BioMaterial>, BioAssayDimension) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Create a matrix based on another one's selected columns.
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix, List<CompositeSequence>) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Create a matrix based on another one's selected rows.
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix, DoubleMatrix<CompositeSequence, BioMaterial>, Collection<QuantitationType>) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Create a data matrix like sourceMatrix but use the values and quantitations from dataMatrix.
ExpressionDataDoubleMatrix(ExpressionExperiment, QuantitationType, DoubleMatrix<CompositeSequence, BioMaterial>) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Create a matrix given a 'raw' matrix that uses the same samples as the experiment.
ExpressionDataDoubleMatrixUtil - Class in ubic.gemma.core.datastructure.matrix: Perform various computations on ExpressionDataMatrices (usually in-place).
ExpressionDataDoubleMatrixUtil() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil
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
ExpressionDataFileUploadController - Class in ubic.gemma.web.controller.expression.experiment: Replaces SimpleExpressionExperimentLoadController
ExpressionDataFileUploadController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
ExpressionDataIntegerMatrix - Class in ubic.gemma.core.datastructure.matrix: Warning, not fully tested.
ExpressionDataIntegerMatrix(Collection<? extends DesignElementDataVector>) - 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 expression experiment.
ExpressionDataMatrixBuilder - Class in ubic.gemma.core.analysis.preprocess: Utility methods for taking an ExpressionExperiment and returning various types of ExpressionDataMatrices, such as the processed data, preferred data, background, etc.
ExpressionDataMatrixBuilder(Collection<? extends DesignElementDataVector>) - Constructor for class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
ExpressionDataMatrixBuilder(Collection<ProcessedExpressionDataVector>, Collection<? extends DesignElementDataVector>) - Constructor for class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
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 - Variable in class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer
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
ExpressionDataMatrixWriterCLI - Class in ubic.gemma.core.apps: Prints preferred data matrix to a file.
ExpressionDataMatrixWriterCLI() - Constructor for class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
ExpressionDataStringMatrix - Class in ubic.gemma.core.datastructure.matrix
ExpressionDataStringMatrix(Collection<? extends DesignElementDataVector>) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
ExpressionDataStringMatrix(Collection<? extends DesignElementDataVector>, QuantitationType) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
ExpressionDataStringMatrix(ExpressionExperiment, Collection<CompositeSequence>, QuantitationType) - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
ExpressionDataStringMatrix(ExpressionExperiment, QuantitationType) - 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
ExpressionDataWriterUtils() - Constructor for class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
ExpressionExperiment - Class in ubic.gemma.model.expression.experiment
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: No-arg constructor added to satisfy javabean contract
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
ExpressionExperimentBibRefFinder - Class in ubic.gemma.core.loader.entrez.pubmed
ExpressionExperimentBibRefFinder() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder
ExpressionExperimentController - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
ExpressionExperimentDao - Interface in ubic.gemma.persistence.service.expression.experiment: Created by tesarst on 13/03/17.
ExpressionExperimentDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
ExpressionExperimentDataFetchCommand - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentDataFetchCommand() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
ExpressionExperimentDataFetchController - Class in ubic.gemma.web.controller.expression.experiment: For the download of data files from the browser.
ExpressionExperimentDataFetchController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
ExpressionExperimentDataFileGeneratorCli - Class in ubic.gemma.core.apps
ExpressionExperimentDataFileGeneratorCli() - Constructor for class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
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, AclObjectIdentity, AclSid) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
ExpressionExperimentDetailsValueObject(ExpressionExperimentValueObject) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
ExpressionExperimentEditValueObject - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentEditValueObject() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject: Required when using the class as a spring bean.
ExpressionExperimentEditValueObject(ExpressionExperimentValueObject) - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
ExpressionExperimentExperimentalFactorValueObject - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentExperimentalFactorValueObject() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
ExpressionExperimentFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Methods to handle filtering expression experiments for analysis.
ExpressionExperimentFilter(Collection<ArrayDesign>, FilterConfig) - Constructor for class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
ExpressionExperimentFormController - Class in ubic.gemma.web.controller.expression.experiment: Handle editing of expression experiments.
ExpressionExperimentFormController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
ExpressionExperimentLoadController - Class in ubic.gemma.web.controller.expression.experiment: Handles loading of Expression data into the system when the source is GEO or ArrayExpress, via Spring MVC or AJAX.
ExpressionExperimentLoadController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController
ExpressionExperimentLoadTask - Interface in ubic.gemma.core.tasks.analysis.expression
ExpressionExperimentLoadTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
ExpressionExperimentLoadTaskCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
ExpressionExperimentLoadTaskCommand(boolean, boolean, String, boolean, boolean, String) - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
ExpressionExperimentLoadTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression
ExpressionExperimentLoadTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskImpl
ExpressionExperimentManipulatingCLI - Class in ubic.gemma.core.apps: Base class for CLIs that needs one or more expression experiment as an input.
ExpressionExperimentManipulatingCLI() - Constructor for class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
ExpressionExperimentMetaFileType - Enum in ubic.gemma.core.expression.experiment: Types of metadata files that can be attached to an ExpressionExperiment.
ExpressionExperimentPlatformSwitchCli - Class in ubic.gemma.core.apps: Switch the array design used to the merged one.
ExpressionExperimentPlatformSwitchCli() - Constructor for class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
ExpressionExperimentPlatformSwitchEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: The event that this expressionexperiment 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
ExpressionExperimentPrePersistService - Interface in ubic.gemma.persistence.service: Sets up the array designs before saving an experiment.
ExpressionExperimentPrePersistServiceImpl - Class in ubic.gemma.persistence.service: Sets up the array designs, put the designelements in the data vectors.
ExpressionExperimentPrePersistServiceImpl() - Constructor for class ubic.gemma.persistence.service.ExpressionExperimentPrePersistServiceImpl
ExpressionExperimentPrimaryPubCli - Class in ubic.gemma.core.apps: Update the primary publication for experiments.
ExpressionExperimentPrimaryPubCli() - Constructor for class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
ExpressionExperimentQCController - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentQCController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
ExpressionExperimentQCUtils - Class in ubic.gemma.web.controller.expression.experiment: Helper functions for checking existence etc.
ExpressionExperimentQCUtils() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils
ExpressionExperimentReportGenerationController - Class in ubic.gemma.web.controller
ExpressionExperimentReportGenerationController() - Constructor for class ubic.gemma.web.controller.ExpressionExperimentReportGenerationController
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
expressionExperiments - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
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.core.expression.experiment.service
ExpressionExperimentSearchServiceImpl - Class in ubic.gemma.core.expression.experiment.service: Handles searching for experiments and experiment sets
ExpressionExperimentSearchServiceImpl(ExpressionExperimentSetService, CoexpressionAnalysisService, DifferentialExpressionAnalysisService, SecurityService, SearchService, TaxonService, ExpressionExperimentService) - Constructor for class ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchServiceImpl
expressionExperimentService - Variable in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
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
ExpressionExperimentSetController - Class in ubic.gemma.web.controller.expression.experiment: For fetching and manipulating ExpressionExperimentSets.
ExpressionExperimentSetController() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
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
ExpressionExperimentSetIDsEndpoint - Class in ubic.gemma.web.services: A service to return the full list of Expression Experiment Set IDs along with the corresponding name and experiment ids it contains.
ExpressionExperimentSetIDsEndpoint() - Constructor for class ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint
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) - 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.core.expression.experiment
ExpressionExperimentSetValueObjectHelperImpl - Class in ubic.gemma.core.expression.experiment: This class will handle population of ExpressionExperimentSetValueObjects.
ExpressionExperimentSetValueObjectHelperImpl() - Constructor for class ubic.gemma.core.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
ExpressionExperimentSubSet - Class in ubic.gemma.model.expression.experiment: A subset of samples 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
ExpressionExperimentSubSetService - Interface in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentSubSetServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
ExpressionExperimentSubSetServiceImpl(ExpressionExperimentSubSetDao, DifferentialExpressionAnalysisService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
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
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
ExpressionExperimentUploadResponse - Class in ubic.gemma.web.controller.expression.experiment
ExpressionExperimentUploadResponse() - Constructor for class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
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(ExpressionExperiment, boolean, boolean) - Constructor for class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Creates a new value object out of given Expression Experiment.
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
ExpressionExperimentVectorManipulatingService - Class in ubic.gemma.core.analysis.service
ExpressionExperimentVectorManipulatingService() - Constructor for class ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService
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
ExpressionExperimentVisualizationCommand - Class in ubic.gemma.web.controller.visualization: Expression experiment command object that wraps expression experiment visualization preferences.
ExpressionExperimentVisualizationCommand() - Constructor for class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject, SearchResult<ExpressionExperiment>) - Constructor for class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
ExpressionPersister - Class in ubic.gemma.persistence.persister
ExpressionPersister() - Constructor for class ubic.gemma.persistence.persister.ExpressionPersister
ExpressionProfileDataObject - Class in ubic.gemma.web.controller.visualization: A lightweight object to hold expression data for a single probe.
ExpressionProfileDataObject(DoubleVectorValueObject) - Constructor for class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
extendAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis) - 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) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
ExternalDatabase - Class in ubic.gemma.model.common.description
ExternalDatabase() - Constructor for class ubic.gemma.model.common.description.ExternalDatabase: No-arg constructor added to satisfy javabean contract
ExternalDatabase.Factory - Class in ubic.gemma.model.common.description
ExternalDatabaseAdderCli - Class in ubic.gemma.core.apps: Add a new external database, but requires editing the code to do so.
ExternalDatabaseAdderCli() - Constructor for class ubic.gemma.core.apps.ExternalDatabaseAdderCli
ExternalDatabaseDao - Interface in ubic.gemma.persistence.service.common.description
ExternalDatabaseDaoImpl - Class in ubic.gemma.persistence.service.common.description
ExternalDatabaseDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl
ExternalDatabaseEvidenceImporterAbstractCLI - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
ExternalDatabaseEvidenceImporterAbstractCLI() - Constructor for class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
ExternalDatabaseOverviewCli - Class in ubic.gemma.core.apps
ExternalDatabaseOverviewCli() - Constructor for class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
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
ExternalDatabaseStatisticsValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
ExternalDatabaseStatisticsValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
ExternalDatabaseStatisticsValueObject(String, String, String, Long, Long, Long, Long, Date, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
ExternalDatabaseUpdaterCli - Class in ubic.gemma.core.apps
ExternalDatabaseUpdaterCli() - Constructor for class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
ExternalDatabaseUtils - Class in ubic.gemma.core.loader.util.parser: Provides convenience methods to provide ExternalDatabases and DatabaseEntries for common cases, such as Genbank.
ExternalDatabaseUtils() - Constructor for class ubic.gemma.core.loader.util.parser.ExternalDatabaseUtils
ExternalDatabaseValueObject - Class in ubic.gemma.model.common.description
ExternalDatabaseValueObject() - Constructor for class ubic.gemma.model.common.description.ExternalDatabaseValueObject
ExternalDatabaseValueObject(Long, String, boolean) - Constructor for class ubic.gemma.model.common.description.ExternalDatabaseValueObject
ExternalDatabaseValueObject(ExternalDatabase) - Constructor for class ubic.gemma.model.common.description.ExternalDatabaseValueObject
ExternalFileGeneLoaderCLI - Class in ubic.gemma.core.apps: CLI for loading genes from a non NCBI files.
ExternalFileGeneLoaderCLI() - Constructor for class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
ExternalFileGeneLoaderService - Interface in ubic.gemma.core.loader.genome.gene
ExternalFileGeneLoaderServiceImpl - Class in ubic.gemma.core.loader.genome.gene: Class to provide functionality to load genes from a tab delimited file.
ExternalFileGeneLoaderServiceImpl() - Constructor for class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl
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
extractAuditables(Object) - Static method in class ubic.gemma.core.security.audit.AuditAdvice: Efficiently extract all auditable of a given type in an object's tree.
extractBookPublicationYear(BibliographicReference, Node) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
extractGenePix(BufferedReader) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor: This method should be generic for GenePix/GPR/ATR file formats.
extractIds(String) - Static method in class ubic.gemma.web.controller.ControllerUtils: Returns a collection of Long ids from strings.
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) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
extractTagData(Document, String) - Static method in class ubic.gemma.core.util.XMLUtils
extractTerms(SearchSettings) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Extract terms, regardless of their logical organization.
extractTermsDnf(SearchSettings) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Extract a DNF (Disjunctive Normal Form) from the terms of a query.

F

F - ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
FACTOR_VALUE_RNAME_PREFIX - Static variable in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
FACTOR_VALUE_RNAME_PREFIX - Static variable in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
FactorAssociatedAnalysisResultSet<R extends AnalysisResult> - Class in ubic.gemma.model.analysis.expression
FactorAssociatedAnalysisResultSet() - Constructor for class ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet: No-arg constructor added to satisfy javabean contract
FactorProfile - Class in ubic.gemma.web.controller.visualization: Represents data for displaying a factor (+ factor values) in a chart.
FactorProfile() - Constructor for class ubic.gemma.web.controller.visualization.FactorProfile
FactorProfile(List<Double>, boolean) - Constructor for class ubic.gemma.web.controller.visualization.FactorProfile
FactorProfile(ExperimentalFactor, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>) - Constructor for class ubic.gemma.web.controller.visualization.FactorProfile
factorsWithoutBatch(Collection<ExperimentalFactor>) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
FactorType - Enum 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: No-arg constructor added to satisfy javabean contract
FactorValue.Factory - Class in ubic.gemma.model.expression.experiment
FactorValueArg<A> - Class in ubic.gemma.rest.util.args: Represents an API arguments that maps to a FactorValue by its ID or name.
FactorValueArg(String, Class<A>, A) - Constructor for class ubic.gemma.rest.util.args.FactorValueArg
FactorValueArrayArg - Class in ubic.gemma.rest.util.args
FactorValueArrayArg(List<String>) - Constructor for class ubic.gemma.rest.util.args.FactorValueArrayArg
FactorValueBasicValueObject - Class in ubic.gemma.model.expression.experiment: Each factorvalue can be associated with multiple characteristics (or with a measurement).
FactorValueBasicValueObject() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject: Required when using the class as a spring bean.
FactorValueBasicValueObject(Long) - Constructor for class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
FactorValueBasicValueObject(FactorValue) - Constructor for class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
FactorValueBasicValueObjectSerializer - Class in ubic.gemma.rest.serializers
FactorValueBasicValueObjectSerializer() - Constructor for class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer
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.core.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.core.expression.experiment: Handles deletions of a factor values.
FactorValueDeletionImpl() - Constructor for class ubic.gemma.core.expression.experiment.FactorValueDeletionImpl
FactorValueIdArg - Class in ubic.gemma.rest.util.args: Maps a long identifier to a FactorValue.
FactorValueIdArg(long) - Constructor for class ubic.gemma.rest.util.args.FactorValueIdArg
FactorValueMigratorCLI - Class in ubic.gemma.core.apps: Deprecated.
this will be removed as soon as all the old-style characteristics are migrated
FactorValueMigratorCLI() - Constructor for class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
FactorValueMigratorService - Interface in ubic.gemma.persistence.service.expression.experiment
FactorValueMigratorService.Migration - Class in ubic.gemma.persistence.service.expression.experiment
FactorValueMigratorService.MigrationFailedException - Exception in ubic.gemma.persistence.service.expression.experiment: Keep track of the first failed migration when multiple migrations are performed in a single transaction.
FactorValueMigratorService.MigrationResult - Class in ubic.gemma.persistence.service.expression.experiment
FactorValueMigratorServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment: Deprecated.
FactorValueMigratorServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorServiceImpl: Deprecated.
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
FactorValueOntologyService - Interface in ubic.gemma.core.ontology: Ontology service for factor values and their annotations.
FactorValueOntologyService.OntologyStatement - Class in ubic.gemma.core.ontology: Represents an ontology statement.
FactorValueOntologyServiceImpl - Class in ubic.gemma.core.ontology
FactorValueOntologyServiceImpl(FactorValueService) - 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 extends Throwable> - Interface in ubic.gemma.core.ontology
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(ExpressionExperimentService, AuditTrailService, AuditEventService, FactorValueDao, StatementDao) - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
FactorValueUtils - Class in ubic.gemma.model.expression.experiment
FactorValueUtils() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueUtils
FactorValueValueArg - Class in ubic.gemma.rest.util.args: Deprecated.
FactorValueValueArg(String) - Constructor for class ubic.gemma.rest.util.args.FactorValueValueArg: Deprecated.
FactorValueValueObject - Class in ubic.gemma.model.expression.experiment: Deprecated.
aim towards using the FactorValueBasicValueObject. This one is confusing. Once usage of this type has been completely phased out, revise the BioMaterialValueObject and relevant DAOs and Services.
FactorValueValueObject() - Constructor for class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.

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

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

Create a FactorValue VO focusing on a specific statement.
FactorValueValueObjectSerializer - Class in ubic.gemma.rest.serializers
FactorValueValueObjectSerializer() - Constructor for class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer
FactorValueVector - Class in ubic.gemma.persistence.util
FactorValueVector(Collection<ExperimentalFactor>, Collection<FactorValue>) - 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.CoexpCorrelationDistribution.Factory
Factory() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.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.coexpression.GeneCoexpressionNodeDegree.Factory
Factory() - Constructor for class ubic.gemma.model.association.coexpression.HumanGeneCoExpression.Factory
Factory() - Constructor for class ubic.gemma.model.association.coexpression.MouseGeneCoExpression.Factory
Factory() - Constructor for class ubic.gemma.model.association.coexpression.OtherGeneCoExpression.Factory
Factory() - Constructor for class ubic.gemma.model.association.coexpression.RatGeneCoExpression.Factory
Factory() - Constructor for class ubic.gemma.model.association.Gene2GOAssociation.Factory
Factory() - Constructor for class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence.Factory: Deprecated.
Factory() - Constructor for class ubic.gemma.model.association.phenotype.ExperimentalEvidence.Factory: Deprecated.
Factory() - Constructor for class ubic.gemma.model.association.phenotype.GenericEvidence.Factory: Deprecated.
Factory() - Constructor for class ubic.gemma.model.association.phenotype.GenericExperiment.Factory: Deprecated.
Factory() - Constructor for class ubic.gemma.model.association.phenotype.LiteratureEvidence.Factory: Deprecated.
Factory() - Constructor for class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication.Factory: Deprecated.
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.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.auditAndSecurity.UserQuery.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.LocalFile.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.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.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
Factory() - Constructor for class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject.Factory
FAILED - ubic.gemma.core.job.SubmittedTask.Status
FAILED - ubic.gemma.model.common.quantitationtype.StandardQuantitationType
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
FailedMultipartHttpServletRequest - Class in ubic.gemma.web.util.upload: Used to allow downstream processing to figure out multipart resolution failed without throwing an exception.
FailedMultipartHttpServletRequest(HttpServletRequest) - Constructor for class ubic.gemma.web.util.upload.FailedMultipartHttpServletRequest
FailedMultipartHttpServletRequest(HttpServletRequest, String) - Constructor for class ubic.gemma.web.util.upload.FailedMultipartHttpServletRequest
FailedPCAAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
FailedPCAAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.FailedPCAAnalysisEvent
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
FailedToComputeSingularValueDecomposition - Exception in ubic.gemma.core.analysis.preprocess
FailedToComputeSingularValueDecomposition(ExpressionExperiment, SVDException) - Constructor for exception ubic.gemma.core.analysis.preprocess.FailedToComputeSingularValueDecomposition
FAILURE - Static variable in class ubic.gemma.core.util.AbstractCLI: Exit code used for a failed AbstractCLI.doWork() execution.
FAILURE_FROM_ERROR_OBJECTS - Static variable in class ubic.gemma.core.util.AbstractCLI: Exit code used for a successful doWork execution that resulted in failed error objects.
FAST - ubic.gemma.model.common.search.SearchSettings.SearchMode: Fast search mode, designed for autocompletion.
FASTA_CMD_ENV_VAR - Static variable in class ubic.gemma.core.loader.genome.SimpleFastaCmd
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 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 ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException
FeedReader - Class in ubic.gemma.web.feed
FeedReader() - Constructor for class ubic.gemma.web.feed.FeedReader
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 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, String, int) - Static method in class ubic.gemma.core.loader.entrez.EutilFetch: Attempts to fetch data via Eutils; failures will be re-attempted several times.
fetch(Collection<Taxon>) - 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.
fetchAndLoad(String, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
fetchAndLoad(String, boolean, boolean, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService: Load data, no restrictions on superseries or subseries
fetchAndLoad(String, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
fetchAndLoad(String, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
fetchAndLoad(String, boolean, boolean, boolean, boolean, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService
fetchAndLoad(String, boolean, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl: Given a GEO GSE or GDS (or GPL, but support might not be complete) Check that it doesn't already exist in the system, filter samples Download and parse GDS files and GSE file needed Convert the GDS and GSE into a ExpressionExperiment (or just the ArrayDesigns) Load the resulting ExpressionExperiment and/or ArrayDesigns into Gemma
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.
FieldAwareSearchSource - Interface in ubic.gemma.core.search: Search source that can retrieve results matching specific fields.
FILE_ALL_PHENOCARTA_ANNOTATIONS - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
FILE_MANUAL_CURATION - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
FileFormatException - Exception in ubic.gemma.core.loader.util.parser: Use to indicate a file format error.
FileFormatException(String) - Constructor for exception ubic.gemma.core.loader.util.parser.FileFormatException
FileFormatException(Throwable) - Constructor for exception ubic.gemma.core.loader.util.parser.FileFormatException
FileService<T> - Interface in ubic.gemma.core.analysis.service: Interface for a service that serialize entities.
FileUpload - Class in ubic.gemma.web.controller.common.auditAndSecurity: Command class to handle uploading of a file
FileUpload() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
FileUploadController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Controller class to upload Files.
FileUploadController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController
FileUploadUtil - Class in ubic.gemma.web.util.upload: Utility methods for uploading files.
FileUploadUtil() - Constructor for class ubic.gemma.web.util.upload.FileUploadUtil
FileUtils - Class in ubic.gemma.core.util
FileUtils() - Constructor for class ubic.gemma.core.util.FileUtils
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<ArrayDesignValueObject>) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
fillEventInformation(Collection<ArrayDesignValueObject>) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl: Fill in event information
fillInDatabaseEntry(DatabaseEntry, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.CommonPersister
fillInSubsumptionInfo(Collection<ArrayDesignValueObject>) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
fillInSubsumptionInfo(Collection<ArrayDesignValueObject>) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
fillInValueObjects(Collection<ArrayDesignValueObject>) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
fillInValueObjects(Collection<ArrayDesignValueObject>) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl: Fill in the probe summary statistics
filter() - Method in class ubic.gemma.rest.util.args.FilterArgParser
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: returns ids of search results
filter(String) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController: Show array designs that match search criteria.
filter(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
filter(List<T>, Filters) - Static method in class ubic.gemma.rest.util.Responder: Produce a FilteredResponseDataObject for a given filtered List.
filter(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
filter(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter
filter(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter
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 - Class in ubic.gemma.persistence.util: Holds the necessary information to filter an entity with a property, operator and right-hand side value.
Filter.Operator - Enum in ubic.gemma.persistence.util
FilterablePropertiesConfigurer() - Constructor for class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
FilterablePropertyMeta() - Constructor for class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
filterAndLog2Transform(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil: Log2 transform if necessary, do any required filtering prior to analysis.
FilterArg<O extends Identifiable> - Class in ubic.gemma.rest.util.args: Represent a filter argument designed to generate a Filters from user input.
FilterArg.Filter - Class in ubic.gemma.rest.util.args: Represents the internal value of a FilterArg.
FilterArgBaseListener - Class in ubic.gemma.rest.util.args: This class provides an empty implementation of FilterArgListener, which can be extended to create a listener which only needs to handle a subset of the available methods.
FilterArgBaseListener() - Constructor for class ubic.gemma.rest.util.args.FilterArgBaseListener
FilterArgLexer - Class in ubic.gemma.rest.util.args
FilterArgLexer(CharStream) - Constructor for class ubic.gemma.rest.util.args.FilterArgLexer
FilterArgListener - Interface in ubic.gemma.rest.util.args: This interface defines a complete listener for a parse tree produced by FilterArgParser.
FilterArgParser - Class in ubic.gemma.rest.util.args
FilterArgParser(TokenStream) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser
FilterArgParser.ClauseContext - Class in ubic.gemma.rest.util.args
FilterArgParser.CollectionContext - Class in ubic.gemma.rest.util.args
FilterArgParser.CollectionOperatorContext - Class in ubic.gemma.rest.util.args
FilterArgParser.DisjunctionContext - Class in ubic.gemma.rest.util.args
FilterArgParser.FilterContext - Class in ubic.gemma.rest.util.args
FilterArgParser.OperatorContext - Class in ubic.gemma.rest.util.args
FilterArgParser.ScalarContext - Class in ubic.gemma.rest.util.args
FilterArgParser.SubClauseContext - Class in ubic.gemma.rest.util.args
filterByTaxon(Collection<Long>, Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
filterByTaxon(Collection<Long>, Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
filterByTaxon(Collection<Long>, Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Remove IDs of Experiments that are not from the given taxon.
filterByTaxon(Collection<Long>, Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
FilterConfig - Class in ubic.gemma.core.analysis.preprocess.filter: Holds settings for filtering.
FilterConfig() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
FilterContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
FilterCriteriaUtils - Class in ubic.gemma.persistence.util: Utilities for integrating Filter with Hibernate Criteria API.
FilterCriteriaUtils() - Constructor for class ubic.gemma.persistence.util.FilterCriteriaUtils
FilteredAndPaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util
FilteredAndPaginatedResponseDataObject(Slice<T>, Filters, String[]) - Constructor for class ubic.gemma.rest.util.FilteredAndPaginatedResponseDataObject
FilteredResponseDataObject<T> - Class in ubic.gemma.rest.util
FilteredResponseDataObject(List<T>, Filters) - Constructor for class ubic.gemma.rest.util.FilteredResponseDataObject
FilteringDao<O extends Identifiable> - Interface in ubic.gemma.persistence.service: Interface for filtering-capable DAO.
FilteringException - Exception in ubic.gemma.core.analysis.preprocess.filter
FilteringException(ExpressionExperiment, String) - Constructor for exception ubic.gemma.core.analysis.preprocess.filter.FilteringException
FilteringService<O extends Identifiable> - Interface in ubic.gemma.persistence.service: Interface for filtering-capable services.
FilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Interface in ubic.gemma.persistence.service: Interface for VO-enabled DAO with filtering capabilities.
FilteringVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>> - Interface in ubic.gemma.persistence.service: Interface VO-enabled service with filtering capabilities.
filterProbesByPlatform(Collection<Long>, Collection<Long>, 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.
FiltersUtils - Class in ubic.gemma.persistence.util: Utilities for working with Filters and Filter.
FiltersUtils() - Constructor for class ubic.gemma.persistence.util.FiltersUtils
find(C) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
find(String, Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX TODO --- include a search of subsets.
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<Long>, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService: Given a list of experiments and a threshold value finds all the probes that met the cut off in the given experiments
find(Collection<Long>, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
find(Collection<QuantitationType>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
find(Collection<QuantitationType>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService
find(Collection<QuantitationType>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
find(Collection<CompositeSequence>, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao
find(Collection<CompositeSequence>, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl
find(Collection<CompositeSequence>, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService
find(Collection<CompositeSequence>, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorServiceImpl
find(Collection<GeneProduct>) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao
find(Collection<GeneProduct>) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
find(Collection<GeneProduct>) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao
find(Collection<GeneProduct>) - 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: Does a search for the entity in the persistent storage
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 ( either id or a string property).
find(Gene2GOAssociation) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
find(Gene2GOAssociation) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
find(PhenotypeAssociation) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
find(Contact) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.ContactDaoImpl
find(Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.ContactService
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 interface ubic.gemma.core.annotation.reference.BibliographicReferenceService: check to see if the object already exists
find(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
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 interface ubic.gemma.persistence.service.common.protocol.ProtocolDao
find(Protocol) - Method in class ubic.gemma.persistence.service.common.protocol.ProtocolDaoImpl
find(Protocol) - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolService
find(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
find(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
find(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService
find(QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
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.AbstractDesignElementDataVectorDao
find(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService
find(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl
find(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
find(DesignElementDataVector) - 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(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
find(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
find(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
find(BioAssaySet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
find(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
find(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl
find(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
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(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
find(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
find(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao: 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) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
find(ExpressionExperiment, QuantitationType) - 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) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
find(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao
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.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.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 interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService: Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
find(Gene) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
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.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.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(Gene, 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)
find(Gene, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
find(Gene, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService: Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
find(Gene, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
find(Gene, Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService: Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
find(Gene, Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
find(Gene, Collection<Long>, double, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService: Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
find(Gene, Collection<Long>, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
find(Gene, ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
find(Gene, ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
find(Gene, ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
find(PhysicalLocation) - Method in interface ubic.gemma.core.genome.gene.service.GeneService: Find all genes at a physical location.
find(PhysicalLocation) - Method in class ubic.gemma.core.genome.gene.service.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
findAlignments(String) - Method in class ubic.gemma.core.externalDb.GoldenPathQuery: Locate the alignment for the given sequence, if it exists in the goldenpath database.
findAllByNameIn(Collection<String>) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseDao
findAllByNameIn(Collection<String>) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl
findAllByNameIn(List<String>) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
findAllByNameIn(List<String>) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
findAllGroups() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findAllPhenotpyesOnGene() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject: Deprecated.
findAllUsers() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findAndThaw(Collection<QuantitationType>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService
findAndThaw(Collection<QuantitationType>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl
findAndThaw(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService
findAndThaw(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService
findAndThaw(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl
findAndThaw(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
findAndThaw(BioSequence) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl
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.Gene2GOAssociationService
findAssociationByGene(Gene) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findAssociationByGenes(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findAssociationByGenes(Collection<Gene>) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findAssociationByGenes(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findAssociationByGenes(Collection<Gene>) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findAssociations(String, Long, Long, String, String, String, ThreePrimeDistanceMethod, ProbeMapperConfig) - Method in class ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis: Given a physical location, identify overlapping genes or predicted genes.
findAttribute(String) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
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.CharacteristicService: Find the best possible characteristic for a given URI.
findBestByUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findBibliographicReference(String) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Find all phenotypes associated to a pubmedID
findBibliographicReference(String) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findBibliographicReference(String, Long) - Method in class ubic.gemma.web.controller.PhenotypeController: Finds bibliographic reference with the given pubmed id.
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.BioAssayService: Locate all BioAssayDimensions in which the selected BioAssay occurs
findBioAssayDimensions(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
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.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.BioAssayService
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDao
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl
findByAccession(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityService
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceImpl
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.ExpressionExperimentService
findByAccession(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByAccession(String, ExternalDatabase) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
findByAccession(String, ExternalDatabase) - Method in class ubic.gemma.core.genome.gene.service.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.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.BioSequenceService
findByAccession(DatabaseEntry) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
findByAlias(String) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
findByAlias(String) - Method in class ubic.gemma.core.genome.gene.service.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.ArrayDesignService
findByAlternateName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findByBibliographicReference(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByBibliographicReference(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
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.ExpressionExperimentService
findByBioAssay(BioAssay) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet>, Collection<DatabaseEntry>, 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<BioAssaySet>, Collection<DatabaseEntry>, Filters, int, int, Sort) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet>, Collection<DatabaseEntry>, Filters, int, int, Sort) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet>, Collection<DatabaseEntry>, 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.ExpressionExperimentService
findByBioMaterial(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByBioMaterials(Collection<BioMaterial>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByBioMaterials(Collection<BioMaterial>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByBioMaterials(Collection<BioMaterial>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByBioMaterials(Collection<BioMaterial>) - 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.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.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.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
findByCategory(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findByCategory(String) - 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.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.BioSequenceService
findByCompositeSequence(CompositeSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
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.ExpressionExperimentService
findByDesign(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
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.UserManager
findByEmail(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
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.core.genome.gene.service.GeneService: Searches for a gene based on its ensembl ID.
findByEnsemblId(String) - Method in class ubic.gemma.core.genome.gene.service.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 class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
findByExperiment(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
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(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDao: Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().
findByExperiment(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDaoBase
findByExperiment(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService
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.BioMaterialService
findByExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
findByExperimentAnalyzed(Collection<Long>, 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<Long>, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByExperimentIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
findByExperimentIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
findByExperimentIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
findByExperiments(Collection<? extends BioAssaySet>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
findByExperiments(Collection<? extends BioAssaySet>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
findByExperiments(Collection<? extends BioAssaySet>) - Method in interface ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDao: Given a collection of experiments returns a Map of Analysis --> collection of Experiments The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with
findByExperiments(Collection<? extends BioAssaySet>) - Method in class ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDaoBase
findByExperiments(Collection<BioAssaySet>) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
findByExperiments(Collection<BioAssaySet>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
findByExperiments(Collection<BioAssaySet>) - Method in interface ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService
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 class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
findByExpressionExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
findByExpressionExperiment(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao
findByExpressionExperiment(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl
findByExpressionExperiment(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService
findByExpressionExperiment(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorServiceImpl
findByExternalId(String) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService: Get a reference by the unqualified external id.
findByExternalId(String) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
findByExternalId(String, String) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService: Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
findByExternalId(String, String) - Method in class ubic.gemma.core.annotation.reference.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(DatabaseEntry) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
findByExternalId(DatabaseEntry) - Method in class ubic.gemma.core.annotation.reference.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
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.DifferentialExpressionAnalysisService
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
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.ExpressionExperimentService
findByFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByFactors(Collection<ExperimentalFactor>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
findByFactorValue(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByFactorValue(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByFactorValue(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByFactorValue(Long) - 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.ExpressionExperimentService
findByFactorValue(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByFactorValues(Collection<FactorValue>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByFactorValues(Collection<FactorValue>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByFactorValues(Collection<FactorValue>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
findByFactorValues(Collection<FactorValue>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByGene(Gene) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService: Return all sets that contain the given gene.
findByGene(Gene) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
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.analysis.expression.diff.DifferentialExpressionResultDao: Find differential expression results for a given gene, grouped by experiment.
findByGene(Gene) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
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.Gene2GOAssociationService
findByGene(Gene) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
findByGene(Gene) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByGene(Gene) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByGene(Gene) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByGene(Gene) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
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, int, int) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
findByGene(Gene, int, int) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByGene(Gene, ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
findByGene(Gene, ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
findByGene(Gene, ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByGene(Gene, ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByGeneAndExperimentAnalyzed(Gene, Collection<Long>) - 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, Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByGeneAndExperimentAnalyzed(Gene, Collection<Long>, 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, Collection<Long>, double, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findByGenes(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findByGenes(Collection<Gene>) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findByGenes(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findByGenes(Collection<Gene>) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findByGenes(Collection<Gene>) - 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<Gene>) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
findByGenes(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
findByGenes(Collection<Gene>) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
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
findByGoTerm(String, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findByGoTerm(String, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findByGOTerm(String, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findByGOTerm(String, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
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
findByGOTerms(Collection<String>, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findByGOTerms(Collection<String>, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
findByGoTermsPerTaxon(Collection<String>) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findByGoTermsPerTaxon(Collection<String>) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
findByGOTermsPerTaxon(Collection<String>) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findByGOTermsPerTaxon(Collection<String>) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
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.ArrayDesignService
findByManufacturer(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
findByName(String) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
findByName(String) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
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.AnalysisDao
findByName(String) - Method in interface ubic.gemma.persistence.service.analysis.AnalysisService
findByName(String) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
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 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 class ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDaoBase
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.ExternalDatabaseService
findByName(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
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.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.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.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.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, Taxon) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
findByName(String, Taxon) - Method in class ubic.gemma.core.genome.gene.service.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.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(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.CompositeSequenceService
findByName(ArrayDesign, String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
findByNamesInArrayDesigns(Collection<String>, Collection<ArrayDesign>) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
findByNamesInArrayDesigns(Collection<String>, Collection<ArrayDesign>) - 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.ExternalDatabaseService
findByNameWithAuditTrail(String) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
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.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.core.genome.gene.service.GeneService
findByNCBIId(Integer) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
findByNcbiIds(Collection<Integer>) - Method in interface ubic.gemma.core.genome.gene.service.GeneService: Quickly load exact matches.
findByNcbiIds(Collection<Integer>) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
findByNcbiIds(Collection<Integer>) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Quickly load exact matches.
findByNcbiIds(Collection<Integer>) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByNCBIIdValueObject(Integer) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
findByNCBIIdValueObject(Integer) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
findByOfficialName(String) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
findByOfficialName(String) - Method in class ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneService
findByOfficialNameInexact(String) - Method in class ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneService
findByOfficialSymbol(String) - Method in class ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneService
findByOfficialSymbol(String, Taxon) - Method in class ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneService
findByOfficialSymbolInexact(String) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
findByOfficialSymbolInexact(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
findByOfficialSymbolInexact(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByOfficialSymbols(Collection<String>, Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneService: Quickly load exact matches.
findByOfficialSymbols(Collection<String>, Long) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
findByOfficialSymbols(Collection<String>, Long) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Quickly load exact matches.
findByOfficialSymbols(Collection<String>, Long) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByPhenotypeName(String, Taxon) - Method in interface ubic.gemma.core.search.GeneSetSearch
findByPhenotypeName(String, Taxon) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
findByPhysicalLocation(PhysicalLocation) - Method in interface ubic.gemma.persistence.service.genome.GeneDao: Deprecated.
findByPhysicalLocation(PhysicalLocation) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
findByProperty(String, Object) - Method in class ubic.gemma.persistence.service.AbstractDao: Does a search on given property and its value.
findByPropertyIn(String, Collection<?>) - Method in class ubic.gemma.persistence.service.AbstractDao: Perform a search on a given property and all its possible values.
findByPubmedID(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.GenericExperimentDao
findByPubmedID(String) - Method in class ubic.gemma.persistence.service.association.phenotype.GenericExperimentDaoImpl: Find all Investigations for a specific pubmed
findByPubmedID(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findByPubmedID(String) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
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.ExpressionExperimentService
findByQuantitationType(QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
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.TaxonService
findByScientificName(String) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
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.ArrayDesignService
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
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.ExpressionExperimentService
findByShortName(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.AnalysisDao
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.AnalysisService
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
findByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
findByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
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 class ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDaoBase
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.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.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.ExpressionExperimentService
findByUpdatedLimit(int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
findByUpdatedLimit(Collection<Long>, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findByUpdatedLimit(Collection<Long>, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
findByUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
findByUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByUri(String) - 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) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByUri(Collection<String>) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
findByUri(Collection<String>) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByUri(Collection<String>) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService: given a collection of strings that represent URI's will find all the characteristics that are used in the system with URI's matching anyone in the given collection
findByUri(Collection<String>) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
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.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: Finds all Characteristics whose value match the given search term
findByValue(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findByValue(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Deprecated.
findByValue(String) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
findByValue(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Deprecated.
findByValue(String) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl: Deprecated.
findByValueLike(String) - 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) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findByValueStartingWith(String) - 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) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findCandidateGenes(Long, boolean, Collection<Long>, String[]) - Method in class ubic.gemma.web.controller.PhenotypeController
findCandidateGenes(Collection<String>, Taxon) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Given an set of phenotypes returns the genes that have all those phenotypes or children phenotypes
findCandidateGenes(Collection<String>, Taxon) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findCandidateGenes(EvidenceFilter, Set<String>) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Given set of phenotypes returns the genes that have all those phenotypes or children phenotypes
findCandidateGenes(EvidenceFilter, Set<String>) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findCandidateGenesForEach(Set<String>, Taxon) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.
findCandidateGenesForEach(Set<String>, Taxon) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findCandidateGenesInTaxon(TaxonArg<?>, StringArrayArg, Boolean) - Method in class ubic.gemma.rest.TaxaWebService: Deprecated.
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.
findCharacteristics(String) - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController
findCharacteristicsByValueUriOrValueLike(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findCharacteristicsByValueUriOrValueLike(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Find characteristics by value matching the provided LIKE pattern.
findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findCharacteristicsCustom(String, boolean, boolean, boolean, boolean, boolean, boolean, String) - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController
findClosestGene(String, Long, Long, String, int) - Method in class ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis: Given a location, find the nearest gene on the same strand, including only "known", "refseq" or "ensembl" transcripts.
findCoexpressionRelationships(Gene, Collection<Long>, int, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao: Find coexpression links for a gene that are common to all the given datasets.
findCoexpressionRelationships(Gene, Collection<Long>, int, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
findCoexpressionRelationships(Gene, Collection<Long>, int, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService: Find links which are common to all of the given data sets.
findCoexpressionRelationships(Gene, Collection<Long>, int, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
findCoexpressionRelationships(Gene, Collection<Long>, int, int, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService: Search for coexpression across all available data sets, for the given genes considered individually, subject to a stringency constraint.
findCoexpressionRelationships(Gene, Collection<Long>, int, int, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
findCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao: Find coexpression links for the genes that are common to all the given datasets, so stringency = bas.size().
findCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
findCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService: Find coexpression links for the genes that are common to all the given datasets (that is, the stringency is equal to the size of the set of datasets)
findCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
findCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, int, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
findCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, int, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
findCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, int, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService: Find coexpression links for the genes that are common to at least stringency of the given datasets.
findCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, int, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
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
findDetailMetaAnalysisById(Long) - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject>, Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao
findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject>, Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject>, Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService: Retrieve differential expression results in bulk.
findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject>, Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findESTs(String, Long, Long, String) - Method in class ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis: Check to see if there are ESTs that overlap with this region.
findEvidenceByFilters(Long, int, String) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Return evidence satisfying the specified filters.
findEvidenceByFilters(Long, int, String) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findEvidenceByFilters(Long, Integer, String) - Method in class ubic.gemma.web.controller.PhenotypeController
findEvidenceByGeneId(Long) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Return all evidence for a specific gene id
findEvidenceByGeneId(Long) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findEvidenceByGeneId(Long, Set<String>, EvidenceFilter) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Return all evidence for a specific gene id with evidence flagged, indicating more information
findEvidenceByGeneId(Long, Set<String>, EvidenceFilter) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findEvidenceByGeneNCBI(Integer) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Return all evidence for a specific gene NCBI
findEvidenceByGeneNCBI(Integer) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findEvidenceCategoryTerms() - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findEvidenceCategoryTerms() - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find category terms currently used in the database by evidence
findEvidenceCategoryTerms() - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findEvidenceCategoryTerms() - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findEvidenceOwners() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.
findEvidenceOwners() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findEvidenceOwners() - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findEvidenceOwners() - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: return the list of the owners that have evidence in the system
findEvidenceOwners() - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findEvidenceOwners() - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findEvidenceOwners() - Method in class ubic.gemma.web.controller.PhenotypeController: Returns a collection of users who own evidence.
findEvidencesWithExternalDatabaseName(String, int, int) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findEvidencesWithExternalDatabaseName(String, int, int) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: loads all evidences from a specific external database
findEvidencesWithExternalDatabaseName(String, int, int) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findEvidencesWithExternalDatabaseName(String, int, int) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findEvidencesWithoutExternalDatabaseName() - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findEvidencesWithoutExternalDatabaseName() - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find all evidence that doesn't come from an external course
findEvidencesWithoutExternalDatabaseName() - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findEvidencesWithoutExternalDatabaseName() - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findExperimentCategory() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Find category term that were used in the database, used to annotated Experiments
findExperimentCategory() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findExperimentCategory() - Method in class ubic.gemma.web.controller.PhenotypeController: Returns available efo category terms.
findExperimentOntologyValue(String) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

for a given search string look in the database and Ontology for matches
findExperimentOntologyValue(String) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findExperimentOntologyValue(String, String, Long) - Method in class ubic.gemma.web.controller.PhenotypeController
findExperimentReferencesByUris(Collection<String>, Taxon, int, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Similar to CharacteristicDao.findExperimentsByUris(Collection, Taxon, int, boolean), but returns proxies with instead of initializing all the EEs in bulk.
findExperimentReferencesByUris(Collection<String>, 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<String>, 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<String>, Taxon, int, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
findExperimentsByUris(Collection<String>, Taxon, int, boolean, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
findExperimentsByUris(Collection<String>, Taxon, int, boolean, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
findExperimentsCharacteristicTags(String, boolean) - Method in interface ubic.gemma.core.ontology.OntologyService: Deprecated.
findExperimentsCharacteristicTags(String, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Deprecated.
findExperimentsCharacteristicTags(String, 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
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
findExternalDatabaseName() - Method in class ubic.gemma.web.controller.PhenotypeController
findExternalDatabasesWithEvidence() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Gets all External Databases that are used with evidence
findExternalDatabasesWithEvidence() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findExternalDatabasesWithEvidence() - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findExternalDatabasesWithEvidence() - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: Gets all External Databases that are used with evidence
findExternalDatabasesWithEvidence() - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService: Gets all External Databases that are used with evidence
findExternalDatabasesWithEvidence() - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl: Gets all External Databases that are used with evidence
findGDSforGDS(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) - 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.
findGeneByOfficialSymbol(String, Taxon) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
findGeneSetsByGene(Long) - Method in interface ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneSetServiceImpl
findGeneSetsByGene(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: Given a Gemma Gene Id will find all gene groups that the current user is allowed to use
findGeneSetsByName(String, Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
findGeneSetsByName(String, Long) - Method in class ubic.gemma.core.genome.gene.service.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 class ubic.gemma.web.controller.genome.gene.GeneSetController
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
findGenesForPhenotype(String, Long, boolean) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.
findGenesForPhenotype(String, Long, boolean) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findGenesForPhenotype(OntologyTerm, Long, boolean) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findGenesForPhenotype(OntologyTerm, Long, boolean) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
findGenesForPhenotype(OntologyTerm, Long, boolean) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findGenesForPhenotype(OntologyTerm, Long, boolean) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findGenesWithEvidence(String, Long) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Does a Gene search (by name or symbol) for a query and return only Genes with evidence
findGenesWithEvidence(String, Long) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
findGenesWithPhenotypes(Set<String>, Taxon, boolean, Collection<Long>) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findGenesWithPhenotypes(Set<String>, Taxon, boolean, Collection<Long>) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: Key method: find Genes link to a phenotype taking into account private and public evidence Here on the cases : 1- Admin - can see anything 2- user not logged in - only public data 3- user logged in only showing what he has read access - public, shared + owned 4- user logged in only showing what he has write access - owned.
findGenesWithPhenotypes(Set<String>, Taxon, boolean, Collection<Long>) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findGenesWithPhenotypes(Set<String>, Taxon, boolean, Collection<Long>) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findGOTerms(Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
findGOTerms(Long) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
findGOTerms(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
findGroupAuthorities(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findGroupByName(String) - Method in interface ubic.gemma.core.security.authentication.UserManager
findGroupByName(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
findGroupByName(String) - Method in interface ubic.gemma.core.security.authentication.UserService
findGroupByName(String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
findGroupsForUser(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
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.persistence.service.common.auditAndSecurity.UserGroupDao
findGroupsForUser(User) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
findGSECorrespondence(Collection<GeoDataset>) - 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) - 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).
findIds(BioAssaySet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: security at DAO level
findIds(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
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
findInResultSet(ExpressionAnalysisResultSet, Double, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao
findInResultSet(ExpressionAnalysisResultSet, Double, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
findInResultSet(ExpressionAnalysisResultSet, Double, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
findInResultSet(ExpressionAnalysisResultSet, Double, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
findInterCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao: Return coexpression relationships among the given genes, limited to the given data sets.
findInterCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
findInterCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService: Return coexpression relationships among the given genes in the given data sets, in a map of query gene to coexpression objects.
findInterCoexpressionRelationships(Taxon, Collection<Long>, Collection<Long>, int, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
findKnownGenesByLocation(String, Long, Long, String) - Method in class ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis: Find "Known" genes contained in or overlapping a region.
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
findMetaAnalyses(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
findMetaAnalyses(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
findMetaAnalyses(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
findMetaAnalyses(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
FindObsoleteTermsCli - Class in ubic.gemma.core.apps
FindObsoleteTermsCli() - Constructor for class ubic.gemma.core.apps.FindObsoleteTermsCli
findObsoleteTermUsage() - Method in interface ubic.gemma.core.ontology.OntologyService: Locates usages of obsolete terms in Characteristics, ignoring Gene Ontology annotations.
findObsoleteTermUsage() - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
findOneByProperty(String, Object) - Method in class ubic.gemma.persistence.service.AbstractDao: Retrieve one entity whose given property matches the given value.
findOntologyTermByUri(String) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper: Deprecated.

For a valueUri return the OntologyTerm found
findOntologyTermByUri(String) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl: Deprecated.
findOrCreate(C) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
findOrCreate(Collection<BioSequence>) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
findOrCreate(Collection<BioSequence>) - 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: Does a search for the entity in the persistent storage, and if not found, creates it.
findOrCreate(T) - Method in class ubic.gemma.persistence.service.AbstractDao
findOrCreate(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Calls the find method, and if this method returns null, creates a new instance in the persistent storage.
findOrCreate(Gene2GOAssociation) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
findOrCreate(Gene2GOAssociation) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationService
findOrCreate(Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.ContactService
findOrCreate(BibliographicReference) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
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(Protocol) - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolDao
findOrCreate(Protocol) - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolService
findOrCreate(QuantitationType) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
findOrCreate(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
findOrCreate(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
findOrCreate(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
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(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
findOrCreate(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao
findOrCreate(ExpressionExperimentSubSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
findOrCreate(FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService
findOrCreate(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
findOrCreate(Gene) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionNodeDegreeDao
findOrCreate(Gene) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionNodeDegreeDaoImpl
findOrCreate(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
findOrCreate(Taxon) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
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.
findOrFail(Protocol) - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolService
findOrFail(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
findParseLineMethod(Object, String) - Static method in class ubic.gemma.core.loader.util.ParserAndLoaderTools
findPhenotypeAssociationForGeneId(Long) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findPhenotypeAssociationForGeneId(Long) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find all PhenotypeAssociation for a specific gene id
findPhenotypeAssociationForGeneId(Long) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findPhenotypeAssociationForGeneId(Long) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findPhenotypeAssociationForGeneIdAndDatabases(Long, Collection<Long>) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findPhenotypeAssociationForGeneIdAndDatabases(Long, Collection<Long>) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find all PhenotypeAssociation for a specific gene id and external Databases ids
findPhenotypeAssociationForGeneIdAndDatabases(Long, Collection<Long>) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findPhenotypeAssociationForGeneIdAndDatabases(Long, Collection<Long>) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findPhenotypeAssociationForGeneNCBI(Integer) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findPhenotypeAssociationForGeneNCBI(Integer) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find all PhenotypeAssociation for a specific NCBI id
findPhenotypeAssociationForGeneNCBI(Integer) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findPhenotypeAssociationForGeneNCBI(Integer) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findPhenotypeAssociationForGeneNCBI(Integer, Set<String>) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findPhenotypeAssociationForGeneNCBI(Integer, Set<String>) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find all PhenotypeAssociation for a specific NCBI id and phenotypes valueUri
findPhenotypeAssociationForGeneNCBI(Integer, Set<String>) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findPhenotypeAssociationForGeneNCBI(Integer, Set<String>) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findPhenotypeAssociationWithIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findPhenotypeAssociationWithIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find PhenotypeAssociation satisfying the given filters: paIds, taxonId and limit
findPhenotypeAssociationWithIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findPhenotypeAssociationWithIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findPhenotypeMappingAsEnum() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
findPhenotypesForBibliographicReference(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findPhenotypesForBibliographicReference(String) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find PhenotypeAssociations associated with a BibliographicReference
findPhenotypesForBibliographicReference(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findPhenotypesForBibliographicReference(String) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findPhenotypesInOntology(String) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper: Deprecated.

search the disease,hp and mp ontology for a searchQuery and return an ordered set of CharacteristicVO
findPhenotypesInOntology(String) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl: Deprecated.
findPrivateEvidenceId(Long, int) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findPrivateEvidenceId(Long, int) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
findPrivateEvidenceId(String, Collection<String>, Long, int) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findPrivateEvidenceId(String, Collection<String>, Long, int) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findPrivatePhenotypesGenesAssociations(Taxon, Set<String>, boolean, Collection<Long>, boolean) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findPrivatePhenotypesGenesAssociations(Taxon, Set<String>, boolean, Collection<Long>, boolean) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find all private phenotypes associated with genes on a specific taxon and containing the valuesUri
findPrivatePhenotypesGenesAssociations(Taxon, Set<String>, String, Collection<String>, boolean, Collection<Long>, boolean) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findPrivatePhenotypesGenesAssociations(Taxon, Set<String>, String, Collection<String>, boolean, Collection<Long>, boolean) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findPublicPhenotypesGenesAssociations(Taxon, Set<String>, boolean, Collection<Long>, boolean) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
findPublicPhenotypesGenesAssociations(Taxon, Set<String>, boolean, Collection<Long>, boolean) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find all public phenotypes associated with genes on a specific taxon and containing the valuesUri
findPublicPhenotypesGenesAssociations(Taxon, Set<String>, String, Collection<String>, boolean, Collection<Long>, boolean) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
findPublicPhenotypesGenesAssociations(Taxon, Set<String>, String, Collection<String>, boolean, Collection<Long>, boolean) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
findRefGenesByLocation(String, Long, Long, String) - Method in class ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis: Find RefSeq genes contained in or overlapping a region.
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.externalDb.GoldenPathSequenceAnalysis: Check to see if there are mRNAs that overlap with this region.
findSequenceLocations(String) - Method in class ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis
findTaxonUsedInEvidence() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonDao
findTaxonUsedInEvidence() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
findTerm(String) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Search by inexact string
findTerm(String) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
findTerm(String, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController: AJAX.
findTerms(String) - Method in interface ubic.gemma.core.ontology.OntologyService
findTerms(String, 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, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
findTermsInexact(String, Taxon) - Method in interface ubic.gemma.core.ontology.OntologyService
findTermsInexact(String, 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, Taxon, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
findTypeOfEvidence() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.

Look at all Headers and identify them to determine the type of evidence
findUpdatedAfter(Date) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
findUpdatedAfter(Date) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
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
findValueUriInOntology(String) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper: Deprecated.

search the disease, hp and mp ontology for OntologyTerm
findValueUriInOntology(String) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl: Deprecated.
findVOByExternalId(String) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService: Get a reference by the unqualified external id.
findVOByExternalId(String) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
FirstQuartileComparator - Static variable in class ubic.gemma.core.analysis.preprocess.OutlierDetails: Compare outliers by first quartile Note: this comparator imposes orderings that are inconsistent with equals
FishCompletionGenerator - Class in ubic.gemma.core.util: Generates fish completion script.
FishCompletionGenerator(Set<String>) - Constructor for class ubic.gemma.core.util.FishCompletionGenerator
flush() - Method in class ubic.gemma.web.util.upload.MonitoredOutputStream
FOLDCHANGE - ubic.gemma.model.common.quantitationtype.ScaleType: Deprecated, do not use.
FOOTER - Static variable in class ubic.gemma.core.util.AbstractCLI
force - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
force - Variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher: Whether download is required even if the sizes match.
formAclRestrictionClause(String) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Create a HQL restriction clause with the BasePermission.READ permission.
formAclRestrictionClause(String, int) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Create an HQL join clause for AclObjectIdentity, AclGrantedAuthoritySid and a restriction clause to limit the result only to objects the current user can access.
formAclRestrictionClause(String, Class<? extends Securable>) - Static method in class ubic.gemma.persistence.util.AclCriteriaUtils: Form a restriction clause for ACL using the read permission.
formAclRestrictionClause(String, Class<? extends Securable>, int) - Static method in class ubic.gemma.persistence.util.AclCriteriaUtils: Form a restriction clause for ACL.
format(Double) - Method in class ubic.gemma.core.analysis.service.AbstractFileService: Format a Double for TSV.
formBackingObject(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController: Case = GET: Step 1 - return instance of command class (from database).
formBackingObject(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
formBackingObject(HttpServletRequest) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl: This is needed or you will have to specify a commandClass in the DispatcherServlet's context
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
formNativeAclJoinClause(String) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Native SQL flavour of the ACL jointure.
formNativeAclJoinClause(String) - Static method in class ubic.gemma.persistence.util.EE2CAclQueryUtils
formNativeAclRestrictionClause(SessionFactoryImplementor) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Native flavour of the ACL restriction clause with a BasePermission.READ permission.
formNativeAclRestrictionClause(SessionFactoryImplementor, int) - Static method in class ubic.gemma.persistence.util.AclQueryUtils: Native flavour of the ACL restriction clause.
formNativeAclRestrictionClause(SessionFactoryImplementor, String) - Static method in class ubic.gemma.persistence.util.EE2CAclQueryUtils
formNativeAclRestrictionClause(SessionFactoryImplementor, String, int) - Static method in class ubic.gemma.persistence.util.EE2CAclQueryUtils
formNativeNonTroubledClause(String, Class<? extends Curatable>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: Form a native non-troubled clause.
formNonTroubledClause(String, Class<? extends Curatable>) - 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(Filters) - Static method in class ubic.gemma.persistence.util.FilterCriteriaUtils: Form a restriction clause using a Criterion.
formRestrictionClause(Filters) - Static method in class ubic.gemma.persistence.util.FilterQueryUtils: Creates a CNF restriction clause from the given Filters list.
forward(String) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
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.
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<Long>, String) - Constructor for class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject: Method to create a display object from scratch
FreeTextGeneResultsValueObject - Class in ubic.gemma.core.genome.gene: *
FreeTextGeneResultsValueObject() - Constructor for class ubic.gemma.core.genome.gene.FreeTextGeneResultsValueObject: default constructor to satisfy java bean contract
FreeTextGeneResultsValueObject(String, String, Long, String, Collection<Long>, String) - Constructor for class ubic.gemma.core.genome.gene.FreeTextGeneResultsValueObject: Method to create a display object from scratch
from(Class<? extends Identifiable>, long, double, Map<String, String>, Object) - Static method in class ubic.gemma.core.search.SearchResult: Create a new provisional search result with a result type and ID.
from(Class<? extends Identifiable>, T, double, Map<String, String>, Object) - Static method in class ubic.gemma.core.search.SearchResult: Create a search result from a given identifiable entity.
fromClasspath() - Static method in class ubic.gemma.core.util.BuildInfo: Retrieve build information directly from the classpath.
fromEntities(Collection<BioSequence>) - Static method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
fromEntity(Collection<ExternalDatabase>) - Static method in class ubic.gemma.model.common.description.ExternalDatabaseValueObject
fromEntity(BlacklistedEntity) - Static method in class ubic.gemma.model.expression.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
fromString(String) - Static method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
fromXMLString(String) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
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
FtpFetcher - Class in ubic.gemma.core.loader.util.fetcher: Download files by FTP.
FtpFetcher() - Constructor for class ubic.gemma.core.loader.util.fetcher.FtpFetcher
fwe - ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.SingularThreshold

G

G - ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
GE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
GE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
GE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
Geeq - Class in ubic.gemma.model.expression.experiment: Represents quality information about a data set.
Geeq() - Constructor for class ubic.gemma.model.expression.experiment.Geeq
GeeqAdminValueObject - Class in ubic.gemma.model.expression.experiment: Represents administrative geeq information.
GeeqAdminValueObject() - Constructor for class ubic.gemma.model.expression.experiment.GeeqAdminValueObject: Required when using the class as a spring bean
GeeqAdminValueObject(Geeq) - Constructor for class ubic.gemma.model.expression.experiment.GeeqAdminValueObject
GeeqCli - Class in ubic.gemma.core.apps: Generate or update GEEQ scores
GeeqCli() - Constructor for class ubic.gemma.core.apps.GeeqCli
GeeqDao - Interface in ubic.gemma.persistence.service.expression.experiment
GeeqDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment
GeeqDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.GeeqDaoImpl
GeeqEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
GeeqEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.GeeqEvent
GeeqService - Interface in ubic.gemma.persistence.service.expression.experiment
GeeqService.ScoreMode - Enum in ubic.gemma.persistence.service.expression.experiment: Modes for filling GEEQ scores.
GeeqServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
GeeqServiceImpl(GeeqDao, ExpressionExperimentService, ArrayDesignService, ExpressionDataMatrixService, OutlierDetectionService, AuditTrailService, SampleCoexpressionAnalysisService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl
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_PHENOCARTA_HOST_URL - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
GEMMA_PHENOCARTA_HOST_URL_DATASETS - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
GEMMA_PHENOCARTA_HOST_URL_ERMINEJ - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
GemmaClassicHomePageController - Class in ubic.gemma.web.controller.common: Deprecated.
GemmaClassicHomePageController() - Constructor for class ubic.gemma.web.controller.common.GemmaClassicHomePageController: Deprecated.
GemmaCLI - Class in ubic.gemma.core.apps: Generic command line for Gemma.
GemmaCLI() - Constructor for class ubic.gemma.core.apps.GemmaCLI
GemmaCLI.CommandGroup - Enum in ubic.gemma.core.apps
GemmaOntologyService - Class in ubic.gemma.core.ontology.providers: Ontology created for Gemma.
GemmaOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.GemmaOntologyService
GemmaRestOnly - Annotation Type 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
GemmaWebOnly - Annotation Type in ubic.gemma.model.annotations: Indicate that a property is exclusively used for Gemma Web.
gender - 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 - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
GENE_LOCAL_NAME - Static variable in class ubic.gemma.web.services.GeneByNCBIIdEndpoint: The local name of the expected Request/Response.
GENE_LOCAL_NAME - Static variable in class ubic.gemma.web.services.GeneIdEndpoint: The local name of the expected Request/Response.
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.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.TableMaintenanceUtil: Query space used by the GENE2CS table.
Gene2CsStatus - Class in ubic.gemma.persistence.model: Used to store information about what happened when the GENE2CS table was updated.
Gene2CsStatus() - Constructor for class ubic.gemma.persistence.model.Gene2CsStatus
Gene2GeneAssociation - Class in ubic.gemma.model.association: Entity representing a relationship between two genes.
Gene2GeneAssociation() - Constructor for class ubic.gemma.model.association.Gene2GeneAssociation
Gene2GeneCoexpression - Class in ubic.gemma.model.association.coexpression: Represents coexpression of a pair of genes.
Gene2GeneCoexpression() - Constructor for class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
Gene2GeneIdAssociation - Class in ubic.gemma.model.association: Entity representing a relationship between two genes identified by ID, rather than by the Gene entity (for efficiency reasons).
Gene2GeneIdAssociation() - Constructor for class ubic.gemma.model.association.Gene2GeneIdAssociation
GENE2GO_LOCAL_NAME - Static variable in class ubic.gemma.web.services.Gene2GoTermEndpoint: The local name of the expected request/response.
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
Gene2GOAssociationService - Interface in ubic.gemma.persistence.service.association
Gene2GOAssociationServiceImpl - Class in ubic.gemma.persistence.service.association
Gene2GOAssociationServiceImpl(Gene2GOAssociationDao, CacheManager) - Constructor for class ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl
Gene2GOdescriptionEndpoint - Class in ubic.gemma.web.services: Given a collection of Gene ID, will return a collection of Gene Ontology IDs (ie.
Gene2GOdescriptionEndpoint() - Constructor for class ubic.gemma.web.services.Gene2GOdescriptionEndpoint
Gene2GoTermEndpoint - Class in ubic.gemma.web.services: Given a collection of Gene IDs, will return a collection of Gene Ontology URIs for each gene.
Gene2GoTermEndpoint() - Constructor for class ubic.gemma.web.services.Gene2GoTermEndpoint
Gene2OntologyEntryAssociation - Class in ubic.gemma.model.association
Gene2OntologyEntryAssociation() - Constructor for class ubic.gemma.model.association.Gene2OntologyEntryAssociation
Gene2OntologyEntryAssociationImpl - Class in ubic.gemma.model.association
Gene2OntologyEntryAssociationImpl() - Constructor for class ubic.gemma.model.association.Gene2OntologyEntryAssociationImpl
Gene2ProbeEndpoint - Class in ubic.gemma.web.services: for a given Official Gene Symbol and Taxon ID will return all the probes IDs and their array design IDs that assay for that given gene.
Gene2ProbeEndpoint() - Constructor for class ubic.gemma.web.services.Gene2ProbeEndpoint
GeneAlias - Class in ubic.gemma.model.genome.gene
GeneAlias() - Constructor for class ubic.gemma.model.genome.gene.GeneAlias: No-arg constructor added to satisfy javabean contract
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
GeneAnyIdArg<T> - Class in ubic.gemma.rest.util.args: Base class for GeneArg representing any of the identifiers of a Gene.
GeneAnyIdArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.GeneAnyIdArg
GeneArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for Gene API.
GeneArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.GeneArg
GeneArgService - Class in ubic.gemma.rest.util.args
GeneArgService(GeneService, PhenotypeAssociationManagerService, GeneOntologyService) - Constructor for class ubic.gemma.rest.util.args.GeneArgService
GeneArrayArg - Class in ubic.gemma.rest.util.args
GeneByNCBIIdEndpoint - Class in ubic.gemma.web.services: Given an NCBI ID, will return the matching Gemma gene id.
GeneByNCBIIdEndpoint() - Constructor for class ubic.gemma.web.services.GeneByNCBIIdEndpoint
GeneCoexpressedGenes - Class in ubic.gemma.model.analysis.expression.coexpression: Important: this is slightly misnamed, since it potentially includes links that have support of zero.
GeneCoexpressedGenes() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressedGenes
GeneCoexpressedGenes(Long) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressedGenes
GeneCoexpressionEndpoint - Class in ubic.gemma.web.services: Allows access to the gene co-expression analysis.
GeneCoexpressionEndpoint() - Constructor for class ubic.gemma.web.services.GeneCoexpressionEndpoint
GeneCoexpressionNodeDegree - Class in ubic.gemma.model.association.coexpression: Represents the coexpression node degree for a gene summarized across experiments, at each level of support.
GeneCoexpressionNodeDegree() - Constructor for class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
GeneCoexpressionNodeDegree.Factory - Class in ubic.gemma.model.association.coexpression
GeneCoexpressionNodeDegreeValueObject - Class in ubic.gemma.model.association.coexpression: Represents a GeneCoexpressionNodeDegree
GeneCoexpressionNodeDegreeValueObject() - Constructor for class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
GeneCoexpressionNodeDegreeValueObject(GeneCoexpressionNodeDegree) - Constructor for class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
GeneCoexpressionSearchEndpoint - Class in ubic.gemma.web.services
GeneCoexpressionSearchEndpoint() - Constructor for class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint
GeneCoexpressionSearchService - Interface in ubic.gemma.core.analysis.expression.coexpression: Provides access to Gene2Gene links.
GeneCoexpressionSearchServiceImpl - Class in ubic.gemma.core.analysis.expression.coexpression
GeneCoexpressionSearchServiceImpl(ExpressionExperimentService, CoexpressionService, CoexpressionAnalysisService, GeneService) - Constructor for class ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchServiceImpl
GeneCoexpressionTestedIn - Class in ubic.gemma.model.analysis.expression.coexpression: Tracks the datasets in which coexpression for a gene has been tested.
GeneCoexpressionTestedIn() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
GeneCoexpressionTestedIn(Long) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
GeneController - Class in ubic.gemma.web.controller.genome.gene
GeneController() - Constructor for class ubic.gemma.web.controller.genome.gene.GeneController
GeneCoreService - Interface in ubic.gemma.core.genome.gene.service: core service for Gene
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
GeneDetailsByGeneIDEndpoint - Class in ubic.gemma.web.services: Given a collection of Gemma gene IDs, will return the matching NCBI Ids.
GeneDetailsByGeneIDEndpoint() - Constructor for class ubic.gemma.web.services.GeneDetailsByGeneIDEndpoint
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
GeneElementExpressionsValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
GeneElementExpressionsValueObject(String, Integer, List<DoubleVectorValueObject>, boolean, String) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
GeneEnsemblIdArg - Class in ubic.gemma.rest.util.args: Long argument type for Gene API, referencing the Gene Ensembl ID.
GeneEvidenceValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject: Deprecated.
GeneEvidenceValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject: Deprecated.

Required when using the class as a spring bean.
GeneEvidenceValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject: Deprecated.
GeneEvidenceValueObject(Gene, Collection<EvidenceValueObject<? extends PhenotypeAssociation>>) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject: Deprecated.
geneExpressionArraybased - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
geneExpressionByArray - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
geneExpressionBySAGE - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
geneExpressionBySequencing - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
geneExpressionMPSSBased - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
GeneExpressionProfile - Class in ubic.gemma.web.controller.visualization: Expression data for one probe; designed for conveying small amounts of data to clients.
GeneExpressionProfile(DoubleVectorValueObject) - Constructor for class ubic.gemma.web.controller.visualization.GeneExpressionProfile
GeneExpressionProfile(DoubleVectorValueObject, Collection<GeneValueObject>) - Constructor for class ubic.gemma.web.controller.visualization.GeneExpressionProfile
GeneExpressionProfile(DoubleVectorValueObject, Collection<GeneValueObject>, String, Integer, Double) - Constructor for class ubic.gemma.web.controller.visualization.GeneExpressionProfile
GeneExpressionProfile(DoubleVectorValueObject, Collection<GeneValueObject>, String, Integer, Double, boolean) - Constructor for class ubic.gemma.web.controller.visualization.GeneExpressionProfile
geneExpressionRTPCRbased - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
geneExpressionSAGEbased - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
GeneIDbyTaxonEndpoint - Class in ubic.gemma.web.services: Given the Taxon (eg.
GeneIDbyTaxonEndpoint() - Constructor for class ubic.gemma.web.services.GeneIDbyTaxonEndpoint
GeneIdEndpoint - Class in ubic.gemma.web.services: Given the official symbol and taxon of a gene, will return the matching gene ID.
GeneIdEndpoint() - Constructor for class ubic.gemma.web.services.GeneIdEndpoint
GENELIST - 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.core.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.core.analysis.sequence.GeneMappingSummary
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
GeneNameEndpoint - Class in ubic.gemma.web.services: Given a gene ID, will return the matching gene official symbol eg) 938103--> Grin1
GeneNameEndpoint() - Constructor for class ubic.gemma.web.services.GeneNameEndpoint
GeneNcbiIdArg - Class in ubic.gemma.rest.util.args: Long argument type for Gene API, referencing the Gene NCBI ID.
GeneOntologyService - Interface in ubic.gemma.core.ontology.providers
GeneOntologyServiceImpl - Class in ubic.gemma.core.ontology.providers: Holds a complete copy of the GeneOntology.
GeneOntologyServiceImpl() - Constructor for class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
GeneOntologyServiceImpl.GOAspect - Enum 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
GeneOverlapEndpoint - Class in ubic.gemma.web.services: given a query gene id & collection of target gene ids will determine the overlapping Go terms (intersection) between each pair of Query Gene and Target Gene.
GeneOverlapEndpoint() - Constructor for class ubic.gemma.web.services.GeneOverlapEndpoint
GenePickerController - Class in ubic.gemma.web.controller.genome.gene: For 'live searches' from the web interface.
GenePickerController() - Constructor for class ubic.gemma.web.controller.genome.gene.GenePickerController
GENEPIX_DATETIME_HEADER_REGEXP - Static variable in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
GeneProduct - Class in ubic.gemma.model.genome.gene
GeneProduct() - Constructor for class ubic.gemma.model.genome.gene.GeneProduct
GeneProduct.Factory - Class in ubic.gemma.model.genome.gene
GeneProductDao - Interface in ubic.gemma.persistence.service.genome.gene
GeneProductDaoImpl - Class in ubic.gemma.persistence.service.genome.gene
GeneProductDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
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.
GeneralSearchController - Interface in ubic.gemma.web.controller: Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
GeneralSearchController.SearchResultValueObject<T extends IdentifiableValueObject<?>> - Class in ubic.gemma.web.controller
GeneralSearchControllerImpl - Class in ubic.gemma.web.controller: Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
GeneralSearchControllerImpl() - Constructor for class ubic.gemma.web.controller.GeneralSearchControllerImpl
GeneralType - Enum 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<Taxon>) - 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<NcbiGeneData>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
generateAllArrayDesignReport() - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService: Report summarizing _all_ array designs.
generateAllArrayDesignReport() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
generateAnnotationFile(Writer, Collection<Gene>, Boolean) - Method in interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService: Generate an annotation for a list of genes, instead of probes.
generateAnnotationFile(Writer, Collection<Gene>, Boolean) - Method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
generateArrayDesignReport() - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService: Generate reports for all array designs, as well as the "global" report.
generateArrayDesignReport() - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
generateArrayDesignReport(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
generateArrayDesignReport(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
generateArrayDesignReport(ArrayDesignValueObject) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
generateArrayDesignReport(ArrayDesignValueObject) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
generateBeanName(BeanDefinition, BeanDefinitionRegistry) - Method in class ubic.gemma.persistence.util.BeanNameGenerator: Automatically produce camel-case names for the beans.
generateCache(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController
generateCompletion(Options, PrintWriter) - Method in class ubic.gemma.core.util.BashCompletionGenerator
generateCompletion(Options, PrintWriter) - Method in interface ubic.gemma.core.util.CompletionGenerator
generateCompletion(Options, PrintWriter) - Method in class ubic.gemma.core.util.FishCompletionGenerator
generateLocal(String, String, String, String, BlockingQueue<NcbiGeneData>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
generateRemote(Collection<Taxon>) - Method in class ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
generateSignupToken(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in class ubic.gemma.core.util.BashCompletionGenerator
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in interface ubic.gemma.core.util.CompletionGenerator
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in class ubic.gemma.core.util.FishCompletionGenerator
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
generateSummary(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController: Build summary report for an array design
generateSummary(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
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
generateWeeklyReport() - Method in interface ubic.gemma.core.analysis.report.WhatsNewService: Generate and save the report from last week.
generateWeeklyReport() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
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
GenericEvidence - Class in ubic.gemma.model.association.phenotype: Deprecated.
GenericEvidence() - Constructor for class ubic.gemma.model.association.phenotype.GenericEvidence: Deprecated.
GenericEvidence.Factory - Class in ubic.gemma.model.association.phenotype: Deprecated.
GenericEvidenceDao - Interface in ubic.gemma.persistence.service.association.phenotype
GenericEvidenceDaoImpl - Class in ubic.gemma.persistence.service.association.phenotype
GenericEvidenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.phenotype.GenericEvidenceDaoImpl
GenericEvidenceValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
GenericEvidenceValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.GenericEvidenceValueObject: Required when using the class as a spring bean.
GenericEvidenceValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.GenericEvidenceValueObject
GenericEvidenceValueObject(Long, Integer, SortedSet<CharacteristicValueObject>, String, String, boolean, EvidenceSourceValueObject) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.GenericEvidenceValueObject
GenericEvidenceValueObject(GenericEvidence) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.GenericEvidenceValueObject
GenericExperiment - Class in ubic.gemma.model.association.phenotype: Deprecated.
GenericExperiment() - Constructor for class ubic.gemma.model.association.phenotype.GenericExperiment: Deprecated.
GenericExperiment.Factory - Class in ubic.gemma.model.association.phenotype: Deprecated.
GenericExperimentDao - Interface in ubic.gemma.persistence.service.association.phenotype
GenericExperimentDaoImpl - Class in ubic.gemma.persistence.service.association.phenotype
GenericExperimentDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.phenotype.GenericExperimentDaoImpl
GenericGenelistDesignGenerator - Class in ubic.gemma.core.apps: Create (or update) an array design based on a list of NCBI gene IDs desired to be on the platform.
GenericGenelistDesignGenerator() - Constructor for class ubic.gemma.core.apps.GenericGenelistDesignGenerator
GENERICLM - ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType
GenericMeterRegistryConfigurer - Class in ubic.gemma.core.metrics: Attach all the given MeterBinder to the registry.
GenericMeterRegistryConfigurer(MeterRegistry, List<MeterBinder>) - Constructor for class ubic.gemma.core.metrics.GenericMeterRegistryConfigurer
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
GenericStreamConsumer - Class in ubic.gemma.core.util.concurrent: See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html
GenericStreamConsumer(InputStream) - Constructor for class ubic.gemma.core.util.concurrent.GenericStreamConsumer
GenericStreamConsumer(InputStream, boolean) - Constructor for class ubic.gemma.core.util.concurrent.GenericStreamConsumer
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.core.genome.gene.service: Service for searching genes (and gene sets)
GeneSearchServiceImpl - Class in ubic.gemma.core.genome.gene.service: Service for searching genes (and gene sets)
GeneSearchServiceImpl() - Constructor for class ubic.gemma.core.genome.gene.service.GeneSearchServiceImpl
GeneSearchServiceImpl(SearchService, SecurityService, TaxonService, GeneSetSearch, GeneSetService, GeneService, GeneOntologyService, GeneSetValueObjectHelper) - Constructor for class ubic.gemma.core.genome.gene.service.GeneSearchServiceImpl
geneService - Variable in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
GeneService - Interface in ubic.gemma.core.genome.gene.service
GeneServiceImpl - Class in ubic.gemma.core.genome.gene.service
GeneServiceImpl(GeneDao) - Constructor for class ubic.gemma.core.genome.gene.service.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
GeneSetController - Class in ubic.gemma.web.controller.genome.gene: Exposes GeneSetServices methods over ajax.
GeneSetController() - Constructor for class ubic.gemma.web.controller.genome.gene.GeneSetController
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
GeneSetListContainer - Class in ubic.gemma.web.persistence
GeneSetListContainer() - Constructor for class ubic.gemma.web.persistence.GeneSetListContainer
GeneSetMember - Class in ubic.gemma.model.genome.gene
GeneSetMember() - Constructor for class ubic.gemma.model.genome.gene.GeneSetMember: No-arg constructor added to satisfy javabean contract
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
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.core.genome.gene.service: Service for managing gene sets
GeneSetServiceImpl - Class in ubic.gemma.core.genome.gene.service: Service for managing gene sets
GeneSetServiceImpl(GeneSetDao) - Constructor for class ubic.gemma.core.genome.gene.service.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.core.genome.gene: * @author tvrossum
GeneSetValueObjectHelperImpl - Class in ubic.gemma.core.genome.gene: This class will handle population of GeneSetValueObjects.
GeneSetValueObjectHelperImpl() - Constructor for class ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl
GeneSymbolArg - Class in ubic.gemma.rest.util.args: String argument type for Gene API.
GeneSymbolComparator - Class in ubic.gemma.web.util
GeneSymbolComparator() - Constructor for class ubic.gemma.web.util.GeneSymbolComparator
GeneTestedInCache - Interface in ubic.gemma.persistence.service.association.coexpression: Cache of the 'tested-in' information for genes.
GeneTestedInCacheImpl - Class in ubic.gemma.persistence.service.association.coexpression
GeneTestedInCacheImpl() - Constructor for class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
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: Aliases are not filled in.
GeneValueObject(GeneValueObject) - Constructor for class ubic.gemma.model.genome.gene.GeneValueObject: Copies constructor from other GeneValueObject
GeneWebService - Class in ubic.gemma.rest: RESTful interface for genes.
GeneWebService() - Constructor for class ubic.gemma.rest.GeneWebService: Required by spring
GeneWebService(GeneService, CompositeSequenceService, GeneCoexpressionSearchService, GeneArgService) - Constructor for class ubic.gemma.rest.GeneWebService: Constructor for service autowiring
GENOME - ubic.gemma.model.common.description.DatabaseType: Represents a genome database such as Golden Path or Ensembl
genomeBindingByArray - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
genomeBindingBySequencing - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
GenomePersister - Class in ubic.gemma.persistence.persister
GenomePersister() - Constructor for class ubic.gemma.persistence.persister.GenomePersister
genomeVariationByArray - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
genomeVariationByGenomeTiling - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
genomic - ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
genomicDNA - ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
genotypeOrVariation - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
GEO - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
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
GeoBrowser - Class in ubic.gemma.core.loader.expression.geo.service: Gets records from GEO and compares them to Gemma.
GeoBrowser() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoBrowser
GeoBrowserService - Interface in ubic.gemma.core.loader.expression.geo.service
GeoBrowserServiceImpl - Class in ubic.gemma.core.loader.expression.geo.service: This is marked as Lazy since we don't use it outside Gemma Web, so it won't be loaded unless it's needed.
GeoBrowserServiceImpl() - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
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 in ubic.gemma.core.loader.expression.geo.model
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 in ubic.gemma.core.loader.expression.geo.model
GeoDataset.PlatformType - Enum in ubic.gemma.core.loader.expression.geo.model
GeoDataset.SampleType - Enum in ubic.gemma.core.loader.expression.geo.model
GeoDataset.ValueType - Enum 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
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() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.GeoFetcher
GeoGrabberCli - Class in ubic.gemma.core.apps: Scans GEO for experiments that are not in Gemma, subject to some filtering criteria, outputs to a file for further screening.
GeoGrabberCli() - Constructor for class ubic.gemma.core.apps.GeoGrabberCli
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
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
GeoRecordBrowserController - Class in ubic.gemma.web.controller.expression.experiment
GeoRecordBrowserController() - Constructor for class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController
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 in ubic.gemma.core.loader.expression.geo.model: Permitted types of replication.
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
GeoSample.LibraryStrategy - Enum in ubic.gemma.core.loader.expression.geo.model
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
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
GeoSeries.SeriesType - Enum in ubic.gemma.core.loader.expression.geo.model
GeoService - Interface 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(ArrayDesignReportService, BioAssayService, ExpressionExperimentReportService, ExpressionExperimentService, ExpressionExperimentPrePersistService, TaxonService, CharacteristicService, BioMaterialService, BibliographicReferenceService, AuditTrailService) - Constructor for class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
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
GeoUtil - Class in ubic.gemma.core.loader.expression.geo.util
GeoUtil() - Constructor for class ubic.gemma.core.loader.expression.geo.util.GeoUtil
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 in ubic.gemma.core.loader.expression.geo.model: Permitted descriptions of terms.
GEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
GEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
GEQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
get() - Method in class ubic.gemma.rest.analytics.ga4.AuthenticationBasedUserIdRetrievalStrategy
get() - Method in interface ubic.gemma.rest.analytics.ga4.ClientIdRetrievalStrategy
get() - Method in class ubic.gemma.rest.analytics.ga4.CompositeClientIdRetrievalStrategy
get() - Method in class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy
get() - Method in class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy
get() - Method in interface ubic.gemma.rest.analytics.ga4.UserIdRetrievalStrategy
get(int) - Method in class ubic.gemma.persistence.util.Slice
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
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.
get(int, int) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
get(Integer) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonParser
get(Long) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
get(Long) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
get(Long) - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
get(Long) - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
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<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
get(Long, Collection<Long>) - 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(String, String) - Static method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.SimpleHttp
get(List<CompositeSequence>, List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
get(List<CompositeSequence>, List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
get(List<CompositeSequence>, List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
get(List<CompositeSequence>, List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
get(List<CompositeSequence>, List<BioAssay>) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a submatrix
get(List<CompositeSequence>, List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
get(K) - Method in class ubic.gemma.core.loader.util.parser.BasicLineMapParser
get(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
get(CompositeSequence, BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
get(CompositeSequence, BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
get(CompositeSequence, BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
get(CompositeSequence, BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
get(CompositeSequence, BioAssay) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a single value of the matrix.
get(CompositeSequence, BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
get(CompositeSequence, BioMaterial) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
get(BioAssaySet, Long) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCache
get(BioAssaySet, Long) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
get_id() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
get_id() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
get_parent() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
getAbaGeneImageUrl() - Method in class ubic.gemma.core.image.ABALinkOutValueObject
getAbaGeneImageUrls() - Method in class ubic.gemma.core.image.ABALinkOutValueObject
getAbaGeneUrl() - Method in class ubic.gemma.core.image.ABALinkOutValueObject
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.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
getAccession() - Method in class ubic.gemma.model.common.description.DatabaseEntry
getAccession() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getAccession() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getAccession() - Method in class ubic.gemma.model.expression.BlacklistedValueObject
getAccession() - Method in class ubic.gemma.model.expression.experiment.BioAssaySet
getAccession() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getAccession() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedSearchCommand
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
getAccessionToBioAssayMap(ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
getAccessionVersion() - Method in class ubic.gemma.model.common.description.DatabaseEntry
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
getActiveExperiments() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getActiveSessions() - Static method in class ubic.gemma.web.listener.UserTracker
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclAfterCollectionCompSeqByArrayDesignFilter
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclAfterCollectionDataVectorByExpressionExperimentFilter
getActualDomainObject(Object) - Method in class ubic.gemma.core.security.authorization.acl.AclAfterCompSeqByArrayDesignFilter
getActuallyTroubled() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getAddExpressionPath() - Method in class ubic.gemma.core.image.aba.Image
getAddress() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getAdminEmailAddress() - Method in interface ubic.gemma.persistence.util.MailEngine: Return the admin email address used for MailEngine.sendAdminMessage(String, String)
getAdminEmailAddress() - Method in class ubic.gemma.persistence.util.MailEngineImpl
getAdminUser() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getAdvertisedNumberOfDesignElements() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getAffPath() - Method in class ubic.gemma.core.image.aba.Image
getAfterDistinctValueCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getAfterInitialFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getAfterLowExpressionCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getAfterLowVarianceCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getAfterMinPresentFilter() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getAfterZeroVarianceCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getAlias() - Method in class ubic.gemma.model.genome.gene.GeneAlias
getAliases() - Method in class ubic.gemma.model.genome.Gene
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) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain all annotations, grouped by applicable level.
getAllAnnotations(ExpressionExperiment) - 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.ArrayDesignService
getAllAssociatedBioAssays(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getAllCharacteristics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment: Obtain all characteristics associated to this EE.
getAllExperimentLinkedReferences() - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService: Return all the BibRefs that are linked to ExpressionExperiments.
getAllExperimentLinkedReferences() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
getAllExperimentLinkedReferences() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
getAllExperimentLinkedReferences() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
getAllExperimentSets() - Method in interface ubic.gemma.web.persistence.SessionListManager
getAllExperimentSets() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getAllGeneSets() - Method in interface ubic.gemma.web.persistence.SessionListManager
getAllGeneSets() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getAllGeneSets(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager
getAllGeneSets(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getAllGEOPlatforms() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowser: A bit hacky, can be improved.
getAllIdOfPhenotype() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
getAllParents(Collection<OntologyTerm>) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getAllParents(Collection<OntologyTerm>) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getAllParents(Collection<OntologyTerm>, boolean) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getAllParents(Collection<OntologyTerm>, boolean) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getAllParentsAnnotationLink() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getAllSessionBoundGroups() - Method in class ubic.gemma.web.persistence.AbstractSetListContainer
getAllTaxonExperimentGroup(Long) - Method in interface ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchService
getAllTaxonExperimentGroup(Long) - Method in class ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchServiceImpl
getAllTaxonExperimentGroup(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
getAlternateNames() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getAlternateNames() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getAlternative() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getAlternativeTo() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getAnalyses(Collection<? extends BioAssaySet>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
getAnalyses(Collection<? extends BioAssaySet>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
getAnalyses(Collection<? extends BioAssaySet>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
getAnalyses(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
getAnalyses(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
getAnalyses(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService
getAnalyses(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
getAnalysesByExperiment(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService: Given a set of ids, find experiments or experimentsubsets that have differential expression analyses.
getAnalysesByExperiment(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
getAnalysesByExperiment(Collection<Long>, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
getAnalysesByExperiment(Collection<Long>, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
getAnalysesByExperimentIds(Collection<Long>, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
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.IncludedResultSetInfoValueObject
getAnalysisId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getAnalysisNotRun() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getAnalysisObj() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getAnalysisResultSetIds() - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
getAnalysisStoragePath() - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getAnalysisType() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getAnalysisType() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
getAnalysisType() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getAnalyticsKey() - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getAnalyzer() - Method in interface ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
getAnalyzer() - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
getAnchor() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getAnnotatedAbstract() - Method in class ubic.gemma.model.common.description.BibliographicReference: Deprecated.
getAnnotation() - Method in class ubic.gemma.persistence.model.Gene2CsStatus
getAnnotation(EntityDelegator<BioMaterial>) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
getAnnotation(EntityDelegator<ExpressionExperiment>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
getAnnotationCounts(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getAnnotationCounts(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getAnnotationCountsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getAnnotationCountsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getAnnotationInformation(Collection<ExpressionExperimentDetailsValueObject>) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService
getAnnotationInformation(Collection<ExpressionExperimentDetailsValueObject>) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl: Populate information about how many annotations there are, and how many factor values there are.
getAnnotations() - Method in class ubic.gemma.model.common.description.BibliographicReference: Deprecated.
getAnnotations() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor: Deprecated.
getAnnotations(DatasetArg<?>) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getAnnotationsByBioMaterials(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getAnnotationsByBioMaterials(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getAnnotationsByFactorValues(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getAnnotationsByFactorValues(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getAnnotationsById(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getAnnotationsById(Long) - 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.
getAnnotationsUsageFrequency(Collection<Long>, Class<? extends Identifiable>, int, int, String, Collection<String>, Collection<String>, Collection<String>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain annotations usage frequency for a set of given ExpressionExperiment IDs.
getAnnotationsUsageFrequency(Collection<Long>, Class<? extends Identifiable>, int, int, String, Collection<String>, Collection<String>, Collection<String>) - 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<Long>, String, Collection<String>, Collection<String>, int, Collection<String>, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain annotation usage frequency for datasets matching the given filters.
getAnnotationsUsageFrequency(Filters, Set<Long>, String, Collection<String>, Collection<String>, int, Collection<String>, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: If the term cannot be resolved via OntologyService.getTerm(String), an attempt is done to resolve its category and assign it as its parent.
getAnnotationValueObjects() - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
getAnswer() - Method in class ubic.gemma.core.job.TaskResult
getApiInfo(HttpServletRequest, ServletConfig) - Method in class ubic.gemma.rest.RootWebService: Returns an object with API information.
getApplicationContext(boolean, boolean, String[]) - Static method in class ubic.gemma.persistence.util.SpringContextUtil: Deprecated.
this method does not support producing Gemma Web contexts, please migrate existing code to use SpringContextUtil.getApplicationContext(String[], String...) instead.
getApplicationContext(String[], String...) - Static method in class ubic.gemma.persistence.util.SpringContextUtil: Obtain an application context for Gemma.
getAppURL(HttpServletRequest) - Static method in class ubic.gemma.web.util.RequestUtil: Convenience method to get the application's URL based on request variables.
getArgsByPropertyName(AbstractEntityArrayArg<T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService: Given a AbstractEntityArrayArg, construct a mapping of properties it refers to values those properties are allowed to take in a filter.
getArgsByPropertyName(AbstractEntityArrayArg<Taxon, TaxonService>) - Method in class ubic.gemma.rest.util.args.TaxonArgService
getArrayDesign() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
getArrayDesign() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getArrayDesign() - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
getArrayDesign() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
getArrayDesign() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
getArrayDesign() - Method in class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
getArrayDesignCache() - Method in class ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
getArrayDesignId() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getArrayDesignIds() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getArrayDesignIdsUsed(Long, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getArrayDesignMismatchProblemMessage() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getArrayDesignName() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getArrayDesignName() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
getArrayDesignName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getArrayDesignReportService() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
getArrayDesigns() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getArrayDesigns() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getArrayDesigns(Long[], boolean, boolean) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getArrayDesigns(Long[], boolean, boolean) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
getArrayDesignService() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
getArrayDesignShortName() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
getArrayDesignsToProcess() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
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<Long>, 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<Long>, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getArrayDesignsUsed(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getArrayDesignsUsed(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getArrayDesignsUsed(Collection<Long>, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getArrayDesignsUsed(BioAssaySet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getArrayDesignsUsed(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getArrayDesignsUsed(BioAssaySet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getArrayDesignsUsed(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getArrayDesignsUsed(ExpressionExperiment, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getArrayDesignsUsedEEMap(Collection<Long>, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getArrayDesignUsed() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters, Set<Long>, 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<Long>, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getArrayName() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getArrayValues(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
getAssemblyDatabase() - Method in class ubic.gemma.model.genome.Chromosome
getAssociationType() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getAsText() - Method in class ubic.gemma.web.propertyeditor.ArrayDesignPropertyEditor
getAsText() - Method in class ubic.gemma.web.propertyeditor.QuantitationTypePropertyEditor
getAsText() - Method in class ubic.gemma.web.propertyeditor.SequenceTypePropertyEditor
getAsText() - Method in class ubic.gemma.web.propertyeditor.TaxonPropertyEditor
getATN() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getATN() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getAttribute(String) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getAttribute(String, int) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getAttributeNamesInScope(int) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getAttributesScope(String) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getAuditEvents(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
getAuditEvents(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getAuditEvents(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getAuditEvents(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getAuditTrail() - Method in class ubic.gemma.model.common.AbstractAuditable
getAuditTrail() - Method in interface ubic.gemma.model.common.Auditable
getAuditTrail() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getAuthenticatedUserCount() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getAuthenticatedUserCount() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
getAuthenticatedUserNames() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getAuthenticatedUserNames() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
getAuthorities() - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup
getAuthority() - Method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority
getAuthority() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
getAuthorList() - Method in class ubic.gemma.model.common.description.BibliographicReference
getAuthorList() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getAutoRunFrequencyHours() - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
getAutoSeekEventType() - Method in class ubic.gemma.core.util.AbstractCLI
getAvailableGroups() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController: AJAX
getAvailableGroups() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
getAvailableGroups() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getAvailablePrincipalSids() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController: Return a list of principals that is users
getAvailablePrincipalSids() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
getAvailableSids() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController: AJAX, but administrator-only!
getAvailableSids() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
getBackgroundChannelA() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getBackgroundChannelB() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getBaseDifferentialDirectory(String) - Static method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionFileUtils
getBaselineConditions(List<BioMaterial>, List<ExperimentalFactor>) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
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
getBaseLineFactorValues() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getBaselineGroup() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
getBaselineGroup() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getBaselineLevels(Collection<ExperimentalFactor>) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort: Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
getBaselineLevels(List<BioMaterial>, Collection<ExperimentalFactor>) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort: Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
getBatchAccessions(Collection<String>, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getBatchAccessions(Collection<String>, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getBatchAccessions(Collection<String>, String, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getBatchAccessions(Collection<String>, String, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getBatchConfound() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getBatchConfound(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Checks the experiment for a batch confound.
getBatchConfound(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBatchEffect() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getBatchEffect(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain a BatchEffectType describing the batch effect state of the given experiment.
getBatchEffect(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBatchEffectDetails(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain the full batch effect details of a given experiment.
getBatchEffectDetails(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBatchEffectStatistics() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
getBatchEffectStatistics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getBatchEffectStatistics(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain a string describing the summary statistics of a batch effect is present in the given experiment.
getBatchEffectStatistics(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBatchFactor(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService: For convenience of some testing classes
getBatchFactor(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl
getBatchFetchEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getBatchIdentifiers(Collection<Integer>, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getBatchIdentifiers(Collection<Integer>, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getBatchIdentifiers(Collection<Integer>, String, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getBatchIdentifiers(Collection<Integer>, String, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getBatchInfo(ExpressionExperiment, Collection<LocalFile>) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
getBatchSize() - Method in class ubic.gemma.persistence.service.AbstractDao
getBatchSize(SessionFactory, ClassMetadata) - Static method in class ubic.gemma.persistence.util.HibernateUtils: Obtain the batch fetch size for the given class.
getBean(Class<T>) - Method in class ubic.gemma.core.util.AbstractCLI: Deprecated.
getBean(String, Class<T>) - Method in class ubic.gemma.core.util.AbstractCLI: Deprecated.
Use Autowired to specify your dependencies, this is just a wrapper around the current BeanFactory.
getBestBioAssayDimension() - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getBestBioAssayDimension() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
getBestCoexpressionMatrix() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis
getBibliographicPhenotypes() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getBigDecimal(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getBigDecimal(String, BigDecimal) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getBigInteger(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getBigInteger(String, BigInteger) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
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.coexpression.CoexpCorrelationDistribution
getBinCounts() - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
getBioAssay() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
getBioAssayCount() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject: Deprecated.
use #getNumberOfBioAssays() instead.
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.DataVectorValueObject: Represents the order of the bioassays for this.
getBioAssayDimension() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
getBioAssayDimension(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getBioAssayDimension(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Produce a BioAssayDimension representing the matrix columns for a specific row.
getBioAssayDimensions() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
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) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getBioAssayDimensions(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBioAssayExpressionLevels() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
getBioAssayIds() - Method in class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
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.experiment.BioAssaySet
getBioAssays() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getBioAssays() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
getBioAssays(Long) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
getBioAssaysForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getBioAssaysForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
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) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain sample-level annotations.
getBioMaterialAnnotations(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getBioMaterialCharacteristicCategories(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController: Extract just the categories from the biomaterial's characteristics.
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.ExpressionExperimentService
getBioMaterialCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getBioMaterialForColumn(int) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getBioMaterialForColumn(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
getBioMaterialIdList(Collection<BioMaterial>) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
getBioMaterialIdList(Collection<BioMaterial>) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
getBioMaterialIds() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
getBioMaterialLink(BioMaterial, String, ServletContext) - Static method in class ubic.gemma.web.util.AnchorTagUtil
getBioMaterialProvider() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getBioMaterials(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
getBioMaterials(EntityDelegator<ExpressionExperiment>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
getBioMaterialsForBioAssays(ExpressionDataMatrix<?>) - Static method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil: Returns a List of all the different types of biomaterials across all bioassays in the experiment.
getBioMaterialsForEE(Long) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
getBioProcessAnnotationLink() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
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.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.analysis.preprocess.ExpressionDataMatrixBuilder
getBlacklistedDatasets(FilterArg<ExpressionExperiment>, SortArg<ExpressionExperiment>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService: Browse blacklisted datasets.
getBlacklistedPlatforms(FilterArg<ArrayDesign>, SortArg<ArrayDesign>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService
getBlatResult() - Method in class ubic.gemma.core.analysis.sequence.GeneMappingSummary
getBlatResult() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
getBlatResultId() - Method in class ubic.gemma.core.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 interface ubic.gemma.core.apps.Blat
getBlatScoreThreshold() - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
getBlockCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getBlockCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
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.web.feed.NewsItem
getBoolean(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getBoolean(String) - Method in class ubic.gemma.web.util.ConfigurationCookie
getBoolean(String, boolean) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getBoolean(String, Boolean) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getByAccession(String, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getByAccession(String, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getByAccession(String, String, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getByAccession(String, String, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
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
getByIdentifier(int, String, String) - Method in interface ubic.gemma.core.loader.genome.FastaCmd
getByIdentifier(int, String, String) - Method in class ubic.gemma.core.loader.genome.SimpleFastaCmd
getByResultObjectType(Class<T>) - 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<? extends Identifiable>) - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap
getByte(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getByte(String, byte) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getByte(String, Byte) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getBytes() - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
getBytes() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.
getBytesRead() - Method in class ubic.gemma.web.util.upload.UploadInfo
getCache(CacheManager, String) - Static method in class ubic.gemma.persistence.util.CacheUtils: Obtain a cache by its name, raising an exception if unavailable.
getCacheStatus() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
getCancelView(HttpServletRequest) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.

Override this to control which cancelView is used.
getCancelView(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
getCatalogNumbers() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getCategoriesUsageFrequency(Collection<Long>, Collection<String>, Collection<String>, Collection<String>, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getCategoriesUsageFrequency(Collection<Long>, Collection<String>, Collection<String>, Collection<String>, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getCategoriesUsageFrequency(Filters, Set<Long>, Collection<String>, Collection<String>, Collection<String>, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Obtain category usage frequency for datasets matching the given filter.
getCategoriesUsageFrequency(Filters, Set<Long>, Collection<String>, Collection<String>, Collection<String>, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getCategory() - Method in class ubic.gemma.model.common.description.Characteristic
getCategory() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor: Obtain the category of this experimental factor.
getCategory(Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Create a new characteristic that represents the category of a given characteristic.
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
getCategoryTerms() - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
getCategoryUri() - Method in class ubic.gemma.model.common.description.Characteristic
getCause() - Method in exception ubic.gemma.core.analysis.preprocess.QuantitationMismatchPreprocessingException
getCause() - Method in exception ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException
getCause() - Method in exception ubic.gemma.core.search.BaseCodeOntologySearchException
getCause() - Method in exception ubic.gemma.core.search.source.HibernateSearchException
getCdfCut() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getCellData() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
getChannel(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getChannelCount() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getChannelNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getChannelNumber() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getChannels() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getCharacteristic() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getCharacteristics() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getCharacteristics() - Method in class ubic.gemma.model.analysis.Investigation
getCharacteristics() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getCharacteristics() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getCharacteristics() - Method in class ubic.gemma.model.expression.experiment.FactorValue
getCharacteristics() - Method in class ubic.gemma.model.genome.gene.GeneSet
getChemicals() - Method in class ubic.gemma.model.common.description.BibliographicReference
getChemicalsTerms() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getChildren() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
getChildren() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
getChildren(Collection<OntologyTerm>, boolean, boolean) - Method in interface ubic.gemma.core.ontology.OntologyService
getChildren(Collection<OntologyTerm>, boolean, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain the children of a collection of terms.
getChildren(Collection<OntologyTerm>, boolean, boolean, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getChildrenOccurrence(Map<String, Integer>, String) - Method in interface ubic.gemma.core.ontology.GoMetric
getChildrenOccurrence(Map<String, Integer>, String) - Method in class ubic.gemma.core.ontology.GoMetricImpl
getChipTypes(ExpressionExperiment, Collection<LocalFile>) - 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.association.phenotype.PhenotypeAssociationPublication: Deprecated.
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
getCitationValueObject() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
getCity() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getClassDelegatingFor() - Method in class ubic.gemma.web.remote.EntityDelegator
getClassName() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getClassName() - Method in class ubic.gemma.web.taglib.ConstantsTag
getCoating() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getCode() - Method in class ubic.gemma.rest.util.WellComposedErrorBody: Used by JSON Serializer.
getCoefficient() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getCoexGeneId() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
getCoexGeneSymbol() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
getCoexpCorrelationDistribution() - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis
getCoexpCorrelationDistribution(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDao
getCoexpCorrelationDistribution(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDaoImpl
getCoexpCorrelationDistribution(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
getCoexpCorrelationDistribution(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
getCoexpNodeDegree() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
getCoexpression(BioAssaySet, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
getCoexpression(BioAssaySet, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
getCoexpression(Taxon, BioAssaySet, boolean) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
getCoexpression(Taxon, BioAssaySet, boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
getCoExpressionDataFile(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController: AJAX Method - kicks off a job to start generating (if need be) the text based tab delimited co-expression data file
getCoexpressionMatrix() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
getCol() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getColor() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getColorString() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getColumn(Integer) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
getColumn(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
getColumn(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getColumn(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getColumn(Integer) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a single column of the matrix.
getColumn(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
getColumn(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
getColumn(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
getColumn(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getColumn(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getColumn(BioAssay) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a single column of the matrix.
getColumn(BioAssay) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
getColumnData(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getColumnData(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getColumnDescriptions() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
getColumnIndex(BioMaterial) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getColumnIndex(BioMaterial) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
getColumnNames() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData: The column names mean different things in different subclasses.
getColumns(List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
getColumns(List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
getColumns(List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getColumns(List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getColumns(List<BioAssay>) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a submatrix slice by columns
getColumns(List<BioAssay>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
getCommandGroup() - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
getCommandGroup() - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
getCommandGroup() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
getCommandGroup() - Method in class ubic.gemma.core.apps.BlacklistCli
getCommandGroup() - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
getCommandGroup() - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
getCommandGroup() - Method in class ubic.gemma.core.apps.GeoGrabberCli
getCommandGroup() - Method in class ubic.gemma.core.apps.IndexGemmaCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
getCommandGroup() - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
getCommandGroup() - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
getCommandGroup() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.OrderVectorsByDesignCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.PubMedLoaderCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ReplaceDataCli
getCommandGroup() - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
getCommandGroup() - Method in class ubic.gemma.core.apps.SplitExperimentCli
getCommandGroup() - Method in class ubic.gemma.core.apps.SVDCli
getCommandGroup() - Method in class ubic.gemma.core.apps.TaxonLoaderCli
getCommandGroup() - Method in class ubic.gemma.core.apps.UpdateEE2CCli
getCommandGroup() - Method in class ubic.gemma.core.apps.UpdatePubMedCli
getCommandGroup() - Method in class ubic.gemma.core.apps.VectorMergingCli
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
getCommandGroup() - Method in interface ubic.gemma.core.util.CLI: Obtain the command group for this CLI.
getCommandName() - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
getCommandName() - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
getCommandName() - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
getCommandName() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
getCommandName() - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
getCommandName() - Method in class ubic.gemma.core.apps.BlacklistCli
getCommandName() - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
getCommandName() - Method in class ubic.gemma.core.apps.DeleteDiffExCli
getCommandName() - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
getCommandName() - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
getCommandName() - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
getCommandName() - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
getCommandName() - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
getCommandName() - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
getCommandName() - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
getCommandName() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
getCommandName() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
getCommandName() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
getCommandName() - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
getCommandName() - Method in class ubic.gemma.core.apps.GeeqCli
getCommandName() - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
getCommandName() - Method in class ubic.gemma.core.apps.GeoGrabberCli
getCommandName() - Method in class ubic.gemma.core.apps.IndexGemmaCLI
getCommandName() - Method in class ubic.gemma.core.apps.LinkAnalysisCli
getCommandName() - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
getCommandName() - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
getCommandName() - Method in class ubic.gemma.core.apps.MakeExperimentPrivateCli
getCommandName() - Method in class ubic.gemma.core.apps.MakeExperimentsPublicCli
getCommandName() - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
getCommandName() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
getCommandName() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
getCommandName() - Method in class ubic.gemma.core.apps.OrderVectorsByDesignCli
getCommandName() - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
getCommandName() - Method in class ubic.gemma.core.apps.PubMedLoaderCli
getCommandName() - Method in class ubic.gemma.core.apps.ReplaceDataCli
getCommandName() - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
getCommandName() - Method in class ubic.gemma.core.apps.SplitExperimentCli
getCommandName() - Method in class ubic.gemma.core.apps.SVDCli
getCommandName() - Method in class ubic.gemma.core.apps.TaxonLoaderCli
getCommandName() - Method in class ubic.gemma.core.apps.UpdateEE2CCli
getCommandName() - Method in class ubic.gemma.core.apps.UpdatePubMedCli
getCommandName() - Method in class ubic.gemma.core.apps.VectorMergingCli
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
getCommandName() - Method in interface ubic.gemma.core.util.CLI: A short memorable name for the command that can be used to locate this class.
getComment() - Method in class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
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.analysis.sequence.GeneMappingSummary
getCompositeSequence() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getCompositeSequenceCount(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getCompositeSequenceCount(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getCompositeSequenceCountById(long) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
getCompositeSequenceCountById(long) - 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) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
getCompositeSequenceCountById(Long) - Method in class ubic.gemma.core.genome.gene.service.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.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.ArrayDesignService
getCompositeSequences(ArrayDesign, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
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) - Method in interface ubic.gemma.core.genome.gene.service.GeneService: Returns a list of compositeSequences associated with the given gene and array design
getCompositeSequences(Gene, ArrayDesign) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
getCompositeSequences(Gene, ArrayDesign) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
getCompositeSequences(Gene, ArrayDesign) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getCompositeSequencesById(long) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
getCompositeSequencesById(long) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl: Gets all the CompositeSequences related to the gene identified by the given id.
getCompositeSequencesById(Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
getCompositeSequencesById(Long) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
getConditions() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
getConfig() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getConfiguration(int) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getConfirmNewPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getContact() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
getContactName() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getContainsMyData() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getContentType() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.
getContentType() - Method in class ubic.gemma.web.view.JSONView
getContext(Class<?>) - Method in class ubic.gemma.rest.providers.ObjectMapperResolver
getContextUploadPath() - Static method in class ubic.gemma.web.util.upload.FileUploadUtil
getContrastFactorValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
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.DifferentialExpressionValueObject
getContrastsFactorValueIds() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getContrastsFactorValues() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getContributer() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getContributers() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
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(HttpServletRequest, String) - Static method in class ubic.gemma.web.util.RequestUtil: Convenience method to get a cookie by name
getCorrectedPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getCorrectedPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getCorrectedPValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getCorrectedPValueBin() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getCorrelationCacheThreshold() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getCorrelationDistribution() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
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.loader.association.NCBIGene2GOAssociationLoader
getCount() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
getCount() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
getCount() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
getCount(InputStream) - Method in class ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParser
getCountry() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getCountsForTaxonPieChart() - Method in class ubic.gemma.web.controller.common.HomePageController: For the show-off graph that shows number of data sets per taxon.
getCreateDate(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getCreateDate(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
getCreateEvents(Collection<? extends Auditable>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao
getCreateEvents(Collection<? extends Auditable>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getCreateEvents(Collection<? extends Auditable>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getCreateEvents(Collection<? extends Auditable>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getCreationEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
getCrossHybridizationRejections() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
getCrossHybridizationRejections() - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis: Use after analysis.
getCs2GeneIdMap(Collection<Long>, Collection<Long>, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getCs2GeneMap(Collection<Gene>, Collection<ArrayDesign>, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getCs2GeneMap(Collection<Gene>, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getCs2GeneMapForProbes(Collection<Long>, Session) - Static method in class ubic.gemma.persistence.util.CommonQueries
getCsSummaries(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController: Exposed for AJAX calls (Probe browser) FIXME can probably remove soon since we should use getGeneCsSummaries? Might be another use for this
getCsSummaries(EntityDelegator<ArrayDesign>) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController: Exposed for AJAX calls.
getCsSummaries(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
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
getCurationNote() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getCurationNote() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getCurrentGroup() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getCurrentGroup() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject: Deprecated.
use UserValueObject.getGroups() instead
getCurrentId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
getCurrentUser() - Method in interface ubic.gemma.core.security.authentication.UserManager
getCurrentUser() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
getCurrentUserCanwrite() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getCurrentUserIsOwner() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getCurrentUsername() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
getCurrentUserOwns() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
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 ubic.gemma.core.loader.util.AlreadyExistsInSystemException
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
getData() - Method in class ubic.gemma.rest.util.ResponseDataObject
getData() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getDatabaseSupplier() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getDataFile(ExpressionExperimentDataFetchCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController: AJAX Method - kicks off a job to start generating (if need be) the text based tab delimited experiment design data file
getDataFileFormatProblemMessage() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getDataMatrix() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getDataProcessing() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getDataSet() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
getDatasetAnnotations(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the annotations for the given dataset.
getDatasetDesign(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the design for the given dataset.
getDatasetDifferentialExpression(DatasetArrayArg, Long, Double, LimitArg, Boolean, ExpLevelConsolidationArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the expression levels of genes highly expressed in the given component on given datasets.
getDatasetDifferentialExpressionAnalyses(DatasetArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the differential analysis results for the given dataset.
getDatasetDifferentialExpressionAnalysesResultSets(DatasetArg<?>, HttpServletRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the result sets of all the differential expression analyses of a dataset.
getDatasetExpression(DatasetArg<?>, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the data for the given dataset.
getDatasetExpressionForGenes(DatasetArrayArg, GeneArrayArg, Boolean, ExpLevelConsolidationArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the expression levels of given genes on given datasets.
getDatasetExpressionPca(DatasetArrayArg, Integer, LimitArg, Boolean, ExpLevelConsolidationArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the expression levels of genes highly expressed in the given component on given datasets.
getDatasetHasBatchInformation(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Returns true if the experiment has had batch information successfully filled in.
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
getDatasetLink() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getDatasetMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getDatasetName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getDatasetName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getDatasetPlatforms(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves platforms for the given dataset.
getDatasetProcessedExpression(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve processed expression data.
getDatasetQuantitationTypes(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve all available quantitation types for a dataset.
getDatasetRawExpression(DatasetArg<?>, QuantitationTypeArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve raw expression data.
getDatasets() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getDatasets(QueryArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.DatasetsWebService
getDataSets() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getDatasetSamples(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the samples for the given dataset.
getDatasetsAnnotationsUsageStatistics(QueryArg, FilterArg<ExpressionExperiment>, ExcludeArg<DatasetsWebService.AnnotationWithUsageStatisticsValueObject>, LimitArg, Integer, String, StringArrayArg, Boolean, StringArrayArg, Boolean, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsAvailable() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
getDatasetsByIds(DatasetArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves all datasets matching the given identifiers.
getDatasetsCategoriesUsageStatistics(QueryArg, FilterArg<ExpressionExperiment>, LimitArg, StringArrayArg, Boolean, StringArrayArg, Boolean, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetShortName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getDatasetShortName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getDatasetsPlatformsUsageStatistics(QueryArg, FilterArg<ExpressionExperiment>, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDataSetsSupporting() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
getDatasetsTaxaUsageStatistics(QueryArg, FilterArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsTested() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
getDatasetSvd(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the design for the given dataset.
getDatasetType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getDataWasBatchCorrected() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
getDate() - Method in class ubic.gemma.core.analysis.report.AuditableObject
getDate() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getDate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getDate() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
getDate() - Method in class ubic.gemma.web.feed.NewsItem
getDateArrayDesignLastUpdated() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDateBatchFetch() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDateCached() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDateCorrelations() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
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.SVDValueObject
getDates() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
getDbXrefs() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getDEDV(Collection<Long>, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: Given a collection of expression experiment Ids and a geneId returns a map of DEDV value objects to a collection of genes.
getDEDVForCoexpressionVisualization(Collection<Long>, Long, Long) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method
getDEDVForDiffExVisualization(Collection<Long>, Collection<Long>, Double, Collection<DiffExpressionSelectedFactorCommand>) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method - for ProbeLevelDiffExGrid, VisualizationDifferentialWindow, DifferentialExpressionAnalysesSummaryTree
getDEDVForDiffExVisualizationByExperiment(Long, Long, Double, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method Batch factor value analyses are filtered out; for ProbeLevelDiffExGrid:VisualizationDifferentialWindow.
getDEDVForDiffExVisualizationByThreshold(Long, Double, Long) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method
getDEDVForPcaVisualization(Long, int, int) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX
getDEDVForVisualization(Collection<Long>, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method
getDEDVForVisualizationByProbe(Collection<Long>, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: AJAX exposed method
getDedvId() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getDefaultSearchOperator() - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getDefaultSymbol() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getDefinition(String) - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain a definition for the given URI.
getDefinition(String) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getDepartment() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getDescription() - Method in class ubic.gemma.core.job.progress.ProgressData
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.genome.gene.ncbi.model.NCBIGeneInfo
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.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.expression.arrayDesign.ArrayDesign
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
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.ExperimentalFactor
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDescription() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getDescription() - Method in class ubic.gemma.model.genome.gene.GeneSet
getDescription() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getDescription() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
getDescription() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getDescription() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getDescription(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX call
getDescriptions() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
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
getDesignElementDataVectorCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getDesignElementDataVectorCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getDesignElementDataVectorCount(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getDesignElementDataVectorCount(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getDesignElementForRow(int) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getDesignElementForRow(int) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
getDesignElementName() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
getDesignElements() - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
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.loader.expression.geo.model.GeoPlatform
getDesignMatrix() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBat
getDesignMatrix(ExpressionExperiment, boolean, boolean) - Static method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject.Factory
getDesignMatrixRows(EntityDelegator<ExpressionExperiment>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
getDesignProvider() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getDesignSummaries(ArrayDesign) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getDesignSummaries(ArrayDesign) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
getDetail() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getDetail() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
getDetails(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getDetails(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
getDetails(String) - Method in class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController
getDetails(String, String) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowserService: Get details from GEO about an accession.
getDetails(String, String) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
getDetectedQualityScore() - Method in class ubic.gemma.model.expression.experiment.Geeq
getDetectedSuitabilityScore() - Method in class ubic.gemma.model.expression.experiment.Geeq
getDf() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
getDifferentialExpression(Long, double) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController: AJAX entry which returns results on a non-meta analysis basis.
getDifferentialExpression(Long, double, Integer) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController: AJAX entry which returns results on a non-meta analysis basis.
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<DiffExpressionSelectedFactorCommand>) - 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<DiffExpressionSelectedFactorCommand>) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
getDifferentialExpression(Gene, Collection<BioAssaySet>) - 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<BioAssaySet>) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
getDifferentialExpression(Gene, BioAssaySet, 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, double, int) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
getDifferentialExpressionAnalyses() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getDifferentialExpressionMetaAnalysis(double, Gene, Map<Long, Long>, Collection<BioAssaySet>) - 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<Long, Long>, Collection<BioAssaySet>) - Method in class ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl
getDifferentialExpressionWithoutBatch(Long, double, Integer) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController: AJAX entry which returns results on a non-meta analysis basis.
getDiffExpressionAnalysisArchiveFile(Long, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create the differential expression data file(s) for a given experiment.
getDiffExpressionAnalysisArchiveFile(Long, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getDiffExpressionDataFile(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController: AJAX Method - kicks off a job to start generating (if need be) the text based tab delimited differential expression data file
getDiffExpressionEvidence() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
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
getDir() - Method in class ubic.gemma.web.remote.ListBatchCommand
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
getDiscontinuedId() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getDisplayName() - Method in enum ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType
getDisplayName() - Method in class ubic.gemma.core.image.aba.Image
getDisplayName() - Method in class ubic.gemma.web.controller.expression.experiment.MetaFile
getDistribution() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getDone() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getDouble(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getDouble(String) - Method in class ubic.gemma.web.util.ConfigurationCookie
getDouble(String, double) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getDouble(String, Double) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getDownloadName(ExpressionExperiment) - Method in enum ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType
getDownloadPath() - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getDownregulatedCount() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Deprecated.
use DiffExResultSetSummaryValueObject.getNumberOfDownregulatedProbes() instead.
getEditor() - Method in class ubic.gemma.model.common.description.BibliographicReference
getEe() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
getEeCountPerTaxon() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getEeId() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
getEeId() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getEeIds() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
getEeIds() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
getEeQuery() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
getEeQuery() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
getEeSetId() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
getEeSetId() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
getEeSetName() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
getEeSetName() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
getEevo() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getEf() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
getEfId() - Method in class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
getEigenGene(int) - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
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
getELContext() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
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 BaseDao.
getElementClass() - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService
getElementClass() - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
getElementClass() - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getElementClass() - Method in interface ubic.gemma.rest.util.args.EntityArgService
getElements(PlatformArg<?>, int, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Retrieves the Elements of the Platform that this argument represents.
getEmail() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getEmail() - Method in class ubic.gemma.model.common.auditAndSecurity.Contact
getEmail() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getEmail() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
getEmailAlert() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getEnabled() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getEnabled() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getEndPosition() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getEndTime() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
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
getEnsemblPeptideId() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getEnsemblTranscriptId() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getEntities(AbstractEntityArg<?, T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getEntities(AbstractEntityArg<?, T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getEntities(AbstractEntityArrayArg<T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getEntities(AbstractEntityArrayArg<T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getEntity(AbstractEntityArg<?, T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getEntity(AbstractEntityArg<?, T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getEntity(QuantitationTypeArg<?>, ExpressionExperiment, Class<? extends DesignElementDataVector>) - Method in class ubic.gemma.rest.util.args.QuantitationTypeArgService
getEntityClazz() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEntityDescription() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEntityId() - Method in class ubic.gemma.core.job.TaskCommand
getEntityId() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEntityName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEntityShortName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getEntityTransformer() - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao: Obtain an entity transformer for the results of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
getEntityWithContrastsAndResults(ExpressionAnalysisResultSetService) - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArg
getEntityWithPlatform(CompositeSequenceArg<?>, ArrayDesign) - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgService
getEntityWithTaxon(GeneService, Taxon) - Method in class ubic.gemma.rest.util.args.GeneEnsemblIdArg
getEntityWithTaxon(GeneService, Taxon) - Method in class ubic.gemma.rest.util.args.GeneSymbolArg
getEntityWithTaxon(GeneArg<?>, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService
getEntrezgenes() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getError() - Method in class ubic.gemma.persistence.model.Gene2CsStatus
getErrorFromPreviousAttempt() - Method in exception ubic.gemma.core.loader.expression.geo.service.IOExceptionWithRetry
getErrorMessage() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaResponse
getErrorMessage() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
getErrorMessage() - Method in class ubic.gemma.web.util.upload.FailedMultipartHttpServletRequest
getErrors() - Method in class ubic.gemma.rest.util.WellComposedErrorBody: Used by JSON Serializer.
getErrorState() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
getEvents() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
getEvents(Auditable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao
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
getEvents(Auditable) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
getEvents(Auditable) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl
getEvents(EntityDelegator<? extends Auditable>) - Method in class ubic.gemma.web.remote.AuditController
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.genome.gene.phenotype.valueObject.GeneEvidenceValueObject: Deprecated.
getEvidenceCode() - Method in class ubic.gemma.model.association.Gene2GOAssociation
getEvidenceCode() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getEvidenceCode() - Method in class ubic.gemma.model.common.description.Characteristic
getEvidenceCode() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getEvidenceId() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
getEvidenceSecurityValueObject() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getEvidenceSource() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getEvidenceSource() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getException() - Method in class ubic.gemma.core.job.TaskResult
getException() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getExcludedUris(StringArrayArg, boolean, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Obtain a list of exclude URIs from an argument containing excluded URIs.
getExistingFile(File, String) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher: Wrap the existing file in the required Collection<LocalFile>
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.
getExpectedSize(String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
getExperiment() - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
getExperiment() - Method in class ubic.gemma.model.association.phenotype.ExperimentalEvidence: Deprecated.
getExperimentalDesign() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getExperimentalDesign() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getExperimentalDesignAnnotations(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain experimental design-level annotations.
getExperimentalDesignAnnotations(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getExperimentalDesignDescription() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getExperimentalDesignId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getExperimentalDesignLink(ExperimentalDesign, String, ServletContext) - Static method in class ubic.gemma.web.util.AnchorTagUtil
getExperimentalDesignName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getExperimentalFactor() - Method in class ubic.gemma.model.expression.experiment.FactorValue
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.FactorAssociatedAnalysisResultSet
getExperimentalFactors() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getExperimentalFactors() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
getExperimentalFactors(EntityDelegator<?>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
getExperimentalFactors(EntityDelegator<ExpressionExperiment>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
getExperimentAnalyzed() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis
getExperimentAnnotations(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain experiment-level annotations.
getExperimentAnnotations(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getExperimentCharacteristics() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject: Deprecated.
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.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getExperimentId() - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
getExperimentIdsInSet(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
getExperimentIdsInSet(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager
getExperimentIdsInSet(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getExperimentName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getExperiments() - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
getExperiments() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getExperiments(PlatformArg<?>, int, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Retrieves the Datasets of the Platform that this argument represents.
getExperimentSetById(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager: Get the session-bound group using the group's id
getExperimentSetById(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
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
getExperimentsInSet(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager
getExperimentsInSet(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getExperimentsInSet(Long, Integer) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
getExperimentsLackingPublications() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getExperimentsLackingPublications() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getExperimentsLackingPublications() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getExperimentsLackingPublications() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getExperimentsWithAnalysis(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.AnalysisService: Not secured: for internal use only
getExperimentsWithAnalysis(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDao
getExperimentsWithAnalysis(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDaoImpl
getExperimentsWithAnalysis(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService: Not secured: for internal use only
getExperimentsWithAnalysis(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
getExperimentsWithAnalysis(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
getExperimentsWithAnalysis(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
getExperimentsWithAnalysis(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
getExperimentsWithAnalysis(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
getExperimentsWithAnalysis(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
getExperimentsWithAnalysis(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService: Not secured: for internal use only
getExperimentsWithAnalysis(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.AnalysisService: Not secured: for internal use only
getExperimentsWithAnalysis(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService: Not secured: for internal use only
getExperimentsWithAnalysis(Taxon) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
getExperimentsWithAnalysis(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
getExperimentsWithAnalysis(Taxon) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
getExperimentsWithAnalysis(Taxon) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
getExperimentsWithAnalysis(Taxon) - Method in interface ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService: Not secured: for internal use only
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.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
getExpressionEvaluator() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getExpressionExperiment() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getExpressionExperiment() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getExpressionExperiment() - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix: The associated ExpressionExperiment, if known.
getExpressionExperiment() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Return the expression experiment this matrix is holding data for.
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
getExpressionExperiment() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getExpressionExperiment() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
getExpressionExperiment() - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
getExpressionExperiment() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
getExpressionExperiment() - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
getExpressionExperiment() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
getExpressionExperiment(Long) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao
getExpressionExperiment(Long) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
getExpressionExperiment(Long) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
getExpressionExperiment(Long) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
getExpressionExperiment(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDao
getExpressionExperiment(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl
getExpressionExperiment(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService: Gets the expression experiment for the specified experimental design object
getExpressionExperiment(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignServiceImpl
getExpressionExperimentCount() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Deprecated.
use ArrayDesignValueObject.getNumberOfExpressionExperiments() instead.
getExpressionExperimentId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getExpressionExperimentId() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
getExpressionExperimentIds() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getExpressionExperimentLink(ExpressionExperiment, String, ServletContext) - Static method in class ubic.gemma.web.util.AnchorTagUtil
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.ArrayDesignService
getExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getExpressionExperimentsCount(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Obtain the number of associated expression experiments.
getExpressionExperimentsCount(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getExpressionExperimentsCount(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getExpressionExperimentsCount(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getExpressionExperimentSets() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getExpressionExperimentUrl(ExpressionExperiment, ServletContext) - Static method in class ubic.gemma.web.util.AnchorTagUtil
getExpressionLevels(Collection<ExpressionExperiment>, Collection<Gene>, boolean, String) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getExpressionLevels(Collection<ExpressionExperiment>, Collection<Gene>, boolean, String) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getExpressionLevelsDiffEx(Collection<ExpressionExperiment>, Long, double, int, boolean, String) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getExpressionLevelsDiffEx(Collection<ExpressionExperiment>, Long, double, int, boolean, String) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getExpressionLevelsPca(Collection<ExpressionExperiment>, int, int, boolean, String) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getExpressionLevelsPca(Collection<ExpressionExperiment>, int, int, boolean, String) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getExternalAccession() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getExternalAccession() - Method in class ubic.gemma.model.expression.BlacklistedEntity
getExternalDatabase() - Method in class ubic.gemma.model.common.description.DatabaseEntry
getExternalDatabase() - Method in class ubic.gemma.model.expression.BlacklistedValueObject
getExternalDatabase() - Method in class ubic.gemma.model.genome.Taxon
getExternalDatabase() - Method in class ubic.gemma.model.genome.TaxonValueObject
getExternalDatabaseIds() - Method in class ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
getExternalDatabases() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getExternalId(BioMaterial, Collection<BioAssay>) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils
getExternalReference() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getExternalReferences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getExternalUrl() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSourceValueObject
getExternalUrl() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getExtractProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getExtraMissingValueIndicators() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
getFactor() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
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.SVDValueObject
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
getFactorName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getFactorName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getFactorNames() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getFactorProfiles() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getFactorPvals() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
getFactors() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
getFactors() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
getFactors() - Method in class ubic.gemma.persistence.util.FactorValueVector
getFactors() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo
getFactors() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
getFactors(Collection<Long>) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController: AJAX entry.
getFactorsToInclude() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getFactorTypes() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
getFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getFactorValue(Long, String) - Method in class ubic.gemma.web.controller.OntologyController
getFactorValueAnnotation(Long, Long, String) - Method in class ubic.gemma.web.controller.OntologyController
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
getFactorValueId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getFactorValueId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
getFactorValueMap() - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
getFactorValueObjects() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject: Deprecated.
use BioMaterialValueObject.getFactorValues()
getFactorValues() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
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.web.controller.visualization.VisualizationValueObject
getFactorValues(EntityDelegator<BioMaterial>) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
getFactorValues(EntityDelegator<ExperimentalFactor>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
getFactorValues(EntityDelegator<ExperimentalFactor>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX
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
getFactorValuesToNames() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
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
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.ExpressionExperimentSubSetService
getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
getFactorValuesUsedByExperimentalFactorId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject: Produce a mapping of ExperimentalFactor IDs to FactorValue VOs used in this analysis.
getFactorValuesWithCharacteristics(EntityDelegator<ExperimentalFactor>) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
getFailedMessage() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getFastqHeaders() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getFax() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getFeatureCount() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getFields(Class<? extends Identifiable>) - Method in interface ubic.gemma.core.search.FieldAwareSearchSource: Obtain a list of fields that can be searched on.
getFields(Class<? extends Identifiable>) - Method in interface ubic.gemma.core.search.SearchService: Obtain a list of fields that can be searched on for the given result type.
getFields(Class<? extends Identifiable>) - Method in class ubic.gemma.core.search.SearchServiceImpl
getFields(Class<? extends Identifiable>) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
getFile() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
getFile() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
getFileIndex() - Method in class ubic.gemma.web.util.upload.UploadInfo
getFileItem() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.

Return the underlying org.apache.commons.fileupload.FileItem instance.
getFileName(String) - Static method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
getFileName(ExpressionExperiment) - Method in enum ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType
getFilter(String, Class<T>, Filter.Operator, Collection<T>) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(String, Class<T>, Filter.Operator, Collection<T>) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(String, Class<T>, Filter.Operator, Collection<T>) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(String, Class<T>, Filter.Operator, Collection<T>) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a Filter with an already parsed collection of values.
getFilter(String, Class<T>, Filter.Operator, Collection<T>) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilter(String, Class<T>, Filter.Operator, T) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(String, Class<T>, Filter.Operator, T) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(String, Class<T>, Filter.Operator, T) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(String, Class<T>, Filter.Operator, T) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a Filter with an already parsed value.
getFilter(String, Class<T>, 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.common.description.CharacteristicService
getFilter(String, Filter.Operator, String) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
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, Collection<String>) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilter(String, Filter.Operator, Collection<String>) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilter(String, Filter.Operator, Collection<String>) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilter(String, Filter.Operator, Collection<String>) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
getFilter(String, Filter.Operator, Collection<String>) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
getFilter(String, Filter.Operator, Collection<String>) - 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<String>) - 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.common.description.CharacteristicService
getFilterableProperties() - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
getFilterableProperties() - Method in interface ubic.gemma.persistence.service.FilteringDao: List all properties availble for filtering.
getFilterableProperties() - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterableProperties() - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterableProperties() - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilterablePropertyAllowedValues(String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a short list of allowed values for the given property, or null if unrestricted.
getFilterablePropertyAllowedValues(String) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyAllowedValues(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyConfigAttributes(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyConfigAttributes(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: Checks for special properties that are allowed to be referenced on certain objects.
getFilterablePropertyConfigAttributes(String) - Method in interface ubic.gemma.persistence.service.FilteringService: Obtain the Spring Security config attributes for a given property.
getFilterablePropertyConfigAttributes(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyConfigAttributes(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyDescription(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterablePropertyDescription(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyDescription(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilterablePropertyDescription(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
getFilterablePropertyDescription(String) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
getFilterablePropertyDescription(String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a short description for a given filterable property.
getFilterablePropertyDescription(String) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterablePropertyDescription(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyDescription(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyIsUsingSubquery(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterablePropertyIsUsingSubquery(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyIsUsingSubquery(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilterablePropertyIsUsingSubquery(String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Indicate if the given property is using a subquery for filtering.
getFilterablePropertyIsUsingSubquery(String) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterablePropertyIsUsingSubquery(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyIsUsingSubquery(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao
getFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao: Obtain various meta-information used to infer what to use in a Filter or Sort.
getFilterablePropertyMeta(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.
getFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl: Checks for special properties that are allowed to be referenced on certain objects.
getFilterablePropertyMeta(String, String, Class<?>) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in interface ubic.gemma.persistence.service.FilteringService: Obtain a list of resolvable MessageSourceResolvables to be used for user display purposes.
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyType(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getFilterablePropertyType(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getFilterablePropertyType(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getFilterablePropertyType(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
getFilterablePropertyType(String) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
getFilterablePropertyType(String) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain the type of the given filterable property.
getFilterablePropertyType(String) - Method in interface ubic.gemma.persistence.service.FilteringService
getFilterablePropertyType(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyType(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterConfig() - Method in class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand
getFilteredMatrix(String, FilterConfig, Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService
getFilteredMatrix(String, FilterConfig, Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getFilteredMatrix(Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter: Provides a ready-to-use expression data matrix that is transformed and filtered.
getFilteredMatrix(ExpressionExperiment, FilterConfig) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService: Provide a filtered expression data matrix.
getFilteredMatrix(ExpressionExperiment, FilterConfig) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getFilteredMatrix(ExpressionExperiment, FilterConfig, Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService: Provide a filtered expression data matrix.
getFilteredMatrix(ExpressionExperiment, FilterConfig, Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getFilteringCountQuery(Filters) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao: Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
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(Filters) - Method in class ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao: Obtain a Criteria for loading VOs.
getFilteringCriteria(Filters) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
getFilteringIdQuery(Filters, Sort) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao: Produce a query that will be used to retrieve IDs of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
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 value objects after applying a set of filters and a given 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(AbstractEntityArg<A, T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilters(AbstractEntityArg<A, T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilters(AbstractEntityArg<A, Taxon, TaxonService>) - Method in class ubic.gemma.rest.util.args.TaxonArgService
getFilters(AbstractEntityArrayArg<T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilters(AbstractEntityArrayArg<T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilters(FilterArg<T>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilters(FilterArg<T>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilters(FilterArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getFilters(FilterArg<ExpressionExperiment>, Collection<OntologyTerm>) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getFiltersWithInferredAnnotations(Filters, Collection<OntologyTerm>, long, TimeUnit) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Apply ontological inference to augment a filter with additional terms.
getFiltersWithInferredAnnotations(Filters, Collection<OntologyTerm>, long, TimeUnit) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl: The approach here is to construct a collection for each sub-clause in the expression that regroups all the predicates that apply to characteristics as well as their inferred terms.
getFinishTime() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
getFinishTime() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getFinishTime() - Method in interface ubic.gemma.core.job.SubmittedTask
getFirstGene() - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
getFirstGene() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
getFirstGene() - Method in class ubic.gemma.model.association.Gene2GeneIdAssociation
getFirstGene() - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
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
getFloat(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getFloat(String, float) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getFloat(String, Float) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getForm() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
getFormat() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getFormatter() - Method in class ubic.gemma.core.search.DefaultHighlighter
getFormatter() - Method in interface ubic.gemma.core.search.lucene.LuceneHighlighter: Obtain a formatter for highlights.
getForwardingURL() - Method in class ubic.gemma.core.job.progress.ProgressData
getFoundGene() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getFoundGeneNodeDegree() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getFoundGeneNodeDegreeRank() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
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.util.ArrayDesignsForExperimentCache
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.
getFullName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getFullTextUri() - Method in class ubic.gemma.model.common.description.BibliographicReference
getFwe() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getGeeq() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getGenbank() - Static method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
getGenbankAccession(String) - Static method in class ubic.gemma.core.loader.util.parser.ExternalDatabaseUtils
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.Gene2OntologyEntryAssociation
getGene() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getGene() - Method in class ubic.gemma.model.genome.gene.GeneProduct
getGene() - Method in class ubic.gemma.model.genome.gene.GeneSetMember
getGene(Gene) - Method in interface ubic.gemma.core.image.aba.AllenBrainAtlasService
getGene(Gene) - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl: Given a gene too look for for will return the corresponding abaGene (useful for finding images)
getGene(GeneProductValueObject) - Method in class ubic.gemma.core.analysis.sequence.GeneMappingSummary
getGene2ProbeMapByOfficialSymbols(Collection<String>, Collection<ArrayDesign>) - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService
getGeneABALink(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
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
getGeneCsSummaries(Long) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController: Exposed for AJAX calls (Elements tab on gene details page)
getGeneDifferentialExpressionMetaAnalysisId() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getGeneDifferentialExpressionMetaAnalysisResult() - Method in class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence: Deprecated.
getGeneDifferentialExpressionMetaAnalysisResultId() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getGeneDifferentialExpressionMetaAnalysisSummaryValueObject() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getGeneEvidence(GeneArg<?>) - Method in class ubic.gemma.rest.GeneWebService: Deprecated.
getGeneEvidence(GeneArg<?>, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService: Deprecated.
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
getGeneGeneCoexpression(GeneArg<?>, GeneArg<?>, LimitArg, Integer) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the coexpression of two given genes.
getGeneGoTerms(GeneArg<?>) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the GO terms of the given gene.
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.analysis.expression.coexpression.CoexpressionSummaryValueObject
getGeneId() - Method in class ubic.gemma.core.image.aba.AbaGene
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.coexpression.GeneCoexpressedGenes
getGeneId() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
getGeneId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getGeneId() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
getGeneId() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
getGeneId() - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
getGeneId() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getGeneIds() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
getGeneIds() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
getGeneIds() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getGeneIdsInGroup(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX
getGeneIdsInGroup(GeneSetValueObject) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
getGeneIdsInGroup(GeneSetValueObject) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
getGeneInfo() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
getGeneLocation(GeneArg<?>) - Method in class ubic.gemma.rest.util.args.GeneArgService: Returns all known locations of the gene(s) that this GeneArg represents.
getGeneLocation(GeneArg<?>, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService: Returns all known locations of the gene that this GeneArg represents.
getGeneLocations(GeneArg<?>) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the physical location of the given gene.
getGeneLocationsInTaxon(TaxonArg<?>, GeneArg<?>) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves gene location for the gene on the given taxon.
getGeneMappingSummaries() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
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
getGeneMappingSummary(EntityDelegator<CompositeSequence>) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController: Exposed for AJAX calls.
getGeneName() - Method in class ubic.gemma.core.image.aba.AbaGene
getGeneName() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getGeneName() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
getGeneNCBI() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
getGeneNCBI() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getGeneNcbiId() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
getGeneOfficialName() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getGeneOfficialSymbol() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
getGeneOfficialSymbol() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getGeneProbes(GeneArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the probes (composite sequences) with this gene.
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.core.analysis.sequence.GeneMappingSummary
getGeneProductIdMap() - Method in class ubic.gemma.core.analysis.sequence.GeneMappingSummary
getGeneProductMap() - Method in class ubic.gemma.core.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.core.analysis.sequence.GeneMappingSummary
getGeneralType() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getGeneralType() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
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.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
getGenes() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
getGenes() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getGenes(String, Taxon) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getGenes(String, Taxon) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getGenes(Collection<Long>) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getGenes(Collection<String>) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
getGenes(Collection<String>) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
getGenes(Collection<String>, Taxon) - Method in interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao
getGenes(Collection<String>, Taxon) - Method in class ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl
getGenes(Collection<CompositeSequence>) - 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<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getGenes(Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService: Given a Collection of composite sequences returns of map of a composite sequence to a collection of genes
getGenes(Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGenes(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getGenes(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGenes(CompositeSequence, int, int) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao: given a composite sequence returns a collection of genes
getGenes(CompositeSequence, int, int) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getGenes(CompositeSequence, int, int) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getGenes(CompositeSequence, int, int) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGenes(GeneArrayArg) - Method in class ubic.gemma.rest.GeneWebService: Retrieves all genes matching the identifier.
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.BioSequenceService
getGenesByAccession(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
getGenesByGOId(String, Long) - Method in interface ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneSearchServiceImpl
getGenesByGOId(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: for AJAX get all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy
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.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.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.GeneProductService
getGenesByNcbiId(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
getGenesByTaxon(Taxon) - Method in interface ubic.gemma.core.genome.gene.service.GeneService: Gets all the genes for a given taxon
getGenesByTaxon(Taxon) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
getGenesByTaxon(Taxon) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
getGenesByTaxon(Taxon) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getGeneSetByGOId(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: for AJAX get a gene set with all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy
getGeneSetById(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager: Get the session-bound group using the group's id
getGeneSetById(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getGeneSetId() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
getGenesEvidenceInTaxon(TaxonArg<?>, GeneArg<?>) - Method in class ubic.gemma.rest.TaxaWebService: Deprecated.
getGenesInGroup(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager: AJAX If the current user has access to given gene group will return the gene ids in the gene group
getGenesInGroup(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getGenesInGroup(Long, Integer) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX If the current user has access to given gene group, will return the gene value objects in the gene group
getGenesInGroup(GeneSetValueObject) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService: Get the gene value objects for the members of the group param
getGenesInGroup(GeneSetValueObject) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
getGenesOnChromosome(TaxonArg<?>, String, String, long, int) - Method in class ubic.gemma.rest.util.args.TaxonArgService: Lists Genes overlapping a location on a specific chromosome on a taxon that this TaxonArg represents.
getGenesOnTaxon(GeneArg<?>, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService
getGenesTested() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis: Gene the genes that were tested, according to the rows that are currently in the dataMatrix (so call this after filtering!)
getGenesWithSpecificity(Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
getGenesWithSpecificity(Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getGenesWithSpecificity(Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getGenesWithSpecificity(Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getGeneSymbol() - Method in class ubic.gemma.core.image.aba.AbaGene
getGeneSymbol() - Method in class ubic.gemma.core.image.ABALinkOutValueObject
getGeneSymbol() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getGeneType() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getGeneUrl() - Method in class ubic.gemma.core.image.aba.AbaGene
getGeneUrl(Gene) - Method in interface ubic.gemma.core.image.aba.AllenBrainAtlasService: Given a Gemma gene object returns an allen brain atlas gene URL
getGeneUrl(Gene) - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl
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
getGeoDomainObjectGenerator() - Method in class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
getGeoDomainObjectGenerator() - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService: This is supplied to allow clients to check that the generator has been set correctly.
getGeoRecords(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Retrieve records for experiments
getGeoRecordsBySearchTerm(String, int, int, boolean, Collection<String>, Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Provides more details than getRecentGeoRecords.
getGfClientExe() - Method in interface ubic.gemma.core.apps.Blat
getGfClientExe() - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
getGfServerExe() - Method in interface ubic.gemma.core.apps.Blat
getGfServerExe() - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
getGitHash() - Method in class ubic.gemma.core.util.BuildInfo
getGOGroupGenes(String, Taxon) - Method in interface ubic.gemma.core.genome.gene.service.GeneSearchService
getGOGroupGenes(String, Taxon) - Method in class ubic.gemma.core.genome.gene.service.GeneSearchServiceImpl
getGoId() - Method in class ubic.gemma.core.genome.gene.GOGroupValueObject
getGoTerms(GeneArg<?>) - Method in class ubic.gemma.rest.util.args.GeneArgService: Returns GO terms for the gene that this GeneArg represents.
getGOTerms(Long, boolean, GeneOntologyServiceImpl.GOAspect) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getGOTerms(Gene) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getGOTerms(Gene) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getGOTerms(Gene, boolean, GeneOntologyServiceImpl.GOAspect) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Get all GO terms for a gene, including parents of terms via is-a relationships; and optionally also parents via part-of relationships.
getGOTerms(Gene, boolean, GeneOntologyServiceImpl.GOAspect) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getGrammarFileName() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getGrammarFileName() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getGroupMembers() - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup
getGroupMembers(String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getGroupMembers(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
getGroupName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
getGroupName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
getGroups() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getGroups() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
getGroupsThatCanRead() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getGroupsThatCanWrite() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getGrowthProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
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
getHasMultiplePreferredQuantitationTypes() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getHasMultipleTechnologyTypes() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getHasSingletonBatches() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
getHasUninformativeBatchInformation() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
getHeight() - Method in class ubic.gemma.core.image.aba.Image
getHgnc_id() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
getHibernateStatus() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
getHighExpressionCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getHistogramArrayList() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis: Read back the histogram as a DoubleArrayList of counts.
getHistogramArrayList() - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
getHistory() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
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(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 interface ubic.gemma.core.apps.Blat
getHost() - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
getHost() - Method in class ubic.gemma.core.util.NetDatasourceUtil
getHostUrl() - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getHumanServerPort() - Method in interface ubic.gemma.core.apps.Blat
getHumanServerPort() - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
getHybProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getId() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
getId() - Method in class ubic.gemma.core.analysis.report.AuditableObject
getId() - Method in enum ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType
getId() - Method in class ubic.gemma.core.image.aba.Image
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.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
getId() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
getId() - Method in class ubic.gemma.model.analysis.AnalysisResultSet
getId() - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution
getId() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
getId() - Method in class ubic.gemma.model.analysis.expression.coexpression.SupportDetails
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.GeneDifferentialExpressionMetaAnalysisResult
getId() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getId() - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
getId() - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
getId() - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
getId() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
getId() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
getId() - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
getId() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getId() - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
getId() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
getId() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
getId() - Method in class ubic.gemma.model.association.Gene2GeneIdAssociation
getId() - Method in class ubic.gemma.model.association.Gene2OntologyEntryAssociation
getId() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication: Deprecated.
getId() - Method in class ubic.gemma.model.common.AbstractDescribable
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.Contact
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
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.GroupAuthority
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getId() - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
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
getId() - Method in class ubic.gemma.model.common.description.DatabaseEntry
getId() - Method in class ubic.gemma.model.common.description.LocalFile
getId() - Method in interface ubic.gemma.model.common.Identifiable
getId() - Method in class ubic.gemma.model.common.measurement.Measurement
getId() - Method in class ubic.gemma.model.common.measurement.Unit
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.bioAssay.BioAssay
getId() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getId() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
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.ExperimentalDesign
getId() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getId() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getId() - Method in class ubic.gemma.model.expression.experiment.FactorValue
getId() - Method in class ubic.gemma.model.expression.experiment.Geeq
getId() - Method in interface ubic.gemma.model.GemmaSessionBackedValueObject
getId() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getId() - Method in class ubic.gemma.model.genome.Chromosome
getId() - Method in class ubic.gemma.model.genome.ChromosomeLocation
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.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.genome.gene.Multifunctionality
getId() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
getId() - Method in class ubic.gemma.model.genome.Taxon
getId() - Method in class ubic.gemma.model.IdentifiableValueObject
getId() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getId() - Method in class ubic.gemma.web.remote.EntityDelegator
getIdColumnName() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getIdentifier(BioSequence) - Static method in class ubic.gemma.core.analysis.sequence.SequenceWriter: Modify the identifier for the purposes of using in temporary Fasta files.
getIdentifierPropertyName() - Method in class ubic.gemma.persistence.service.AbstractDao
getIdentifierPropertyName() - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getIdentifierPropertyName() - Method in interface ubic.gemma.persistence.service.BaseDao: Obtain the identifiable property name for BaseDao.
getIdentifierPropertyName() - Method in interface ubic.gemma.persistence.service.FilteringService
getIdentity() - Method in class ubic.gemma.core.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<T>) - Static method in class ubic.gemma.persistence.util.EntityUtils: Given a set of entities, create a map of their ids to the entities.
getIds() - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
getIds(Collection<T>) - Static method in class ubic.gemma.persistence.util.EntityUtils
getIdsForSearchQuery(QueryArg, Map<Long, Double>) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Obtain a Filter for the result of a ExpressionExperiment search.
getIdsSet() - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
getImages() - Method in class ubic.gemma.core.image.aba.ImageSeries
getImageSeries() - Method in class ubic.gemma.core.image.aba.AbaGene
getImageSeriesId() - Method in class ubic.gemma.core.image.aba.ImageSeries
getImagesFromImageSeries(Collection<ImageSeries>) - Method in interface ubic.gemma.core.image.aba.AllenBrainAtlasService: Returns a collection of images from all the imageSeries given.
getImagesFromImageSeries(Collection<ImageSeries>) - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl
getImmobilizedCharacteristic() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getImplClass(Class<?>) - Static method in class ubic.gemma.persistence.util.EntityUtils
getImplementationForProxy(Object) - Static method in class ubic.gemma.persistence.util.EntityUtils: Expert only.
getImportantFactors(ExpressionExperiment, Collection<ExperimentalFactor>, Double) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper
getImportantFactors(ExpressionExperiment, Collection<ExperimentalFactor>, Double) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl
getIncludedResultSetsInfo() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
getIndex() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
getIndices(GeoPlatform, List<GeoSample>, Integer) - 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
getInferredQuantitationType() - Method in exception ubic.gemma.core.datastructure.matrix.InferredQuantitationMismatchException
getInfo() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getInMemoryConfiguration() - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getInputStream() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.
getInstance() - Static method in class ubic.gemma.persistence.util.DescribableComparator
getInstance() - Static method in class ubic.gemma.persistence.util.FactorValueComparator
getInstanceOf() - Method in class ubic.gemma.core.ontology.OntologyIndividualSimple
getInstitute() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getInt(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getInt(String) - Method in class ubic.gemma.web.util.ConfigurationCookie
getInt(String, int) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getInteger(String, Integer) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getIntensities(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper
getIntensity() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getInteractionsToInclude() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getIsApproximateLength() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getIsBackground() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsBackgroundSubtracted() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsBaseline() - Method in class ubic.gemma.model.expression.experiment.FactorValue
getIsBatchCorrected() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getIsBatchCorrected() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsCircular() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getIsContinuous() - Method in class ubic.gemma.web.controller.visualization.FactorProfile
getIsGenesUsable() - Method in class ubic.gemma.model.genome.Taxon
getIsGenesUsable() - Method in class ubic.gemma.model.genome.TaxonValueObject
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.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getIsMaskedPreferred() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType: Deprecated.
getIsNegativeEvidence() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getIsNegativeEvidence() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getIsNormalized() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsOutlier() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getIsPreferred() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
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 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.ExpressionExperimentValueObject
getIsPublic() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getIsRatio() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getIsRatio() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getIsRecomputedFromRawData() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
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 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.ExpressionExperimentValueObject
getIsShared() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
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
getIssue() - Method in class ubic.gemma.model.common.description.BibliographicReference
getIssue() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getJobs() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getJobs() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getKeep() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getKeepers() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis: Identify the correlations that are above the set thresholds.
getKeepers() - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
getKey(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
getKey(Collection<Reporter>) - 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.persistence.util.Settings: Deprecated.
getKeys() - Method in class ubic.gemma.web.util.ConfigurationCookie
getKeys(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getKeys(Cache) - Static method in class ubic.gemma.persistence.util.CacheUtils: Obtain the keys of all elements of a cache.
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
getKeywords() - Method in class ubic.gemma.model.common.description.BibliographicReference
getKeyWords() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getKindCV() - Method in class ubic.gemma.model.common.measurement.Measurement
getLabel() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getLabel() - Method in class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
getLabel() - Method in class ubic.gemma.web.util.LabelValue
getLabelProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getLaboratory() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getLast() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
getLastArrayDesignUpdate(Collection<ExpressionExperiment>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getLastArrayDesignUpdate(Collection<ExpressionExperiment>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getLastArrayDesignUpdate(Collection<ExpressionExperiment>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getLastArrayDesignUpdate(Collection<ExpressionExperiment>) - 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.ExpressionExperimentService
getLastArrayDesignUpdate(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getLastArrayDesignUpdateDate() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getLastEvent(Auditable, Class<? extends AuditEventType>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao
getLastEvent(Auditable, Class<? extends AuditEventType>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getLastEvent(Auditable, Class<? extends AuditEventType>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getLastEvent(Auditable, Class<? extends AuditEventType>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getLastEvent(Auditable, Class<? extends AuditEventType>, Collection<Class<? extends AuditEventType>>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Obtain the latest AuditEvent of a specified type, excluding a certain number of types.
getLastEvent(Auditable, Class<? extends AuditEventType>, Collection<Class<? extends AuditEventType>>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getLastEvent(Auditable, Class<? extends AuditEventType>, Collection<Class<? extends AuditEventType>>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getLastEvent(Auditable, Class<? extends AuditEventType>, Collection<Class<? extends AuditEventType>>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getLastEvents(Collection<? extends Auditable>, Collection<Class<? extends AuditEventType>>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService: Fast method to retrieve auditEventTypes of multiple classes.
getLastEvents(Collection<? extends Auditable>, Collection<Class<? extends AuditEventType>>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getLastEventsByType(Collection<? extends Auditable>, Collection<Class<? extends AuditEventType>>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao
getLastEventsByType(Collection<? extends Auditable>, Collection<Class<? extends AuditEventType>>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
getLastGeneMapping(Collection<Long>) - 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<Long>) - 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<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getLastLinkAnalysis(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getLastLogMessage() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getLastMissingValueAnalysis(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getLastMissingValueAnalysis(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getLastName() - Method in class ubic.gemma.model.common.auditAndSecurity.Person: Deprecated.
getLastName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getLastNeedsAttentionEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getLastNeedsAttentionEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getLastNoteUpdateEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getLastNoteUpdateEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getLastProcessedDataUpdate(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getLastProcessedDataUpdate(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getLastProgressUpdates() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
getLastProgressUpdates() - Method in interface ubic.gemma.core.job.SubmittedTask
getLastRepeatAnalysis(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getLastRepeatAnalysis(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getLastRepeatMaskEvent(Long) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getLastRepeatMaskEvent(Long) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl
getLastSequenceAnalysis(Collection<Long>) - 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<Long>) - 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(Collection<Long>) - 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<Long>) - 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
getLastSingleNodeValue(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint: basically Delegates to getSingleNodeValue and returns the just the last value.
getLastTroubledEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
getLastTroubledEvent() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
getLastUpdate() - Method in class ubic.gemma.persistence.model.Gene2CsStatus
getLastUpdated() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
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.description.ExternalDatabase
getLastUpdated() - Method in interface ubic.gemma.model.common.description.Versioned: The last updated date, if known.
getLastUpdated() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
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: Returns the date the series was last updated.
getLastUpdateDate() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
getLastUsed() - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
getLatestExperiments(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.rss.RssFeedController: Show all experiments
getLatestNews() - Method in class ubic.gemma.web.feed.FeedReader
getLatestWeeklyReport() - Method in interface ubic.gemma.core.analysis.report.WhatsNewService: Retrieve the latest weekly report if available.
getLatestWeeklyReport() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
getLength() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getLength() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getLibraryStrategy() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
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.Slice
getLimit() - Method in class ubic.gemma.web.remote.ListBatchCommand
getLimitingDate() - Method in class ubic.gemma.core.util.AbstractCLI
getLink() - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
getLinkAnalysisConfig() - Method in class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand
getLinkAnalysisEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getLinkCountsNegative() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
getLinkCountsPositive() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
getLinkId() - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
getLinksFound() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
getLinksWithExactSupport(Integer, boolean) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
getLinksWithMinimumSupport(int) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
getLinksWithMinimumSupport(Integer, boolean) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
getList(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getList(String) - Method in class ubic.gemma.web.util.ConfigurationCookie
getList(String, List<Object>) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getLiteratureSources() - Method in class ubic.gemma.model.genome.gene.GeneSet
getLoadedGeneCount() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
getLoader() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
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 class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
getLocalPath() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
getLocalURL() - Method in class ubic.gemma.model.common.description.LocalFile
getLocusTag() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
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.ContrastVO
getLogMessages() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getLong(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getLong(String) - Method in class ubic.gemma.web.util.ConfigurationCookie
getLong(String, long) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getLong(String, Long) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getLowDistinctValueCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getLowerTailCut() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getLowExpressionCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getLowVarianceCut() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getMageMlFile(Collection<LocalFile>) - Method in class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
getMakeArchiveFile() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getManualQualityScore() - Method in class ubic.gemma.model.expression.experiment.Geeq
getManualSuitabilityScore() - Method in class ubic.gemma.model.expression.experiment.Geeq
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
getMappingType() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getMatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getMatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getMatrix() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
getMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getMatrix(Collection<? extends DesignElementDataVector>) - Static method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder: Create a matrix using all the vectors, which are assumed to all be of the same quantitation type.
getMaxEdges() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
getMaximumRepeatFraction() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getMaxNumProbesPerComponent() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getMaxQueueMinutes() - Method in class ubic.gemma.core.job.TaskCommand
getMaxResults() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getMaxResults() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
getMaxRuntime() - Method in class ubic.gemma.core.job.TaskCommand
getMaxSupportNeg() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
getMaxSupportPos() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
getMeanLogFoldChange() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getMeanLogFoldChange() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getMeans() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
getMeanVarianceRelation() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getMeasurement() - Method in class ubic.gemma.model.expression.experiment.FactorValue
getMedianCorrelation() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
getMemberIds() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getMembers() - Method in class ubic.gemma.model.genome.gene.GeneSet
getMergedInto() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getMergees() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getMergees() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getMerger() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getMeshHeadings() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
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.rest.util.WellComposedErrorBody: Used by JSON Serializer.
getMessage() - Method in class ubic.gemma.web.remote.JsonReaderResponse
getMessages() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getMessageUtil() - Method in class ubic.gemma.web.controller.BaseController
getMessageUtil() - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.
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
getMetadataFile(ExpressionExperiment, ExpressionExperimentMetaFileType) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate a metadata file.
getMetadataFile(ExpressionExperiment, ExpressionExperimentMetaFileType) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getMetadataFiles(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController: Scans the metadata directory for any files associated with the given experiment.
getMetaPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getMetaPvalue() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getMetaPvalue() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getMetaPvalueRank() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getMetaPvalueRank() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getMetaQvalue() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getMetaQvalue() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getMetaQvalue() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getMetric() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getMetric() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getMetricMatrix() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getMetricType() - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
getMetricType() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics
getMetricType() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
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
getMigration() - Method in exception ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException
getMinimumExonOverlapFraction() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getMinNumPresent() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getMinPresentFraction() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getMinPvalue() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getMinutesElapsed(StopWatch) - Static method in class ubic.gemma.core.util.TimeUtil
getMismatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
getMismatches() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getMissingValueAnalysisEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getMissingValueData() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getMissingValueQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getModeNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getModerateStatistics() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getModified() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
getModifiedExperimentSets() - Method in interface ubic.gemma.web.persistence.SessionListManager
getModifiedExperimentSets() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getModifiedExperimentSets(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager
getModifiedExperimentSets(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getModifiedGeneSets() - Method in interface ubic.gemma.web.persistence.SessionListManager
getModifiedGeneSets() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
getModifiedGeneSets(Long) - Method in interface ubic.gemma.web.persistence.SessionListManager
getModifiedGeneSets(Long) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
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.
getMouseServerPort() - Method in interface ubic.gemma.core.apps.Blat
getMouseServerPort() - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
getMultifunctionality() - Method in class ubic.gemma.model.genome.Gene
getMultipartContentType(String) - Method in class ubic.gemma.web.util.upload.FailedMultipartHttpServletRequest
getMultipartHeaders(String) - Method in class ubic.gemma.web.util.upload.FailedMultipartHttpServletRequest
getMyself() - Method in class ubic.gemma.rest.RootWebService: Retrieve user information for the current user.
getName() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getName() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
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.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getName() - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
getName() - Method in class ubic.gemma.model.common.AbstractDescribable
getName() - Method in class ubic.gemma.model.common.auditAndSecurity.Contact
getName() - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
getName() - Method in interface ubic.gemma.model.common.Describable: Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
getName() - Method in class ubic.gemma.model.common.description.BibliographicReference
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.bioAssay.BioAssay
getName() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getName() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
getName() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
getName() - Method in class ubic.gemma.model.expression.biomaterial.Compound
getName() - Method in class ubic.gemma.model.expression.BlacklistedValueObject
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.ExperimentalDesign
getName() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
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
getName() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
getName() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
getName() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getName() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
getName() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.
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.image.aba.AbaGene
getNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
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
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
getNegSupp() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
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
getNewObjects() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getNewPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getNewSinceDate(Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Get auditables that have been Created since the given date
getNewSinceDate(Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl: Note that this only returns selected classes of auditables.
getNewSinceDate(Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getNewSinceDate(Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getNodeDegree(Gene) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
getNodeDegree(Gene) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
getNodeDegrees(Collection<Long>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
getNodeDegrees(Collection<Long>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
getNodeValue(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
getNomenclatureStatus() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getNonBlacklistedExpressionExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDao
getNonBlacklistedExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl
getNonMatchingProbeNameExamples() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getNonRepeatNonSpecificSiteCountThreshold() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getNonSpecificSiteCountThreshold() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
getNoParentsAnnotationLink() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getNormalizationDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getNormalizationMethod() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getNote() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
getNote() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
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
getNumAnnotations() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getNumBatches() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
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
getNumberMatchingProbes() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getNumberOfConfigurations() - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getNumberOfDatasets(QueryArg, FilterArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.DatasetsWebService
getNumberOfDataVectors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getNumberOfDownregulatedProbes() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getNumberOfElementsAnalyzed() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis
getNumberOfExpressionExperiments() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getNumberOfExpressionExperiments() - Method in interface ubic.gemma.rest.DatasetsWebService.UsageStatistics
getNumberOfGenes() - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
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
getNumberOfGenesTested(Collection<DifferentialExpressionAnalysisResult>, Map<CompositeSequence, Collection<Gene>>) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer: Utility method
getNumberOfGenesTested(Collection<DifferentialExpressionAnalysisResult>, Map<CompositeSequence, Collection<Gene>>) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
getNumberOfLinks() - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis
getNumberOfNonMatchingProbes() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getNumberOfPlatforms(FilterArg<ArrayDesign>) - Method in class ubic.gemma.rest.PlatformsWebService
getNumberOfProbes() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getNumberOfProbes() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
getNumberOfProbes() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getNumberOfProbes() - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
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
getNumberOfResultSets(FilterArg<ExpressionAnalysisResultSet>) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService
getNumberOfSamples() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getNumberOfUpregulatedProbes() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
getNumBins() - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution
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
getNumColumns() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getNumComponentsStored() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getNumDatasetsQueried() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
getNumDatasetsSupporting() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
getNumDatasetsSupporting() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
getNumDatasetsTestedIn() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
getNumDatasetsTestedIn() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
getNumEvidence() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
getNumEvidenceFromSameMetaAnalysis() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getNumExperimentsInScope() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getNumFactors() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
getNumGenes() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
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.Multifunctionality
getNumIds() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
getNumIds() - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
getNumMetThreshold() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getNumMissingValues(QuantitationType) - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getNumPhenotypes() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
getNumPopulatedFactors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getNumProbes() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getNumPublications() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
getNumResults() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getNumResultSetsIncluded() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
getNumRows() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
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
getNumTestedIn() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getNumThreads() - Method in class ubic.gemma.core.util.AbstractCLI
getNumUniqueGenes() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
getNumUniqueGenes() - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
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.model.expression.experiment.Statement
getObject() - Method in class ubic.gemma.persistence.util.AbstractAsyncFactoryBean
getObject() - Method in interface ubic.gemma.persistence.util.AsyncFactoryBean: Obtain a bean asynchronously.
getObjectAlias() - Method in interface ubic.gemma.persistence.util.PropertyMapping: Alias in the query/criteria space, if applicable.
getObjectType() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory
getObjectType() - Method in class ubic.gemma.persistence.util.AbstractAsyncFactoryBean
getObjectUri() - Method in class ubic.gemma.model.expression.experiment.Statement
getOfficialName() - Method in class ubic.gemma.model.genome.Gene
getOfficialSymbol() - Method in class ubic.gemma.model.genome.Gene
getOffset() - Method in class ubic.gemma.persistence.util.Slice
getOldPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getOldStyleCharacteristics() - Method in class ubic.gemma.model.expression.experiment.FactorValue: Deprecated.
getOntology() - Method in class ubic.gemma.web.controller.OntologyController
getOntologyEntry() - Method in class ubic.gemma.model.association.Gene2OntologyEntryAssociation
getOntologyName() - Method in class ubic.gemma.core.ontology.providers.GemmaOntologyService
getOntologyName() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getOntologyName() - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService
getOntologyName() - Method in class ubic.gemma.core.ontology.providers.PatoOntologyService
getOntologyServices() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper: Deprecated.

Returns the ontology services this helper is using.
getOntologyServices() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl: Deprecated.
getOntologyTermFormatter - Interface in ubic.gemma.core.search
getOntologyUrl() - Method in class ubic.gemma.core.ontology.providers.GemmaOntologyService
getOntologyUrl() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getOntologyUrl() - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService
getOntologyUrl() - Method in class ubic.gemma.core.ontology.providers.PatoOntologyService
getOpenApi(ServletConfig) - Static method in class ubic.gemma.rest.util.OpenApiUtils: Obtain the OpenAPI definition for this RESTful API.
getOptionalNodeValue(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
getOptions() - Method in class ubic.gemma.core.util.AbstractCLI
getOptions() - Method in interface ubic.gemma.core.util.CLI: Obtain the options for the CLI.
getOrder() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getOrder() - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
getOrder() - Method in class ubic.gemma.core.util.BeanInitializationTimeMonitor
getOrderApplied() - Method in class ubic.gemma.model.expression.biomaterial.Treatment
getOrderedSamples(ExpressionDataDoubleMatrix, List<ExperimentalFactor>) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils: This puts the control samples up front if possible.
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
getOrganisms() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getOrganisms() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getOrientation() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getOriginalFilename() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.
getOriginalFileName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getOriginalParseException() - Method in exception ubic.gemma.core.search.ParseSearchException: The original ParseException if this query was reattempted.
getOriginalPhenotype() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getOriginalPhenotype() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getOriginalPlatform() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getOriginalPlatform() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getOriginalPlatforms() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
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<Long>, 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<Long>, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getOriginalProperty() - Method in interface ubic.gemma.persistence.util.PropertyMapping: Obtain the original property, if available.
getOriginalQuery() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getOriginalValue() - Method in class ubic.gemma.model.common.description.Characteristic
getOtherIssues() - Method in class ubic.gemma.model.expression.experiment.Geeq
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.ExpressionExperimentDetailsValueObject
getOtherRelevantPublications() - Method in class ubic.gemma.model.analysis.Investigation
getOtherRelevantPublications() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getOut() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
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
getOutputFile() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getOutputFile(String) - Method in interface ubic.gemma.core.analysis.report.DatabaseViewGenerator
getOutputFile(String) - Method in class ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl
getOutputFile(String) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
getOutputFile(String) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getOutputFile(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
getOutputFile(String, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
getOutputFile(String, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getOutputFile(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
getOutputFile(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getOutputFile(ExpressionExperiment, boolean, boolean, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
getOutputFile(ExpressionExperiment, boolean, boolean, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
getOutputStream() - Method in class ubic.gemma.web.util.upload.MonitoredDiskFileItem
getOverallDesign() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getOverallDesign() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getOverlap() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getOwner() - Method in class ubic.gemma.model.analysis.Investigation
getOwner() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
getOwner() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getOwnersGroups() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
getOwningDataset() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
getP() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
getP() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getPage() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getPages() - Method in class ubic.gemma.model.common.description.BibliographicReference
getPages() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getParents(Collection<OntologyTerm>, boolean, boolean) - Method in interface ubic.gemma.core.ontology.OntologyService
getParents(Collection<OntologyTerm>, boolean, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain the parents of a collection of terms.
getParents(Collection<OntologyTerm>, boolean, boolean, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getParents(Collection<Characteristic>, Collection<Class<?>>, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Obtain the parents (i.e.
getParents(Collection<Characteristic>, Collection<Class<?>>, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
getParents(Collection<Characteristic>, Collection<Class<?>>, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
getParents(Collection<Characteristic>, Collection<Class<?>>, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl
getPassword() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getPassword() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
getPasswordHint() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getPasswordHint() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getPath() - Method in class ubic.gemma.core.image.aba.Image
getPathToDownloadFile() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
getPcaAnalysisEventType() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
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
getPermissions(AclObjectIdentity) - Static method in class ubic.gemma.persistence.util.EntityUtils: Checks ACL related properties from the AclObjectIdentity.
getPersist() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getPersistJobDetails() - Method in class ubic.gemma.core.job.TaskCommand
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.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.ExpressionExperimentService
getPerTaxonCount() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getPerTaxonCount(Collection<Long>) - 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<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPhases() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getPhenotypeAssociationPublications() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getPhenotypeAssociations() - Method in class ubic.gemma.model.genome.Gene: Deprecated.
getPhenotypeAssPubVO() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getPhenotypeCategory() - Method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
getPhenotypeDumps() - Method in class ubic.gemma.rest.PhenotypeWebService: Deprecated.

Finds all dumps.
getPhenotypeEvidence(String, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PhenotypeWebService: Deprecated.

Finds all evidence with the given external database name.
getPhenotypeMapping() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getPhenotypeName() - Method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
getPhenotypes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getPhenotypes() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getPhenotypesValues() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
getPhenotypesValueUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getPhenotypesValueUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject: Deprecated.
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.core.genome.gene.service.GeneService
getPhysicalLocationsValueObjects(Gene) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
getPlatform() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getPlatform() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getPlatformAnnotations(PlatformArg<?>) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the annotation file for the given platform.
getPlatformConstraint() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getPlatformCountById(Long) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
getPlatformCountById(Long) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
getPlatformData() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getPlatformDatasets(PlatformArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves experiments in the given platform.
getPlatformElement(PlatformArg<?>, CompositeSequenceArrayArg, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves composite sequences (elements) of the given platform.
getPlatformElementGenes(PlatformArg<?>, CompositeSequenceArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the genes on the given platform element.
getPlatformElements(PlatformArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the composite sequences (elements) for the given platform.
getPlatformFilter() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg
getPlatformId() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getPlatformInformation() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getPlatformMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getPlatforms() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getPlatforms() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getPlatforms(DatasetArg<?>) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Retrieves the Platforms of the Dataset that this argument represents.
getPlatforms(FilterArg<ArrayDesign>, OffsetArg, LimitArg, SortArg<ArrayDesign>) - Method in class ubic.gemma.rest.PlatformsWebService
getPlatformSampleMap(GeoSeries) - Static method in class ubic.gemma.core.loader.expression.geo.DatasetCombiner
getPlatformsByIds(PlatformArrayArg, FilterArg<ArrayDesign>, OffsetArg, LimitArg, SortArg<ArrayDesign>) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves all datasets matching the given identifiers.
getPlatformTroubled() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getPlatformType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getPlots() - Method in class ubic.gemma.web.controller.visualization.FactorProfile
getPolymerType() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getPopulatedFactorCounts(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getPopulatedFactorCounts(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPopulatedFactorCounts(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getPopulatedFactorCounts(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getPopulatedFactorCountsExcludeBatch(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getPopulatedFactorCountsExcludeBatch(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getPopulatedFactorCountsExcludeBatch(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getPopulatedFactorCountsExcludeBatch(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getPosSupp() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getPostCode() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
getPredicate() - Method in class ubic.gemma.model.expression.experiment.Statement
getPredicateUri() - Method in class ubic.gemma.model.expression.experiment.Statement
getPredictedOutlier() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getPreferredAndMissingQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getPreferredData() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getPreferredQTypes() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getPreferredQuantitationType(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Obtain the preferred quantitation type, 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.analysis.preprocess.ExpressionDataMatrixBuilder
getPreviousClicks() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
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
getPreviousNcbiId() - Method in class ubic.gemma.model.genome.ChromosomeFeature
getPreviousNcbiId() - Method in class ubic.gemma.model.genome.gene.GeneProduct
getPrimaryArrayTaxon(Collection<Taxon>, Collection<String>) - Method in interface ubic.gemma.core.loader.expression.geo.GeoConverter
getPrimaryArrayTaxon(Collection<Taxon>, Collection<String>) - 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
getPrimaryPublication() - Method in class ubic.gemma.model.analysis.Investigation
getPrimaryPublication() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getPrimaryTaxon() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getPrivateGeneCount() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
getProbe() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getProbe() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getProbe() - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
getProbe() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getProbe(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getProbeDegree(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getProbeDegreeThreshold() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getProbeForRow(ExpressionDataMatrixRowElement) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
getProbeForRow(ExpressionDataMatrixRowElement) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
getProbeId() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getProbeId() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getProbeLoadings() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
getProbeName() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
getProbeNamesInGemma() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getProbeResults() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getProbeToGeneMap() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
getProblematicEvidenceIds() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
getProcessDomainObjectClass() - Method in class ubic.gemma.core.security.authorization.acl.AclAfterCollectionCompSeqByArrayDesignFilter
getProcessDomainObjectClass() - Method in class ubic.gemma.core.security.authorization.acl.AclAfterCollectionDataVectorByExpressionExperimentFilter
getProcessDomainObjectClass() - Method in class ubic.gemma.core.security.authorization.acl.AclAfterCompSeqByArrayDesignFilter
getProcessedData() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getProcessedDataArrays(Collection<? extends BioAssaySet>, Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getProcessedDataArrays(Collection<? extends BioAssaySet>, Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessedDataArrays(Collection<ExpressionExperiment>, Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataArrays(Collection<ExpressionExperiment>, Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataArrays(BioAssaySet) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getProcessedDataArrays(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessedDataArrays(BioAssaySet, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getProcessedDataArrays(BioAssaySet, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessedDataArrays(BioAssaySet, Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getProcessedDataArrays(BioAssaySet, Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessedDataArrays(BioAssaySet, Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataArrays(BioAssaySet, Collection<Long>) - 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
getProcessedDataArrays(ExpressionExperiment, int) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataArrays(ExpressionExperiment, int) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataArraysByProbe(Collection<? extends BioAssaySet>, Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getProcessedDataArraysByProbe(Collection<? extends BioAssaySet>, Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessedDataArraysByProbe(Collection<ExpressionExperiment>, Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Retrieves DEDV's by probes and experiments
getProcessedDataArraysByProbe(Collection<ExpressionExperiment>, Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedDataArraysByProbeIds(BioAssaySet, Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getProcessedDataArraysByProbeIds(BioAssaySet, Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessedDataArraysByProbeIds(BioAssaySet, Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataArraysByProbeIds(BioAssaySet, Collection<Long>) - 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
getProcessedDataVectorsAndThaw(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getProcessedDataVectorsAndThaw(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getProcessedExpressionDataMatrix(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService
getProcessedExpressionDataMatrix(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getProcessedExpressionDataVectors() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getProcessedVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getProcessedVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getProcessingDate() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
getProcessingDate() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getProducts() - Method in class ubic.gemma.model.genome.Gene
getProducts(Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
getProducts(Long) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
getProducts(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
getProfile() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getProfiles() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getProgressStatus(String) - Method in interface ubic.gemma.web.job.progress.ProgressStatusService: Get the latest information about how a job is doing.
getProgressStatus(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl
getProgressUpdateCallback() - Method in class ubic.gemma.core.job.executor.common.ProgressUpdateAppender.ProgressUpdateContext
getProgressUpdates() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
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.
getProperties(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getProperties(String) - Method in class ubic.gemma.web.util.ConfigurationCookie
getProperties(String, Properties) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getProperty(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getProperty(String) - Method in class ubic.gemma.web.util.ConfigurationCookie
getPropertyName() - Method in interface ubic.gemma.persistence.util.PropertyMapping: Property name in the query/criteria space.
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
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
getPublicationDate() - Method in class ubic.gemma.model.common.description.BibliographicReference
getPublicationDate() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getPublicGeneCount() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
getPublicGenesNBCI() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
getPublicQualityScore() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getPublicSuitabilityScore() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
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.ExpressionExperimentDetailsValueObject
getPubMedId() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
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.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
getPValue() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getPvalueDistribution() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getQChtml() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getQChtml() - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
getQCTagHTML(ExpressionExperiment) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Used to include the html for the qc table in an ext panel (without using a tag) (This method should probably be in a service?)
getqScoreBatchConfound() - Method in class ubic.gemma.model.expression.experiment.Geeq
getqScoreBatchEffect() - Method in class ubic.gemma.model.expression.experiment.Geeq
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
getQualityScoreArray() - Method in class ubic.gemma.model.expression.experiment.Geeq
getQualityScoreWeightsArray() - Method in class ubic.gemma.model.expression.experiment.Geeq
getQuantitationType() - Method in exception ubic.gemma.core.datastructure.matrix.QuantitationMismatchException: Quantitation type for the data.
getQuantitationType() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
getQuantitationType() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
getQuantitationType() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
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
getQuantitationTypeDescription() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getQuantitationTypeId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
getQuantitationTypeIndex(GeoPlatform, String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
getQuantitationTypeName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getQuantitationTypeProblemMessage() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
getQuantitationTypes() - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getQuantitationTypes() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Return the quantitation types for this matrix.
getQuantitationTypes() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getQuantitationTypes() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
getQuantitationTypes(GeoPlatform) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
getQuantitationTypes(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getQuantitationTypes(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getQuantitationTypes(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getQuantitationTypes(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getQuantitationTypes(DatasetArg<?>) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Retrieve a dataset with quantitation type initialized.
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
getQuery() - Method in exception ubic.gemma.core.search.ParseSearchException
getQuery() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
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
getQueryGene() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getQueryGeneId() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
getQueryGeneNodeDegree() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getQueryGeneNodeDegreeRank() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getQueryGenes() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
getQueryGenesOnly() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
getQueryGeneSymbol() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
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.core.genome.gene.FreeTextGeneResultsValueObject
getQueryString() - Method in class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
getQueryStringency() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
getQueryStringency() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
getqValues() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
getQvalueThresholdForStorage() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
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.ExperimentalDesignService: Obtain a random experimental design that needs attention.
getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignServiceImpl
getRank() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
getRank() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
getRank() - Method in class ubic.gemma.model.genome.gene.Multifunctionality
getRank() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
getRankAtMinimumSupport(Integer, boolean) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
getRankByMax() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
getRankByMean() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
getRankMatrix(Collection<Gene>, Collection<ExpressionExperiment>, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataMatrixService
getRankMatrix(Collection<Gene>, Collection<ExpressionExperiment>, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl
getRanks() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRanks(Collection<ExpressionExperiment>, Collection<Gene>, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getRanks(Collection<ExpressionExperiment>, Collection<Gene>, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getRanks(Collection<ExpressionExperiment>, Collection<Gene>, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getRanks(Collection<ExpressionExperiment>, Collection<Gene>, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getRanks(ExpressionExperiment, Collection<Gene>, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getRanks(ExpressionExperiment, Collection<Gene>, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getRanks(ExpressionExperiment, Collection<Gene>, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getRanks(ExpressionExperiment, Collection<Gene>, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getRanks(ExpressionExperiment, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
getRanks(ExpressionExperiment, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getRanks(ExpressionExperiment, ProcessedExpressionDataVectorDao.RankMethod) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
getRanks(ExpressionExperiment, ProcessedExpressionDataVectorDao.RankMethod) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getRanksByMean() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getRanksByProbe(Collection<ExpressionExperiment>, Collection<Gene>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao: Retrieve expression level information for genes in experiments.
getRanksByProbe(Collection<ExpressionExperiment>, Collection<Gene>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
getRanksByProbe(Collection<ExpressionExperiment>, Collection<Gene>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Retrieve expression level information for genes in experiments.
getRanksByProbe(Collection<ExpressionExperiment>, Collection<Gene>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
getRatServerPort() - Method in interface ubic.gemma.core.apps.Blat
getRatServerPort() - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
getRawCoexpressionFromDbViaGenes(Collection<Long>, Taxon, int) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
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.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 interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access the entire matrix.
getRawMatrix() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
getRawRow(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRawSummary(Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
getRawSummary(Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
getRawSummary(Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
getRawSummary(Collection<CompositeSequence>) - 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.CompositeSequenceService
getRawSummary(ArrayDesign, int) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
getReason() - Method in class ubic.gemma.model.expression.BlacklistedEntity
getReason() - Method in class ubic.gemma.model.expression.BlacklistedValueObject
getRecentGeoRecords(int, int) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowser: Retrieves and parses tab delimited file from GEO.
getRecentGeoRecords(int, int) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowserService
getRecentGeoRecords(int, int) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
getRecords() - Method in class ubic.gemma.web.remote.JsonReaderResponse
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(Collection<BibliographicReference>) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
getRelatedExperiments(Collection<BibliographicReference>) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
getRelatedExperiments(Collection<BibliographicReference>) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
getRelatedExperiments(Collection<BibliographicReference>) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
getRelatedExperiments(BibliographicReference) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService: Get the ExpressionExperiments, if any, that are linked to the given reference.
getRelatedExperiments(BibliographicReference) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
getRelationship() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getRelationship() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
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
getRelationTerms() - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
getRelativeLinkRanksNegative() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
getRelativeLinkRanksPositive() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
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 interface ubic.gemma.model.common.description.Versioned: External URL to the release, if applicable.
getReleaseVersion() - Method in class ubic.gemma.model.common.description.ExternalDatabase
getReleaseVersion() - Method in interface ubic.gemma.model.common.description.Versioned: The version of the release, if applicable.
getRemoteURL() - Method in class ubic.gemma.model.common.description.LocalFile
getReplicateDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
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
getReportHtml(EntityDelegator<ArrayDesign>) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getReportHtml(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
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
getReprocessedFromRawData() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
getRequest() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getRequestParameters(HttpServletRequest) - Static method in class ubic.gemma.web.util.RequestUtil
getResource(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getResponse() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getResult() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
getResult() - Method in interface ubic.gemma.core.job.SubmittedTask: Get the result of the task.
getResultClass() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getResultId() - Method in class ubic.gemma.core.search.SearchResult: Obtain the result ID.
getResultId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject
getResultId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getResults() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject: A sorted list of the results (sorting must be done elsewhere!)
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.ArrayDesignParser: Deprecated.
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
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
getResultSet(ExpressionAnalysisResultSetArg, Boolean) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService: Retrieve a AnalysisResultSet given its identifier.
getResultSetAsTsv(ExpressionAnalysisResultSetArg) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService: Retrieve an AnalysisResultSet in a tabular format.
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.DifferentialExpressionValueObject
getResultSetId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getResultSetId() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Alias for #getId() kept for backward-compatibility in the Gemma Web frontend.
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 ExpressionAnalysis.
getResultSets(DatasetArrayArg, DatabaseEntryArrayArg, FilterArg<ExpressionAnalysisResultSet>, OffsetArg, LimitArg, SortArg<ExpressionAnalysisResultSet>) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService: Retrieve all AnalysisResultSet matching a set of criteria.
getResultSetsIncluded() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
getResultsForSearchQuery(QueryArg, Highlighter) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Obtain the search results for a given query and highlighter.
getResultsUsed() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getResultTypes() - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap
getResultValueObject() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getRetracted() - Method in class ubic.gemma.model.common.description.BibliographicReference
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.web.controller.common.auditAndSecurity.UserValueObject: Deprecated.
use UserValueObject.getGroups() instead
getRolePrefix() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
getRootOfTree() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
getRow() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getRow(Integer) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
getRow(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
getRow(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRow(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getRow(Integer) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a single row of the matrix, by index.
getRow(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRow(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
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.ExpressionDataStringMatrix
getRowElement(int) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getRowElements() - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getRowElements() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
getRowIndex(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
getRowIndex(CompositeSequence) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
getRowMap() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getRowNames() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRows(List<CompositeSequence>) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
getRows(List<CompositeSequence>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
getRows(List<CompositeSequence>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
getRows(List<CompositeSequence>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
getRows(List<CompositeSequence>) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Access a submatrix
getRows(List<CompositeSequence>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
getRuleNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getRuleNames() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getRunningRemotely() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getRunningStatus() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getS() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getS2n() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
getSagittalImageSeries(Gene) - Method in interface ubic.gemma.core.image.aba.AllenBrainAtlasService: Given a Gene, returns all the image series that contain sagittal images for the given gene.
getSagittalImageSeries(Gene) - Method in class ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl
getSample() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getSample() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getSampleCorrespondence() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSampleDetails() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleGEOAccessions() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSampleMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getSampleNames() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
getSampleRemovalEvents(Collection<ExpressionExperiment>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getSampleRemovalEvents(Collection<ExpressionExperiment>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getSampleRemovalEvents(Collection<ExpressionExperiment>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getSampleRemovalEvents(Collection<ExpressionExperiment>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSampleRemovedFlags() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
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(DatasetArg<?>) - Method in class ubic.gemma.rest.util.args.DatasetArgService
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.SimpleExpressionExperimentMetaData
getScale() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
getScanDateExtractor() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
getScanProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getScientificName() - Method in class ubic.gemma.model.genome.Taxon
getScientificName() - Method in class ubic.gemma.model.genome.TaxonValueObject
getScope() - Method in class ubic.gemma.web.taglib.ConstantsTag
getScope(String) - Method in class ubic.gemma.web.taglib.ConstantsTag: Converts the scope name into its corresponding PageContext constant value.
getScore() - Method in class ubic.gemma.core.analysis.sequence.GeneMappingSummary
getScore() - Method in class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
getScore() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
getScore() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getScore() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getScore() - Method in class ubic.gemma.model.genome.gene.GeneSetMember
getScore() - Method in class ubic.gemma.model.genome.gene.Multifunctionality
getScore() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getScoreInBin(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
getScoreInBin(int) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
getScoreName() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject
getScoreType() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getScoreValue() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject
getScoreValueObject() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getSearchBibrefs() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getSearchBioSequences() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getSearchCriteria() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
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.apps.ShellDelegatingBlat
getSearchExperiments() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getSearchExperimentSets() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getSearchGenes() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getSearchGeneSets() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getSearchOptions() - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand
getSearchPhenotypes() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getSearchPlatforms() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getSearchProbes() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getSearchSettings() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject: The original search settings from the client.
getSearchSettings() - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
getSearchSettings() - Method in class ubic.gemma.rest.SearchWebService.SearchResultsResponseDataObject
getSearchString() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
getSearchTerm() - Method in class ubic.gemma.core.genome.gene.GOGroupValueObject
getSearchTerm() - Method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
getSecondaryAccession() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
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
getSecondFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getSecondFactorValueId() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastVO
getSecondGene() - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
getSecondGene() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
getSecondGene() - Method in class ubic.gemma.model.association.Gene2GeneIdAssociation
getSecondGene() - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
getSecondObject() - Method in class ubic.gemma.model.expression.experiment.Statement
getSecondObjectUri() - Method in class ubic.gemma.model.expression.experiment.Statement
getSecondPredicate() - Method in class ubic.gemma.model.expression.experiment.Statement
getSecondPredicateUri() - Method in class ubic.gemma.model.expression.experiment.Statement
getSectionNumber() - Method in class ubic.gemma.core.image.aba.Image
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
getSecurityInfo(EntityDelegator<? extends Securable>) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
getSecurityInfo(EntityDelegator<? extends Securable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
getSecurityOwner() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
getSecurityOwner() - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis
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
getSelectedFactors() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
getSelectionThreshold() - Method in class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence: Deprecated.
getSelectionThreshold() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getSeqDir() - Method in interface ubic.gemma.core.apps.Blat
getSeqDir() - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
getSeqFiles(ShellDelegatingBlat.BlattableGenome) - Method in interface ubic.gemma.core.apps.Blat
getSeqFiles(ShellDelegatingBlat.BlattableGenome) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
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
getSequenceDatabaseEntry() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getSequenceDatabaseEntry() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
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
getSerializedATN() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getSerializedATN() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getSeries() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getSeriesAppearsIn() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getSeriesId() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSeriesMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getSeriesType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSeriesTypes() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getServerFilePath() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getServletConfig() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getServletContext() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getSession() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
getSessionBoundModifiedGroups() - Method in class ubic.gemma.web.persistence.AbstractSetListContainer
getSessionFactory() - Method in class ubic.gemma.persistence.persister.AbstractPersister
getSessionFactory() - Method in class ubic.gemma.persistence.service.AbstractDao
getShort(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getShort(String) - Method in class ubic.gemma.web.util.ConfigurationCookie
getShort(String, short) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getShort(String, Short) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
getShortDesc() - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
getShortDesc() - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
getShortDesc() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
getShortDesc() - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
getShortDesc() - Method in class ubic.gemma.core.apps.BlacklistCli
getShortDesc() - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
getShortDesc() - Method in class ubic.gemma.core.apps.DeleteDiffExCli
getShortDesc() - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
getShortDesc() - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
getShortDesc() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
getShortDesc() - Method in class ubic.gemma.core.apps.GeeqCli
getShortDesc() - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
getShortDesc() - Method in class ubic.gemma.core.apps.GeoGrabberCli
getShortDesc() - Method in class ubic.gemma.core.apps.IndexGemmaCLI
getShortDesc() - Method in class ubic.gemma.core.apps.LinkAnalysisCli
getShortDesc() - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
getShortDesc() - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
getShortDesc() - Method in class ubic.gemma.core.apps.MakeExperimentPrivateCli
getShortDesc() - Method in class ubic.gemma.core.apps.MakeExperimentsPublicCli
getShortDesc() - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
getShortDesc() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
getShortDesc() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
getShortDesc() - Method in class ubic.gemma.core.apps.OrderVectorsByDesignCli
getShortDesc() - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
getShortDesc() - Method in class ubic.gemma.core.apps.PubMedLoaderCli
getShortDesc() - Method in class ubic.gemma.core.apps.ReplaceDataCli
getShortDesc() - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
getShortDesc() - Method in class ubic.gemma.core.apps.SplitExperimentCli
getShortDesc() - Method in class ubic.gemma.core.apps.SVDCli
getShortDesc() - Method in class ubic.gemma.core.apps.TaxonLoaderCli
getShortDesc() - Method in class ubic.gemma.core.apps.UpdateEE2CCli
getShortDesc() - Method in class ubic.gemma.core.apps.UpdatePubMedCli
getShortDesc() - Method in class ubic.gemma.core.apps.VectorMergingCli
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
getShortDesc() - Method in interface ubic.gemma.core.util.CLI: Obtain a short description for this command explaining what it does.
getShortName() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getShortName() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
getShortName() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getShortName() - Method in class ubic.gemma.model.expression.BlacklistedEntity
getShortName() - Method in class ubic.gemma.model.expression.BlacklistedValueObject
getShortName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getSignalChannelA() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getSignalChannelB() - Method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getSignupToken() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getSignupTokenDatestamp() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getSilently(Future<T>, Class<? extends AsyncFactoryBean<T>>) - Static method in class ubic.gemma.persistence.util.AsyncFactoryBeanUtils: Resolve a future obtained from AsyncFactoryBean.getObject() silently.
getSingleNodeValue(Element, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint: Function that handles the retrieval of xml input.
getSingularThreshold() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getSingularValues() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getSize() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getSize() - Method in class ubic.gemma.model.common.description.LocalFile
getSize() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getSize() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getSize() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.
getSize(Cache) - Static method in class ubic.gemma.persistence.util.CacheUtils
getSize(GeneSetValueObject) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
getSize(GeneSetValueObject) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
getSort() - Method in class ubic.gemma.persistence.util.Slice
getSort() - Method in class ubic.gemma.web.remote.ListBatchCommand
getSort(String, Sort.Direction) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
getSort(String, Sort.Direction) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
getSort(String, Sort.Direction) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao
getSort(String, Sort.Direction) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
getSort(String, Sort.Direction) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
getSort(String, Sort.Direction) - Method in interface ubic.gemma.persistence.service.FilteringDao: Obtain a Sort object for a property of the FilteringDao.
getSort(String, Sort.Direction) - Method in interface ubic.gemma.persistence.service.FilteringService
getSort(SortArg<T>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getSort(SortArg<T>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getSort(SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getSortKey() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getSortKey() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
getSortKey() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
getSource() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
getSource() - Method in class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
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
getSourceExperiment() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
getSourceExperiment() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
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.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getSourceVectorId() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
getSpecificity() - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
getSpecificityScore() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
getsScoreAvgPlatformPopularity() - Method in class ubic.gemma.model.expression.experiment.Geeq
getsScoreAvgPlatformPopularity() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getsScoreAvgPlatformSize() - Method in class ubic.gemma.model.expression.experiment.Geeq
getsScoreAvgPlatformSize() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getsScoreMissingValues() - Method in class ubic.gemma.model.expression.experiment.Geeq
getsScoreMissingValues() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getsScorePlatformAmount() - Method in class ubic.gemma.model.expression.experiment.Geeq
getsScorePlatformAmount() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getsScorePlatformsTechMulti() - Method in class ubic.gemma.model.expression.experiment.Geeq
getsScorePlatformsTechMulti() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getsScorePublication() - Method in class ubic.gemma.model.expression.experiment.Geeq
getsScorePublication() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getsScoreRawData() - Method in class ubic.gemma.model.expression.experiment.Geeq
getsScoreRawData() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getsScoreSampleSize() - Method in class ubic.gemma.model.expression.experiment.Geeq
getsScoreSampleSize() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
getStart() - Method in class ubic.gemma.web.remote.ListBatchCommand
getStartInBioChar() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
getStartingRows() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
getStartPosition() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
getStartTime() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
getStartTime() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
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
getStats() - Method in interface ubic.gemma.web.util.HibernateMonitor
getStats() - Method in class ubic.gemma.web.util.HibernateMonitorImpl
getStats(boolean, boolean, boolean) - Method in interface ubic.gemma.web.util.HibernateMonitor: Log some statistics.
getStats(boolean, boolean, boolean) - Method in class ubic.gemma.web.util.HibernateMonitorImpl
getStats(Locale) - Method in interface ubic.gemma.web.util.CacheMonitor: Obtain the cache statistics in HTML format.
getStats(Locale) - Method in class ubic.gemma.web.util.CacheMonitorImpl
getStatus() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
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.rest.util.WellComposedErrorBody
getStatus() - Method in class ubic.gemma.web.util.upload.UploadInfo
getStatus(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper: Translate the exception to an HTTP Response.Status.
getStatus(Throwable) - Method in class ubic.gemma.rest.providers.UnhandledExceptionMapper
getStatus(NotFoundException) - Method in class ubic.gemma.rest.providers.NotFoundExceptionMapper
getStatus(WebApplicationException) - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapper
getStatus(AccessDeniedException) - Method in class ubic.gemma.rest.providers.AccessDeniedExceptionMapper
getStatus(AuthenticationException) - Method in class ubic.gemma.rest.providers.AuthenticationExceptionMapper
getStatus(EntityNotFoundException) - Method in class ubic.gemma.rest.providers.EntityNotFoundExceptionMapper: Deprecated.
getStatus(MalformedArgException) - Method in class ubic.gemma.rest.providers.MalformedArgExceptionMapper
getStopWatch() - Method in class ubic.gemma.core.util.StopWatchUtils.StopWatchRegion
getStorageDescription() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.

Return a description for the storage location of the multipart content.
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
getStrength() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
getStrength() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject
getString(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getString(String) - Method in class ubic.gemma.web.util.ConfigurationCookie
getString(String, String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getStringArray(String) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.
getStringency() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
getSubDelimiter() - Method in class ubic.gemma.core.analysis.service.AbstractFileService: Get the delimiter used within column.
getSubject() - Method in class ubic.gemma.model.expression.experiment.Statement: Obtain the subject of the statement.
getSubjectUri() - Method in class ubic.gemma.model.expression.experiment.Statement: Obtain the subject URI of the statement.
getSubMatrixForArrayDesign(DoubleMatrix<String, String>, Collection<Object>, ArrayDesign) - Method in interface ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService
getSubMatrixForArrayDesign(DoubleMatrix<String, String>, Collection<Object>, ArrayDesign) - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl
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 class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
getSubmissionTime() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getSubmissionTime() - Method in interface ubic.gemma.core.job.SubmittedTask
getSubmittedTask(String) - Method in interface ubic.gemma.core.job.executor.webapp.TaskRunningService
getSubmittedTask(String) - Method in class ubic.gemma.core.job.executor.webapp.TaskRunningServiceImpl
getSubmittedTask(String) - Method in interface ubic.gemma.web.job.progress.ProgressStatusService
getSubmittedTask(String) - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl
getSubmittedTasks() - Method in interface ubic.gemma.core.job.executor.webapp.TaskRunningService
getSubmittedTasks() - Method in class ubic.gemma.core.job.executor.webapp.TaskRunningServiceImpl
getSubmittedTasks() - Method in interface ubic.gemma.web.job.progress.ProgressStatusService
getSubmittedTasks() - Method in class ubic.gemma.web.job.progress.ProgressStatusServiceImpl
getSubmitter() - Method in class ubic.gemma.core.job.EmailNotificationContext
getSubmitter() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getSubmitter() - Method in class ubic.gemma.core.job.TaskCommand
getSubSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSubSeriesOf() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
getSubsetFactor() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getSubsetFactor() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
getSubsetFactorValue() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getSubsetFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
getSubsetMap() - Method in class ubic.gemma.core.loader.expression.geo.GeoParseResult
getSubsets() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
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) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getSubSets(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getSubsetSize() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getSubsumedArrayDesigns() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getSubsumees() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getSubsumer() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
getSubsumingArrayDesign() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
getSuitabilityScoreArray() - Method in class ubic.gemma.model.expression.experiment.Geeq
getSuitabilityScoreWeightsArray() - Method in class ubic.gemma.model.expression.experiment.Geeq
getSummaries() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
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.core.loader.expression.geo.model.GeoSeries
getSummaryForArrayDesign(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
getSummaryForArrayDesign(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
getSummaryHtml(ArrayDesignValueObject) - Static method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignHtmlUtil: Generate a pretty HTML table with the array design stats summary, used for AJAX version.
getSummaryMapValueObjects(Collection<Object[]>) - 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<Object[]>) - 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<Long>) - Method in interface ubic.gemma.core.analysis.report.ArrayDesignReportService
getSummaryObject(Collection<Long>) - Method in class ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl: Get the cached summary objects
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
getSupplementaryFile() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getSupplementaryFile() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getSupplementaryFile() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getSupport() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getSupport() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getSupportDetails() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
getSupportDetailsId() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
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
getSupportedTaxaWithNCBIGenes() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator: Those taxa that are supported by GEMMA and have genes in NCBI.
getSupportingDatasets() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
getSupportingExperiments() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
getSuspiciousValues() - Method in exception ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException
getSvd(Long) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService
getSvd(Long) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl: Get the SVD information for experiment with id given.
getSvdFactorAnalysis(Long) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService
getSvdFactorAnalysis(Long) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
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(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getSwitchedExpressionExperimentCount(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
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.
getSwitchedExpressionExperimentsCount(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao: Count the number of switched ExpressionExperiment from a given platform.
getSwitchedExpressionExperimentsCount(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getSynonyms() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
getTagCount() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getTagLength() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getTargetAlignedRegion() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
getTargetChromosome() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
getTargetChromosomeName() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
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
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
getTaskClass() - Method in class ubic.gemma.core.job.TaskCommand
getTaskClass() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand
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.PreprocessTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
getTaskClass() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
getTaskClass() - Method in class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
getTaskCommand() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskAbstract
getTaskCommand() - Method in interface ubic.gemma.core.job.SubmittedTask
getTaskCommand() - Method in class ubic.gemma.core.tasks.AbstractTask
getTaskCommand() - Method in interface ubic.gemma.core.tasks.Task
getTaskId() - Method in class ubic.gemma.core.job.EmailNotificationContext
getTaskId() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskAbstract
getTaskId() - Method in class ubic.gemma.core.job.progress.ProgressData
getTaskId() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getTaskId() - Method in interface ubic.gemma.core.job.SubmittedTask
getTaskId() - Method in class ubic.gemma.core.job.TaskCommand
getTaskId() - Method in class ubic.gemma.core.job.TaskResult
getTaskId() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getTaskId() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
getTaskName() - Method in class ubic.gemma.core.job.EmailNotificationContext
getTaskStatus() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getTaskType() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
getTaxa() - Method in class ubic.gemma.rest.TaxaWebService: Lists all available taxa.
getTaxa() - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getTaxa(Collection<T>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getTaxa(Collection<T>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getTaxa(Collection<T>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getTaxa(Collection<T>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getTaxa(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
getTaxa(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
getTaxa(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Return the taxa for the array design.
getTaxa(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getTaxa(GeneSet) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService: Obtain all the taxa for the members of a given gene set.
getTaxa(GeneSet) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
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
getTaxaByIds(TaxonArrayArg) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves single taxon based on the given identifier.
getTaxaUsageFrequency(Filters, Set<Long>) - 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<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getTaxaWithArrays() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
getTaxaWithArrays() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
getTaxaWithArrays() - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getTaxaWithDatasets() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
getTaxaWithDatasets() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
getTaxaWithDatasets() - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getTaxaWithEvidence() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
getTaxaWithEvidence() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
getTaxaWithEvidence() - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
getTaxaWithGenes() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
getTaxaWithGenes() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
getTaxaWithGenes() - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX
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.expression.coexpression.links.LinkAnalysis
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.model.analysis.expression.ExpressionExperimentSet
getTaxon() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getTaxon() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
getTaxon() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment: This is a denormalization to speed up queries.
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
getTaxon() - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
getTaxon() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getTaxon() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
getTaxon() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
getTaxon(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
getTaxon(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
getTaxon(BioAssaySet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
getTaxon(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getTaxon(BioAssaySet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Returns the taxon of the given expressionExperiment.
getTaxon(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getTaxon(GeneSet) - Method in interface ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneSetServiceImpl
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
getTaxonByName(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
getTaxonByName(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
getTaxonCommonName() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getTaxonCommonName() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
getTaxonDatasets(TaxonArg<?>, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<Taxon>) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves datasets for the given taxon.
getTaxonGenes(TaxonArg<?>, GeneArg<?>) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves genes matching the identifier on the given taxon.
getTaxonGenesOverlappingChromosome(TaxonArg<?>, String, String, Long, Integer) - Method in class ubic.gemma.rest.TaxaWebService: Finds genes overlapping a given region.
getTaxonId() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
getTaxonId() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
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 #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.model.genome.gene.phenotype.EvidenceFilter
getTaxonId() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
getTaxonID() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject: Deprecated.
use #getTaxonObject() instead
getTaxonName() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
getTaxonName() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
getTaxonName() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getTaxonName() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
getTaxonPhenotypes(TaxonArg<?>, Boolean, Boolean) - Method in class ubic.gemma.rest.TaxaWebService: Loads all phenotypes for the given taxon.
getTaxonScientificName() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneSetServiceImpl
getTeaser() - Method in class ubic.gemma.web.feed.NewsItem
getTechnology() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
getTechnologyType() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getTechnologyType() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
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<Long>) - 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<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getTechnologyTypeUsageFrequency(Filters, Set<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
getTechnologyTypeUsageFrequency(Filters, Set<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
getTerm() - Method in class ubic.gemma.model.common.description.BibRefAnnotation
getTerm(String) - Method in interface ubic.gemma.core.ontology.OntologyService: Obtain a term for the given URI.
getTerm(String) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getTerm(String) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getTerm(String) - Method in class ubic.gemma.web.controller.OntologyController
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
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
getTermForId(String) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
getTermForId(String) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getTermName(String) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Return human-readable term ("protein kinase") for a GO Id.
getTermName(String) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
getTerms(Collection<String>) - Method in interface ubic.gemma.core.ontology.OntologyService
getTerms(Collection<String>, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService: Return all the terms matching the given URIs.
getTerms(Collection<String>, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl
getTermUri() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getTestedInDatasets() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
getText(String, Object[], Locale) - Method in class ubic.gemma.web.controller.BaseController
getText(String, Object[], Locale) - Method in interface ubic.gemma.web.util.MessageUtil: Convenience method for getting a i18n key's value with arguments.
getText(String, Object[], Locale) - Method in class ubic.gemma.web.util.MessageUtilImpl
getText(String, String, Locale) - Method in interface ubic.gemma.web.util.MessageUtil: Convenient method for getting a i18n key's value with a single string argument.
getText(String, String, Locale) - Method in class ubic.gemma.web.util.MessageUtilImpl
getText(String, Locale) - Method in class ubic.gemma.web.controller.BaseController
getText(String, Locale) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.
getText(String, Locale) - Method in interface ubic.gemma.web.util.MessageUtil: Convenience method for getting a i18n key's value.
getText(String, Locale) - Method in class ubic.gemma.web.util.MessageUtilImpl
getTextValue(Element) - 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.externalDb.GoldenPathSequenceAnalysis: Uses default mapping settings
getThreePrimeDistances(BlatResult, ThreePrimeDistanceMethod) - Method in class ubic.gemma.core.externalDb.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.web.controller.diff.DiffExpressionSearchCommand
getThresholdQvalue() - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
getTimestamp() - Method in class ubic.gemma.core.util.BuildInfo
getTitle() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
getTitle() - Method in class ubic.gemma.model.common.description.BibliographicReference
getTitle() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getTitle() - Method in class ubic.gemma.web.feed.NewsItem
getTitleInDataset() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
getTokenNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer: Deprecated.
getTokenNames() - Method in class ubic.gemma.rest.util.args.FilterArgParser: Deprecated.
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
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.PrincipalComponentAnalysisService
getTopLoadedProbes(ExpressionExperiment, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl
getTopLoadedVectors(Long, int, int) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService
getTopLoadedVectors(Long, int, int) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
getTopLoadedVectors(ExpressionExperiment, int, int) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper
getTopLoadedVectors(ExpressionExperiment, int, int) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl
getToRedo() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
getToRemove() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand
getTotalElements() - Method in class ubic.gemma.persistence.util.Slice
getTotalRecords() - Method in class ubic.gemma.web.remote.JsonReaderResponse
getTotalSize() - Method in class ubic.gemma.web.util.upload.UploadInfo
getTreatmentProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
getTreatments() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
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.
getTstat() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
getTsvFormatBuilder(String...) - Method in class ubic.gemma.core.analysis.service.AbstractFileService: Preconfigure a CSVFormat.Builder with desirable defaults.
getType() - Method in class ubic.gemma.core.analysis.report.AuditableObject
getType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
getType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: Returns 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.SimpleExpressionExperimentMetaData
getType() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication: Deprecated.
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.expression.BlacklistedValueObject
getType() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
getType() - Method in class ubic.gemma.model.genome.biosequence.BioSequence
getType() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
getType() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
getType() - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo
getTypeId() - Method in class ubic.gemma.web.controller.expression.experiment.MetaFile
getTypes() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
getU() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getUnit() - Method in class ubic.gemma.model.common.measurement.Measurement
getUnit() - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
getUnitId() - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
getUnitNameCV() - Method in class ubic.gemma.model.common.measurement.Unit
getUpdatedArrayDesigns() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getUpdateDate() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getUpdatedEEIdsPerTaxon() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getUpdatedExpressionExperiments() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getUpdatedObjects() - Method in class ubic.gemma.core.analysis.report.WhatsNew
getUpdatedSinceDate(Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao: Get auditables that have been Updated since the given date
getUpdatedSinceDate(Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl: Note that this only returns selected classes of auditables.
getUpdatedSinceDate(Date) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
getUpdatedSinceDate(Date) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
getUploadPath() - Static method in class ubic.gemma.web.util.upload.FileUploadUtil
getUploadStatus() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController
getUpperTail() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
getUpperTail() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
getUpperTail() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
getUpperTailCut() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
getUpregulatedCount() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject: Deprecated.
use DiffExResultSetSummaryValueObject.getNumberOfUpregulatedProbes() instead.
getUri() - Method in class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
getUri() - Method in class ubic.gemma.model.common.description.DatabaseEntry: Deprecated.
getUri(Long) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Obtain a suitable ontology ID for a given factor value ID.
getUri(FactorValue) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Obtain a suitable ontology ID for a given factor value.
getUrl() - Method in class ubic.gemma.core.image.aba.Image
getUrl() - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
getUrl() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
getUrlId() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
getUseCharacteristics() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getUseDatabase() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getUsefulQuantitationTypes(Collection<QuantitationType>) - Static method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getUsefulQuantitationTypes(ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
getUseGo() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getUseIndices() - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
getUser() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
getUser() - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
getUser(String) - Method in class ubic.gemma.rest.RootWebService: Retrieve user information.
getUserAndSessionGeneGroups(boolean, Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Returns the current users gene sets as well as their session gene sets
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.ExpressionExperimentValueObject
getUserCanWrite() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getUserFlaggedOutlier() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
getUserGroupGrantedAuthority(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
getUserName() - Method in class ubic.gemma.model.common.auditAndSecurity.User
getUserName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
getUserName() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
getUserName(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
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.ExpressionExperimentValueObject
getUserOwned() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
getUsers() - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.UserListController
getUsers() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserListControllerImpl
getUsersData(String, boolean) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController: AJAX
getUsersData(String, boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
getUserSessionGeneGroups(boolean, Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Returns just the current users gene sets
getUsersGeneGroups(boolean, Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Returns just the current users gene sets
getUsersGeneGroups(boolean, Long, boolean) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
getUsersGeneGroups(boolean, Long, boolean) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
getUsersGeneGroupsValueObjects(boolean, Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService: Returns just the current users gene sets
getUsersGeneGroupsValueObjects(boolean, Long) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
getUseWeights() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
getV() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
getValue() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
getValue() - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
getValue() - Method in class ubic.gemma.model.common.description.Characteristic
getValue() - Method in class ubic.gemma.model.common.measurement.Measurement
getValue() - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
getValue() - Method in class ubic.gemma.model.expression.experiment.FactorValue: Deprecated.
use FactorValue.getMeasurement() or FactorValue.getCharacteristics() to retrieve the value.
getValue() - Method in class ubic.gemma.model.expression.experiment.Statement: Deprecated.
use Statement.getSubject() instead
getValue() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
getValue() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
getValue() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject
getValue() - Method in class ubic.gemma.rest.util.args.AbstractArg: Obtain the value represented by this argument.
getValue() - Method in interface ubic.gemma.rest.util.args.Arg: Obtain the value represented by this argument.
getValue() - Method in class ubic.gemma.rest.util.args.LimitArg: Obtain the value of the limit ensuring that it is smaller than LimitArg.MAXIMUM
getValue() - Method in class ubic.gemma.rest.util.args.QueryArg
getValue() - Method in class ubic.gemma.web.util.LabelValue
getValue(Integer) - Method in class ubic.gemma.rest.util.args.LimitArg: Obtain the value of the limit and ensure it is smaller than a given maximum.
getValueNoMaximum() - Method in class ubic.gemma.rest.util.args.LimitArg: Obtain the value of the limit, explicitly disregarding the maximum defined by LimitArg.MAXIMUM.
getValueObject() - Method in class ubic.gemma.model.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<OntologyTerm>) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService: Converts the given collection of Ontology Terms to Gene Ontology Value Objects.
getValueObjects(Collection<OntologyTerm>) - 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
getValueObjects(GeneArg<?>) - Method in class ubic.gemma.rest.util.args.GeneArgService
getValueObjectTransformer() - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao: Obtain a value object transformer for the results of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
getValueObjectTransformer() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
getValues() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
getValues(Collection<GeoSample>) - 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
getValuesForFactor(ExperimentalFactor) - Method in class ubic.gemma.persistence.util.FactorValueVector
getValueType() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
getValueUri() - Method in class ubic.gemma.model.common.description.Characteristic
getValueUri() - Method in class ubic.gemma.model.expression.experiment.Statement: Deprecated.
use Statement.getSubjectUri() instead
getValueUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
getValueUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
getVar() - Method in class ubic.gemma.web.taglib.ConstantsTag
getVariableInfo(TagData) - Method in class ubic.gemma.web.taglib.ConstantsTei: Return information about the scripting variables to be created.
getVariableResolver() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
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.SVDValueObject
getVariances() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
getVector() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
getVectors() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
getVersion() - Method in class ubic.gemma.core.util.BuildInfo
getVersion() - Method in class ubic.gemma.model.common.description.LocalFile
getView() - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController
getView() - Method in interface ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
getView() - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerImpl
getViewNameForRequest(HttpServletRequest) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SystemStatsController
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.SVDValueObject
getVocabulary() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getVocabulary() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getVolume() - Method in class ubic.gemma.model.common.description.BibliographicReference
getVolume() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
getWarnings() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
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
getWebUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
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
getWellComposedErrorBody(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper: Obtain a WellComposedErrorBody for the exception.
getWellComposedErrorBody(NotFoundException) - Method in class ubic.gemma.rest.providers.NotFoundExceptionMapper
getWellComposedErrorBody(MalformedArgException) - Method in class ubic.gemma.rest.providers.MalformedArgExceptionMapper
getWidth() - Method in class ubic.gemma.core.image.aba.Image
GO - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
GO2Gene_LOCAL_NAME - Static variable in class ubic.gemma.web.services.GoTerm2GeneEndpoint: The local name of the expected request/response.
GOEvidenceCode - Enum 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.
GOEvidenceCodeConverter - Class in ubic.gemma.web.remote
GOEvidenceCodeConverter() - Constructor for class ubic.gemma.web.remote.GOEvidenceCodeConverter
GOGroupValueObject - Class in ubic.gemma.core.genome.gene
GOGroupValueObject() - Constructor for class ubic.gemma.core.genome.gene.GOGroupValueObject
GOGroupValueObject(String, String, Long, String, Collection<Long>, String, String) - Constructor for class ubic.gemma.core.genome.gene.GOGroupValueObject: Method to create a display object from scratch
GoldenPath - Class in ubic.gemma.core.externalDb: Perform useful queries against GoldenPath (UCSC) databases.
GoldenPath(Taxon) - Constructor for class ubic.gemma.core.externalDb.GoldenPath: Create a GoldenPath database for a given taxon.
GoldenPathQuery - Class in ubic.gemma.core.externalDb
GoldenPathQuery(Taxon) - Constructor for class ubic.gemma.core.externalDb.GoldenPathQuery
GoldenPathSequenceAnalysis - Class in ubic.gemma.core.externalDb: Using the Goldenpath databases for comparing sequence alignments to gene locations.
GoldenPathSequenceAnalysis(Taxon) - Constructor for class ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis
GoMetric - Interface in ubic.gemma.core.ontology
GoMetric.Metric - Enum in ubic.gemma.core.ontology
GoMetricImpl - Class in ubic.gemma.core.ontology
GoMetricImpl() - Constructor for class ubic.gemma.core.ontology.GoMetricImpl
GoogleAnalytics4Provider - Class in ubic.gemma.rest.analytics.ga4: Implementation of the AnalyticsProvider interface for Google Analytics 4 collect API.
GoogleAnalytics4Provider(String, String) - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
GoogleAnalytics4Provider(RestTemplate, String, String) - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Create a new Google Analytics 4 provider.
GoTerm2GeneEndpoint - Class in ubic.gemma.web.services: Given a Gene Ontology Term URI and a Taxon ID as input, will return a collection of gene IDs that match the GO Term and Taxon.
GoTerm2GeneEndpoint() - Constructor for class ubic.gemma.web.services.GoTerm2GeneEndpoint
greaterOrEq - ubic.gemma.persistence.util.Filter.Operator
greaterThan - ubic.gemma.persistence.util.Filter.Operator
GroupAuthority - Class in ubic.gemma.model.common.auditAndSecurity: Authority for groups (kind of like a "user role", but for group-based authorization)
GroupAuthority() - Constructor for class ubic.gemma.model.common.auditAndSecurity.GroupAuthority: No-arg constructor added to satisfy javabean contract
GroupAuthority.Factory - Class in ubic.gemma.model.common.auditAndSecurity
GroupAuthorityImpl - Class in ubic.gemma.model.common.auditAndSecurity
GroupAuthorityImpl() - Constructor for class ubic.gemma.model.common.auditAndSecurity.GroupAuthorityImpl
groupByIfNecessary(Sort, String...) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao: Similar logic to AbstractCuratableDao.distinctIfNecessary(), but using a group by since it's more efficient.
groupExists(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
groupExists(String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
growthProtocol - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
guessAliases(String, String) - Static method in class ubic.gemma.persistence.service.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
GwasDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
GwasDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
GZIP - Annotation Type in ubic.gemma.rest.annotations: Used to annotate endpoints that will have their payload compressed with GZIPOutputStream unconditionally.
GzipHeaderDecorator - Class in ubic.gemma.rest.providers: Automagically add the Content-Encoding: gzip header to endpoints annotated with GZIP.
GzipHeaderDecorator() - Constructor for class ubic.gemma.rest.providers.GzipHeaderDecorator

H

H2Dialect - Class in ubic.gemma.persistence.hibernate
H2Dialect() - Constructor for class ubic.gemma.persistence.hibernate.H2Dialect
handlePageException(Exception) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
handlePageException(Throwable) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
handleRequest(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.UserListController
handleRequest(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserListControllerImpl
handleRequestInternal(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.DEDVController: Handle case of text export of the results.
handleRequestInternal(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
handleRequestInternal(HttpServletRequest) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.genome.BlatResultTrackController
HARD_LIMIT_MIN_NUM_USED - Static variable in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis: Absolute lower limit to minNumUsed.
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.
hasBatchInformation() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
hasCoexpCorrelationDistribution(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDao
hasCoexpCorrelationDistribution(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDaoImpl
hasCoexpCorrelationDistribution(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
hasCoexpCorrelationDistribution(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
hasData() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
hasEvent(Auditable, Class<? extends AuditEventType>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao
hasEvent(Auditable, Class<? extends AuditEventType>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
hasEvent(Auditable, Class<? extends AuditEventType>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
hasEvent(Auditable, Class<? extends AuditEventType>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
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.coexpression.CoexpressionValueObjectExt
hashCode() - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
hashCode() - Method in class ubic.gemma.core.analysis.report.AuditableObject
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.genome.gene.GOGroupValueObject
hashCode() - Method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
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.genome.gene.ncbi.model.NcbiGeneHistory
hashCode() - Method in class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
hashCode() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
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.model.analysis.AnalysisResultSet: Returns a hash code based on this entity's identifiers.
hashCode() - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution: Returns a hash code based on this entity's identifiers.
hashCode() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressedGenes
hashCode() - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
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.coexpression.SupportDetails
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
hashCode() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
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.GeneDifferentialExpressionMetaAnalysisResult
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.PvalueDistribution
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.association.coexpression.ExperimentCoexpressionLink
hashCode() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
hashCode() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
hashCode() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
hashCode() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
hashCode() - Method in class ubic.gemma.model.association.Gene2GeneIdAssociation
hashCode() - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
hashCode() - Method in class ubic.gemma.model.common.AbstractDescribable: Returns a hash code based on this entity's identifiers.
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
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.JobInfo
hashCode() - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
hashCode() - Method in class ubic.gemma.model.common.description.BibRefAnnotation
hashCode() - Method in class ubic.gemma.model.common.description.Characteristic
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.ExternalDatabase
hashCode() - Method in class ubic.gemma.model.common.description.LocalFile
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.expression.arrayDesign.AlternateName
hashCode() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
hashCode() - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
hashCode() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.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.DoubleVectorValueObject
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector: Returns a hash code based on this entity's identifiers.
hashCode() - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
hashCode() - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
hashCode() - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
hashCode() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
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.Geeq
hashCode() - Method in class ubic.gemma.model.expression.experiment.Statement
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.ChromosomeLocation: Returns a hash code based on this entity's identifiers.
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.GeneSetMember
hashCode() - Method in class ubic.gemma.model.genome.Gene
hashCode() - Method in class ubic.gemma.model.genome.gene.Multifunctionality
hashCode() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
hashCode() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
hashCode() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
hashCode() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject: Deprecated.
hashCode() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
hashCode() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
hashCode() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
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.BioSequenceValueObject
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.persistence.service.association.coexpression.CoexpressionValueObject
hashCode() - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
hashCode() - Method in class ubic.gemma.persistence.util.FactorValueVector
hashCode() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
hashCode() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
hashCode() - Method in class ubic.gemma.web.util.LabelValue
hashCode(Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
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.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 interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
hasMissingValues() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
hasNodeDegreeDistFile(ExpressionExperiment) - Static method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils
hasPca(Long) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService
hasPca(Long) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
hasPca(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper
hasPca(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl
hasProblematicBatchInformation() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
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
hasPvalueDistFiles(ExpressionExperiment) - Static method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils
hasRepresentation - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Relates a Measurement to its representation.
hasResultType(Class<?>) - Method in class ubic.gemma.model.common.search.SearchSettings: Check if this is configured to search a given result type.
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.
HDA - ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Direct Assay (HDA)
HEADER - Static variable in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
HEADER - Static variable in class ubic.gemma.core.util.AbstractCLI
helpFindAllDumps() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Get information about external data sources from Phenocarta, including URLs and timestamps of the most recent update dates/times.
helpFindAllDumps() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
HEP - ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Expression Pattern (HEP)
HGI - ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Genetic Interaction (HGI)
Hibernate4Metrics - Class in ubic.gemma.core.metrics.binder.jpa: Metrics for Hibernate 4.
Hibernate4Metrics(SessionFactory, String, Iterable<Tag>) - 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<Tag>) - Constructor for class ubic.gemma.core.metrics.binder.jpa.Hibernate4QueryMetrics: Create a HibernateQueryMetrics.
HibernateMonitor - Interface in ubic.gemma.web.util
HibernateMonitorImpl - Class in ubic.gemma.web.util: Monitoring of Hibernate status.
HibernateMonitorImpl() - Constructor for class ubic.gemma.web.util.HibernateMonitorImpl
HibernateSearchException - Exception in ubic.gemma.core.search.source
HibernateSearchException(String, SearchException) - Constructor for exception ubic.gemma.core.search.source.HibernateSearchException
HibernateSearchSource - Class in ubic.gemma.core.search.source: Search source based on Hibernate Search.
HibernateSearchSource() - Constructor for class ubic.gemma.core.search.source.HibernateSearchSource
HibernateUtils - Class in ubic.gemma.persistence.util
HibernateUtils() - Constructor for class ubic.gemma.persistence.util.HibernateUtils
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.
highlight(String, String) - Method in class ubic.gemma.model.common.search.SearchSettings: Highlight a given field.
highlightDocument(Document, Highlighter, Analyzer) - Method in class ubic.gemma.core.search.DefaultHighlighter
highlightDocument(Document, Highlighter, Analyzer) - Method in interface ubic.gemma.core.search.lucene.LuceneHighlighter: Highlight a given Lucene document.
highlightDocument(Document, Highlighter, Analyzer) - Method in class ubic.gemma.model.common.search.SearchSettings
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(String, String, String) - Method in class ubic.gemma.model.common.search.SearchSettings: Highlight a given ontology term.
highlightTerm(String, TokenGroup) - Method in class ubic.gemma.core.search.lucene.SimpleHTMLFormatter
highlightTerm(String, TokenGroup) - Method in class ubic.gemma.core.search.lucene.SimpleMarkdownFormatter
HikariCPMetrics - Class in ubic.gemma.core.metrics.binder.database
HikariCPMetrics(HikariDataSource) - Constructor for class ubic.gemma.core.metrics.binder.database.HikariCPMetrics
hitCount() - Method in class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics
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: No-arg constructor added to satisfy javabean contract
HitListSize.Factory - Class in ubic.gemma.model.analysis.expression.diff
HMP - ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Mutant Phenotype (HMP)
holds(Class<?>) - Method in class ubic.gemma.web.remote.EntityDelegator: Check if the entity delegator holds the given type.
HOME_PAGE - Static variable in class ubic.gemma.web.controller.WebConstants
HomePageController - Class in ubic.gemma.web.controller.common: Responsible for display of the Gemma 2.0 home page.
HomePageController() - Constructor for class ubic.gemma.web.controller.common.HomePageController
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 - Interface in ubic.gemma.core.loader.genome.gene.ncbi.homology
HomologeneServiceFactory - Class in ubic.gemma.core.loader.genome.gene.ncbi.homology: Factory for HomologeneService.
HomologeneServiceFactory() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceFactory
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, TaxonService, Resource) - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl
HOST - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
HTML - ubic.gemma.core.loader.entrez.EutilFetch.Mode
HTP - ubic.gemma.model.association.GOEvidenceCode: Inferred from High Throughput Experiment (HTP)
HttpArchiveFetcherInterface - Interface in ubic.gemma.core.loader.util.fetcher: Interface for downloading via http files and unarchiving them
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 - ubic.gemma.core.apps.ShellDelegatingBlat.BlattableGenome
HumanCoexpressionSupportDetailsImpl - Class in ubic.gemma.model.analysis.expression.coexpression
HumanCoexpressionSupportDetailsImpl() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.HumanCoexpressionSupportDetailsImpl
HumanCoexpressionSupportDetailsImpl(Long, Long, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.HumanCoexpressionSupportDetailsImpl
HumanCoexpressionSupportDetailsImpl(Gene, Gene, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.HumanCoexpressionSupportDetailsImpl
HumanExperimentCoexpressionLinkImpl - Class in ubic.gemma.model.association.coexpression
HumanExperimentCoexpressionLinkImpl() - Constructor for class ubic.gemma.model.association.coexpression.HumanExperimentCoexpressionLinkImpl
HumanExperimentCoexpressionLinkImpl(BioAssaySet, Long, Long, Long) - Constructor for class ubic.gemma.model.association.coexpression.HumanExperimentCoexpressionLinkImpl
HumanGeneCoExpression - Class in ubic.gemma.model.association.coexpression
HumanGeneCoExpression() - Constructor for class ubic.gemma.model.association.coexpression.HumanGeneCoExpression
HumanGeneCoExpression.Factory - Class in ubic.gemma.model.association.coexpression
HumanGeneCoExpressionImpl - Class in ubic.gemma.model.association.coexpression
HumanGeneCoExpressionImpl() - Constructor for class ubic.gemma.model.association.coexpression.HumanGeneCoExpressionImpl

I

IAGP - ubic.gemma.model.association.GOEvidenceCode: Inferred from association of genotype and phenotype (RGD code)
IBA - 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 - 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 - ubic.gemma.model.association.GOEvidenceCode
id - Variable in class ubic.gemma.core.analysis.report.AuditableObject
id - Variable in class ubic.gemma.model.IdentifiableValueObject
IDA - ubic.gemma.model.association.GOEvidenceCode
IdArray - Class in ubic.gemma.model.analysis.expression.coexpression: Represents a set of IDs for entities (e.g., genes or experiments), stored in a bitSet.
IdArray() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.IdArray
IdArrayValueObject - Class in ubic.gemma.model.analysis.expression.coexpression
IdArrayValueObject() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.IdArrayValueObject
IdArrayValueObject(byte[]) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.IdArrayValueObject
Identifiable - Interface in ubic.gemma.model.common: Created by tesarst on 31/05/17.
IdentifiableValueObject<O extends Identifiable> - Class in ubic.gemma.model: Base implementations for value objects representing persistent objects
IdentifiableValueObject() - Constructor for class ubic.gemma.model.IdentifiableValueObject: Default empty constructor for bean-style initialization.
IdentifiableValueObject(Long) - Constructor for class ubic.gemma.model.IdentifiableValueObject: Constructor that sets the common property of all identifiable objects, the ID.
IdentifiableValueObject(O) - Constructor for class ubic.gemma.model.IdentifiableValueObject: Constructor for a given entity.
IdentifiableValueObject(IdentifiableValueObject<O>) - Constructor for class ubic.gemma.model.IdentifiableValueObject: Copy constructor.
identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay, BioAssay>) - 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<BioAssay, BioAssay>) - 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
identifyOutliersRemoved(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
identifyPossibleOutliers(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
identity() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult: Fraction identity computation, as in psl.c.
IEA - ubic.gemma.model.association.GOEvidenceCode
IED - ubic.gemma.model.association.GOEvidenceCode: Inferred from experimental data (RGD code)
IEP - ubic.gemma.model.association.GOEvidenceCode
IGC - 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 - ubic.gemma.model.association.GOEvidenceCode
IgnoreAudit - Annotation Type in ubic.gemma.core.security.audit: Mark a DAO method as ignored for auditing.
IIA - ubic.gemma.model.association.GOEvidenceCode: Added by Gemma: Inferred from Imported Annotation.
IKR - 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
Image - Class in ubic.gemma.core.image.aba: allen brain Atlas Image class.
Image(String, int, int, int, String, String, String, int) - Constructor for class ubic.gemma.core.image.aba.Image
ImageSeries - Class in ubic.gemma.core.image.aba: Represents the ImageSeries information returned from the AIBS brain atlas
ImageSeries(Integer) - Constructor for class ubic.gemma.core.image.aba.ImageSeries
IMP - ubic.gemma.model.association.GOEvidenceCode
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 - ubic.gemma.model.association.GOEvidenceCode: Inferred from Missing Residues.
in - ubic.gemma.persistence.util.Filter.Operator
IN - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
IN - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
IN() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
include(String) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
include(String, boolean) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
IncludedResultSetInfoValueObject - Class in ubic.gemma.model.analysis.expression.diff
IncludedResultSetInfoValueObject() - Constructor for class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
increment(Integer, boolean) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
incrementAndGetLargestExperimentSetSessionId() - Method in interface ubic.gemma.web.persistence.SessionListManager
incrementAndGetLargestExperimentSetSessionId() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
incrementAndGetLargestGeneSetSessionId() - Method in interface ubic.gemma.web.persistence.SessionListManager
incrementAndGetLargestGeneSetSessionId() - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
incrementAndGetLargestSessionId() - Method in class ubic.gemma.web.persistence.AbstractSetListContainer
incrementOccurrenceCount() - Method in class ubic.gemma.model.common.description.CharacteristicValueObject
incrementSessions() - Static method in class ubic.gemma.web.listener.UserTracker
incrementWarnings() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
index(Class<? extends Identifiable>) - Method in interface ubic.gemma.core.search.IndexerService: Index the given class.
index(Class<? extends Identifiable>) - Method in class ubic.gemma.core.search.IndexerServiceImpl
index(IndexerTaskCommand) - Method in class ubic.gemma.web.controller.IndexController
IndexController - Class in ubic.gemma.web.controller
IndexController() - Constructor for class ubic.gemma.web.controller.IndexController
IndexerService - Interface in ubic.gemma.core.search: Indexer service.
IndexerServiceImpl - Class in ubic.gemma.core.search
IndexerServiceImpl() - Constructor for class ubic.gemma.core.search.IndexerServiceImpl
IndexerTask - Interface in ubic.gemma.core.tasks.maintenance: Created with IntelliJ IDEA.
IndexerTaskCommand - Class in ubic.gemma.core.tasks.maintenance
IndexerTaskCommand() - Constructor for class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
IndexerTaskImpl - Class in ubic.gemma.core.tasks.maintenance
IndexerTaskImpl() - Constructor for class ubic.gemma.core.tasks.maintenance.IndexerTaskImpl
IndexGemmaCLI - Class in ubic.gemma.core.apps
IndexGemmaCLI() - Constructor for class ubic.gemma.core.apps.IndexGemmaCLI
indexOfCaseInsensitiveStringElements(List<String>) - 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<T>) - Static method in class ubic.gemma.core.util.ListUtils: Get a mapping of element to their first occurrence in a List.
individual - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
infection - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
inferQuantitationType(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil: Infer a QuantitationType from expression data.
INFERRED_CURATED - Static variable in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
INFERRED_XREF - Static variable in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
InferredQuantitationMismatchException - Exception in ubic.gemma.core.datastructure.matrix: Exception raised when the quantitation of an ExpressionDataMatrix does not agree with the one inferred.
InferredQuantitationMismatchException(QuantitationType, QuantitationType, String) - Constructor for exception ubic.gemma.core.datastructure.matrix.InferredQuantitationMismatchException
INFO_UPDATE_INTERVAL - Static variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
inGemma() - Method in class ubic.gemma.core.util.Pointcuts: Matches stuff within Gemma package.
init() - Method in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.

load all needed services and initialize data structures
init() - Method in class ubic.gemma.core.loader.expression.arrayExpress.util.ArrayExpressUtil
init() - Method in class ubic.gemma.core.loader.expression.geo.util.GeoUtil
init() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIUtil
init() - Method in class ubic.gemma.core.util.NetDatasourceUtil
init() - Method in class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
init() - Method in class ubic.gemma.rest.providers.MetricsApplicationEventListener
initArchiveHandler(String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment>, Taxon) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment>, Taxon) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl: Instantiate non-persistent experiment set with description = "Automatically generated for ## EEs.".
initBinder(WebDataBinder) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.

Set up a custom property editor for converting form inputs to real objects.
initBinder(WebDataBinder) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
initBinder(WebDataBinder) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl
initConfig() - Method in class ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.DatasetFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.PlatformFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
initConfig() - Method in class ubic.gemma.core.loader.expression.geo.fetcher.SeriesFetcher
initConfig() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher
initConfig() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
initConfig() - Method in class ubic.gemma.core.loader.genome.taxon.TaxonFetcher
initConfig() - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
initConfig() - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
initFilterBean() - Method in class ubic.gemma.rest.servlet.CorsFilter
initialize() - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator: Initialize fetchers, clear out any data that was already generated by this Generator.
initialize() - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal
initialize(InputStream, boolean) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
initialize(Servlet, ServletRequest, ServletResponse, String, boolean, int, boolean) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
initializeCachedFilteringResult(O) - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao: Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.
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
initializeFromOldData(Gene, Map<Long, Gene>, Map<NonPersistentNonOrderedCoexpLink, SupportDetails>, Set<Long>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
initializeFromOldData(Gene, Map<Long, Gene>, Map<NonPersistentNonOrderedCoexpLink, SupportDetails>, Set<Long>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
initializeLinksFromOldData(Gene, Map<Long, Gene>, Map<NonPersistentNonOrderedCoexpLink, SupportDetails>, Set<Long>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
initializeLinksFromOldData(Gene, Map<Long, Gene>, Map<NonPersistentNonOrderedCoexpLink, SupportDetails>, Set<Long>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
initializeLinksFromOldData(Taxon) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersister: Temporary method.
initializeLinksFromOldData(Taxon) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersisterImpl
inSituOligonucleotide - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
inSubquery - ubic.gemma.persistence.util.Filter.Operator
InsufficientDataException - Exception in ubic.gemma.core.analysis.preprocess.filter: Used to indicate that analysis was skipped, not necessarily an error.
InsufficientDataException(ExpressionExperiment, String) - Constructor for exception ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException
InsufficientProbesException - Exception in ubic.gemma.core.analysis.preprocess
InsufficientProbesException(ExpressionExperiment, String) - Constructor for exception ubic.gemma.core.analysis.preprocess.InsufficientProbesException
InsufficientSamplesException - Exception in ubic.gemma.core.analysis.preprocess.filter
InsufficientSamplesException(ExpressionExperiment, String) - Constructor for exception ubic.gemma.core.analysis.preprocess.filter.InsufficientSamplesException
INT - ubic.gemma.model.common.quantitationtype.PrimitiveType
INTARRAY - ubic.gemma.model.common.quantitationtype.PrimitiveType
INTERIM - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus
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.web.scheduler.SecureMethodInvokingJobDetailFactoryBean
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ArrayDesignUsedEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.DEDVRankEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentAnnotationEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentDEDVEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint: Reads the given requestElement, and sends the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentIdEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentNameEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExperimentNumSamplesEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.Gene2GOdescriptionEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.Gene2GoTermEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.Gene2ProbeEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneByNCBIIdEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneDetailsByGeneIDEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneIDbyTaxonEndpoint: Reads the given requestElement, and sends the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneIdEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneNameEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GeneOverlapEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.GoTerm2GeneEndpoint: Reads the given requestElement, and sends a the response back.
invokeInternal(Element, Document) - Method in class ubic.gemma.web.services.Probe2GeneEndpoint: Reads the given requestElement, and sends a the response back.
involves(Long) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
involvesAny(Set<Long>) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
IOExceptionWithRetry - Exception in ubic.gemma.core.loader.expression.geo.service: Represents an IOException with a chain of retries.
IOExceptionWithRetry(IOException, IOExceptionWithRetry) - Constructor for exception ubic.gemma.core.loader.expression.geo.service.IOExceptionWithRetry
IPI - ubic.gemma.model.association.GOEvidenceCode
IPM - ubic.gemma.model.association.GOEvidenceCode: Inferred from phenotype manipulation (RGD code)
IRD - ubic.gemma.model.association.GOEvidenceCode: Inferred from Rapid Divergence.
is_is_leaf() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
ISA - ubic.gemma.model.association.GOEvidenceCode
isAbsoluteValue() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isAccessDenied() - Method in class ubic.gemma.model.BaseValueObject
isAccessDenied() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
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
isAggressiveQtRemoval() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isAllMissing() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
isAllowArrayExpressDesign() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isAllowModification() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
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
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.analysis.preprocess.ExpressionDataMatrixBuilder
isArrayDesignMatchesDataFile() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isArrayExpress() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isAutomaticallyGenerated(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
isAutomaticallyGenerated(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl: Determines if set was automatically generated by matching the description to that used in ubic.gemma.core.analysis.expression .coexpression.ExpressionExperimentSetService.AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION
isAutoSeek() - Method in class ubic.gemma.core.util.AbstractCLI
isAvailable() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.

Determine whether the multipart content is still available.
isBackgroundChannelA(String) - Static method in class ubic.gemma.persistence.util.ChannelUtils: For two-color arrays: Given the quantitation type name, determine if it represents the channel A background.
isBackgroundChannelB(String) - Static method in class ubic.gemma.persistence.util.ChannelUtils: For two-color arrays: Given the quantitation type name, determine if it represents the channel B background.
isBackgroundSubtracted(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
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.
isBatch(ExperimentalFactor) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
isBatch(ExperimentalFactorValueObject) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
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.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl
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.expression.experiment.BlacklistedEntityDao
isBlacklisted(String) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl
isBlacklisted(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityService
isBlacklisted(String) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceImpl
isBlacklisted(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDao
isBlacklisted(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl
isBlacklisted(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityService
isBlacklisted(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceImpl
isBlacklisted(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDao
isBlacklisted(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl
isBlacklisted(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityService
isBlacklisted(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceImpl
isBlackListed(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
isBlackListed(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
isBlackListed(String) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
isBlackListed(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
isCanEdit() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
isCanonical(Chromosome) - Static method in class ubic.gemma.persistence.util.ChromosomeUtil: 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.
isCheckCorrelationDistribution() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isCheckForBatchEffect() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isCheckForOutliers() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isCompassOn() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isComplete(ExperimentalFactor, List<BioMaterial>, Map<ExperimentalFactor, FactorValue>) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils: Check if a factor has missing values (samples that lack an assigned value)
isConsumerDone() - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
isContainQueryPhenotype() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
isContinuous(ExperimentalFactor) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
isCurrentGroupCanRead() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
isCurrentGroupCanWrite() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
isCurrentUserHasWritePermission() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
isCurrentUserIsOwner() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
isDataFileIsValidFormat() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isDbPhenotype() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
isDbPhenotype() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
isDescriptionInvalidSymbol() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isDirectory() - Method in enum ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType
isDirty() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
isDirty() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
isDoDownload() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
isDone() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskAbstract
isDone() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
isDone() - Method in class ubic.gemma.core.job.progress.ProgressData
isDone() - Method in interface ubic.gemma.core.job.SubmittedTask
isDummy() - Method in class ubic.gemma.model.genome.gene.GeneProduct
isEditable() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
isEeConstraint() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
isEmailAlert() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
isEmailAlert() - Method in interface ubic.gemma.core.job.SubmittedTask
isEmailAlert() - Method in class ubic.gemma.core.job.TaskCommand
isEmpty() - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap
isEmpty() - Method in class ubic.gemma.persistence.util.Filters: Check if this contains an empty conjunction, or if all its clauses are empty.
isEmpty() - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.
isEnableAuthorities() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
isEnabled() - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
isEnabled() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
isEnabled() - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
isEnabled() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
isEnabled() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
isEnableGroups() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
isError() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
isErrorFound() - Method in class ubic.gemma.model.BaseValueObject
isEvidenceNotFound() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isFailed() - Method in class ubic.gemma.core.job.progress.ProgressData
isFilter() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
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.
isForceRewrite() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
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.
isFromCache() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
isFunctional() - Method in class ubic.gemma.core.ontology.OntologyPropertySimple
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.
isHasBatchInformation() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
isHomologueEvidence() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
isHuman(Taxon) - Static method in class ubic.gemma.persistence.util.TaxonUtility
isIgnoreMinimumRowsThreshold() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
isIgnoreMinimumSampleThreshold() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
isIncluded(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray: Use 'and' instead if possible.
isIncludeInteractions() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
isIndexAD() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexBibRef() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexBioSequence() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexEE() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexExperimentSet() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexGene() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexGeneSet() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexOntologies() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isIndexProbe() - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
isInGroup() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
isInitialized() - Method in class ubic.gemma.persistence.util.AbstractAsyncFactoryBean
isInitialized() - Method in interface ubic.gemma.persistence.util.AsyncFactoryBean: Indicate if this bean has been initialized or if its initialization is pending.
isInProgress() - Method in class ubic.gemma.web.util.upload.UploadInfo
isInterQueryLink() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
isLastUpdateDifferent() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isLoaderDone() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
isLoadPlatformOnly() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isLogTransform() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
isLowDistinctValueIsSet() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
isLowerCdfCutUsed() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isLowExpressionCutIsSet() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
isLowVarianceCutIsSet() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
ISM - ubic.gemma.model.association.GOEvidenceCode
isMakeSampleCorrMatImages() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isManualBatchConfoundActive() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualBatchEffectActive() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualHasBatchConfound() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualHasNoBatchEffect() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualHasStrongBatchEffect() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualQualityOverride() - Method in class ubic.gemma.model.expression.experiment.Geeq
isManualSuitabilityOverride() - Method in class ubic.gemma.model.expression.experiment.Geeq
isMasked() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
isMaskMissing() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
isMeasurement() - Method in class ubic.gemma.model.expression.experiment.FactorValueValueObject: Deprecated.

Indicate if this FactorValue is a measurement.
isMember() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
isMerged(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
isMerged(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
isMerged(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
isMerged(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
isMergee(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
isMergee(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
isMergee(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
isMergee(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
isMightNotHaveDataInFile() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
isMigratedToStatement() - Method in class ubic.gemma.model.common.description.Characteristic: Deprecated.
isMinPresentFractionIsSet() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
isModerateStatistics() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
isModifiable() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
isModified() - Method in class ubic.gemma.core.genome.gene.SessionBoundGeneSetValueObject
isModified() - Method in class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject
isModified() - Method in interface ubic.gemma.model.GemmaSessionBackedValueObject
isMouse(Taxon) - Static method in class ubic.gemma.persistence.util.TaxonUtility
isMultipart(HttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver
isMutable() - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
isNameIsFromAuthority() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
isNormalized() - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
isNormalized(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
isNoVectors() - Method in class ubic.gemma.model.expression.experiment.Geeq
isNoVectors() - Method in class ubic.gemma.model.expression.experiment.GeeqValueObject
ISO - ubic.gemma.model.association.GOEvidenceCode
isObjectAlreadyRemoved() - Method in class ubic.gemma.model.BaseValueObject
isObsolete() - Method in class ubic.gemma.core.ontology.AbstractOntologyResourceSimple
isolate - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
isOmitNegLinks() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isOutlier() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
isOwnedByCurrentUser() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
isPersist() - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
isPositiveCorrelation() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
isPositiveCorrelation() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
isPositiveCorrelation() - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
isPostProcessOnly() - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
isPreferred(QuantitationType) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser: Determine if a quantitation type is 'preferred'.
isPrincipal() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
isPrivate() - Method in annotation type ubic.gemma.rest.annotations.CacheControl
isPrivateKeySet() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
isProbeIdsAreImageClones() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
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
isProxy(Object) - Static method in class ubic.gemma.persistence.util.EntityUtils
isPublic() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
isPubliclyReadable() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
isPublik() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
isPubmedIdInvalid() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isQuantitationTypeIsValid() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isQueryGenesOnly() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
isQuick() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
isRat(Taxon) - Static method in class ubic.gemma.persistence.util.TaxonUtility
isRatio(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
isRemove() - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
isRemovePrimaryPublication() - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
isReordered() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
isReorganized() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
isRequireSequences() - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
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
isRunningRemotely() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
isRunningRemotely() - Method in interface ubic.gemma.core.job.SubmittedTask
ISS - ubic.gemma.model.association.GOEvidenceCode
isSameEvidenceFound() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isSameGeneAndOnePhenotypeAnnotated() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isSameGeneAndPhenotypeChildOrParentAnnotated() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isSameGeneAndPhenotypesAnnotated() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isSameGeneAnnotated() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isShared() - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
isShared() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
isShared() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
isShortNameIsUnique() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isShowOnlyEditable() - Method in class ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
isSignalChannelA(String) - Static method in class ubic.gemma.persistence.util.ChannelUtils: For two-color arrays: Given the quantitation type name, determine if it represents the channel A signal.
isSignalChannelB(String) - Static method in class ubic.gemma.persistence.util.ChannelUtils: For two-color arrays: Given the quantitation type name, determine if it represents the channel B signal.
isSingleBatch() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
isSingleton() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceFactory
isSingleton() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory
isSliced() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
isSplitByPlatform() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isStandardized() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
isSubSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
isSubSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
isSubset() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isSubset() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject
isSubsetUsed() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isSubsumed(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
isSubsumed(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
isSubsumed(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
isSubsumed(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
isSubsumedOrMerged(ArrayDesign) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
isSubsumer(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
isSubsumer(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
isSubsumer(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
isSubsumer(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
isSuccess() - Method in class ubic.gemma.web.remote.JsonReaderResponse
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
isSupportedBy(BioAssaySet) - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
isSuppressMatching() - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
isSymbolIsFromAuthority() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
isTextOut() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isTrimNonCanonicalChromosomehits() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
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
isUncategorized(Characteristic) - Static method in class ubic.gemma.model.common.description.CharacteristicUtils: Check if the given characteristic is uncategorized.
isUpperCdfCutUsed() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isUsable() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
isUseDataFromGEO() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
isUseDb() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
isUseEnsembl() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isUseEsts() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
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
isUseMyDatasets() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
isUsePvalueThreshold() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
isUseRefGene() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
isUserNotLoggedIn() - Method in class ubic.gemma.model.BaseValueObject
isUserNotLoggedIn() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
isUserOwned() - Method in class ubic.gemma.core.search.SearchResultDisplayObject
isUseWeights() - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
isValid() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaResponse
isValid() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
isValidateOnly() - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
isViewSampling() - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
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.
iterator() - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
iterator() - Method in class ubic.gemma.core.search.SearchResultSet
iterator() - Method in class ubic.gemma.persistence.util.Filters: Obtain an iterator over the clauses contained in this conjunction.

J

JacksonConfig - Class in ubic.gemma.rest.util: Configure the various beans injected in Swagger's components relating to Jackson's JSON serialization.
JacksonConfig() - Constructor for class ubic.gemma.rest.util.JacksonConfig
JavascriptLogger - Class in ubic.gemma.web.util: Class to handle saving client-side javascript error messages and warnings to a server-side log.
JavascriptLogger() - Constructor for class ubic.gemma.web.util.JavascriptLogger
jiang - 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
JSON_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
JsonFileService<T> - Interface in ubic.gemma.core.analysis.service: Interface for service that provides JSON serialization.
JsonMappingExceptionMapper - Class in ubic.gemma.rest.providers: Mapper that creates a well composed error body response out of a JsonMappingException.
JsonMappingExceptionMapper() - Constructor for class ubic.gemma.rest.providers.JsonMappingExceptionMapper
JsonReaderResponse<T> - Class in ubic.gemma.web.remote: Creates a response that can be consumed by an Ext.data.JsonReader.
JsonReaderResponse(String) - Constructor for class ubic.gemma.web.remote.JsonReaderResponse: Creates an unJsonReaderResponse.successful JsonReaderResponse with null JsonReaderResponse.records.
JsonReaderResponse(Collection<T>, long) - Constructor for class ubic.gemma.web.remote.JsonReaderResponse: Use for remote paging applications.
JsonReaderResponse(List<T>) - Constructor for class ubic.gemma.web.remote.JsonReaderResponse: Creates a successful JsonReaderResponse with the provided objectsToConvertToRecords.
JSONTableRenderer - Class in ubic.gemma.web.view
JSONTableRenderer() - Constructor for class ubic.gemma.web.view.JSONTableRenderer
JsonUtil - Class in ubic.gemma.web.util: Utilities for writing JSON payloads to HttpServletResponse.
JsonUtil() - Constructor for class ubic.gemma.web.util.JsonUtil
JSONView - Class in ubic.gemma.web.view
JSONView() - Constructor for class ubic.gemma.web.view.JSONView
JSONView(String) - Constructor for class ubic.gemma.web.view.JSONView

K

kappa - ubic.gemma.core.ontology.GoMetric.Metric
Keyword - Class in ubic.gemma.model.common.description
Keyword() - Constructor for class ubic.gemma.model.common.description.Keyword
Keyword.Factory - Class in ubic.gemma.model.common.description
kurtosis() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis

L

LabelValue - Class in ubic.gemma.web.util: A simple JavaBean to represent label-value pairs.
LabelValue() - Constructor for class ubic.gemma.web.util.LabelValue: Default constructor.
LabelValue(String, String) - Constructor for class ubic.gemma.web.util.LabelValue: Construct an instance with the supplied property values.
LATEST_EVIDENCE_EXPORT - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
LE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
LE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
LE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
LEFT - ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod
LEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
LEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
LEQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
lessOrEq - ubic.gemma.persistence.util.Filter.Operator
lessThan - ubic.gemma.persistence.util.Filter.Operator
like - ubic.gemma.persistence.util.Filter.Operator
LIKE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
LIKE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
LIKE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
likelyExternalReference(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
likelyId(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
likelyProbeDescription(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
likelyProbeOrganism(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
likelySequence(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants
limit(List<T>, String, Filters, String[], Sort, Integer) - Static method in class ubic.gemma.rest.util.Responder
LimitArg - Class in ubic.gemma.rest.util.args: Argument used to represent a limit.
LimitedResponseDataObject<T> - Class in ubic.gemma.rest.util: Represents a payload with a limited number of results.
LimitedResponseDataObject(List<T>, String, Filters, String[], Sort, Integer) - Constructor for class ubic.gemma.rest.util.LimitedResponseDataObject
lin - ubic.gemma.core.ontology.GoMetric.Metric
LINEAR - 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
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.
LinkAnalysis - Class in ubic.gemma.core.analysis.expression.coexpression.links: Handles the actual coexpression analysis, once handed data that has been prepared.
LinkAnalysis(LinkAnalysisConfig) - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
LinkAnalysisCli - Class in ubic.gemma.core.apps: Commandline tool to conduct link (coexpression) analysis.
LinkAnalysisCli() - Constructor for class ubic.gemma.core.apps.LinkAnalysisCli
LinkAnalysisConfig - Class in ubic.gemma.core.analysis.expression.coexpression.links: Holds parameters needed for LinkAnalysis.
LinkAnalysisConfig() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
LinkAnalysisConfig.NormalizationMethod - Enum in ubic.gemma.core.analysis.expression.coexpression.links
LinkAnalysisConfig.SingularThreshold - Enum in ubic.gemma.core.analysis.expression.coexpression.links: Configures whether only one of the two thresholds should be used.
LinkAnalysisController - Class in ubic.gemma.web.controller.analysis.expression.coexpression.links: A controller to pre-process expression data vectors.
LinkAnalysisController() - Constructor for class ubic.gemma.web.controller.analysis.expression.coexpression.links.LinkAnalysisController
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: No-arg constructor added to satisfy javabean contract
LinkAnalysisPersister - Interface in ubic.gemma.core.analysis.expression.coexpression.links: Handles the persistence phase of a Link analysis.
LinkAnalysisPersisterImpl - Class in ubic.gemma.core.analysis.expression.coexpression.links: Handles moving gene coexpression links from memory into the database; updates related meta-data.
LinkAnalysisPersisterImpl() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersisterImpl
LinkAnalysisService - Interface in ubic.gemma.core.analysis.expression.coexpression.links
LinkAnalysisServiceImpl - Class in ubic.gemma.core.analysis.expression.coexpression.links: Running link analyses through the spring context; will persist the results if the configuration says so.
LinkAnalysisServiceImpl() - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceImpl
LinkAnalysisTaskCommand - Class in ubic.gemma.core.tasks.analysis.coexp: Command object for Link analysis
LinkAnalysisTaskCommand(ExpressionExperiment, LinkAnalysisConfig, FilterConfig) - Constructor for class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand
LinkAnalysisTaskImpl - Class in ubic.gemma.core.tasks.analysis.coexp
LinkAnalysisTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskImpl
LinkCreator - Class in ubic.gemma.persistence.service.association.coexpression: Helper class to use for generating the link objects for persistence.
LinkCreator(Taxon) - Constructor for class ubic.gemma.persistence.service.association.coexpression.LinkCreator
listAll() - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
listAll() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
listAll() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
listAll() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
listAvailableGroups() - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
ListBatchCommand - Class in ubic.gemma.web.remote: Encapsulates information needed for generic list browsing.
ListBatchCommand() - Constructor for class ubic.gemma.web.remote.ListBatchCommand
listByBatch(Query, String, Collection<S>, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
listByBatch(Query, String, Collection<S>, int, int) - Static method in class ubic.gemma.persistence.util.QueryUtils: List the results of a query by a fixed batch size.
listFiles(String, File, Collection<LocalFile>) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
listFiles(String, String) - Method in class ubic.gemma.core.loader.util.fetcher.HttpFetcher
ListUtils - Class in ubic.gemma.core.util: Utilities and algorithms for List.
ListUtils() - Constructor for class ubic.gemma.core.util.ListUtils
LITERATURE - ubic.gemma.model.common.description.DatabaseType
LiteratureEvidence - Class in ubic.gemma.model.association.phenotype: Deprecated.
LiteratureEvidence() - Constructor for class ubic.gemma.model.association.phenotype.LiteratureEvidence: Deprecated.
LiteratureEvidence.Factory - Class in ubic.gemma.model.association.phenotype: Deprecated.
LiteratureEvidenceDao - Interface in ubic.gemma.persistence.service.association.phenotype
LiteratureEvidenceDaoImpl - Class in ubic.gemma.persistence.service.association.phenotype
LiteratureEvidenceDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.phenotype.LiteratureEvidenceDaoImpl
LiteratureEvidenceValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
LiteratureEvidenceValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.LiteratureEvidenceValueObject
LiteratureEvidenceValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.LiteratureEvidenceValueObject
LiteratureEvidenceValueObject(LiteratureEvidence) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.LiteratureEvidenceValueObject
LN - ubic.gemma.model.common.quantitationtype.ScaleType
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.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.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Load an evidence
load(Long) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
load(Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
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.analysis.AnalysisService
load(Long) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
load(Long) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
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: Loads object with given ID.
load(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
load(Long) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
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.biomaterial.BioMaterialService
load(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
load(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService
load(Long) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
load(Long) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
load(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX
load(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX - load with the IDs filled in
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<Long>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
load(Collection<Long>) - Method in class ubic.gemma.persistence.service.AbstractDao: This implementation is temporary and attempts to best replicate the behaviour of loading entities by multiple IDs introduced in Hibernate 5.
load(Collection<Long>) - Method in class ubic.gemma.persistence.service.AbstractService
load(Collection<Long>) - Method in interface ubic.gemma.persistence.service.BaseDao: Loads entities with given ids form the persistent storage.
load(Collection<Long>) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Loads objects with given ids.
load(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
load(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
load(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
load(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
load(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
load(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
load(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
load(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
load(ExpressionExperimentLoadTaskCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController
load(LocalFile) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
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.expression.arrayDesign.CuratableService
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.expression.arrayDesign.CuratableService
load(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.FilteringDao: Load a slice of entities matching the given filters.
load(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.FilteringService
load(Filters, Sort, int, int) - Method in interface ubic.gemma.rest.util.Responder.FilterMethod
load(SimpleExpressionExperimentLoadTaskCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
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.genome.gene.service.GeneSetService
loadAll() - Method in interface ubic.gemma.core.security.authentication.UserManager
loadAll() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
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 interface ubic.gemma.persistence.service.analysis.AnalysisService
loadAll() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
loadAll() - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
loadAll() - Method in interface ubic.gemma.persistence.service.BaseDao: Loads all instanced of specific class from the persistent storage.
loadAll() - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Loads all the entities of specific type.
loadAll() - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolService
loadAll() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
loadAll() - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
loadAll() - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
loadAll() - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
loadAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
loadAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
loadAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
loadAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
loadAll() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX returns all available sets that have a taxon value (so not really all) sets can have *any* number of experiments
loadAll(Taxon) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
loadAll(Taxon) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
loadAll(Taxon) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
loadAll(Taxon) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
loadAll(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
loadAll(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadAllenBrainImages(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController: AJAX NOTE: this method updates the value object passed in
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
loadAllForExperiments() - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
loadAllForExperiments() - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
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
loadAllMetaAnalyses() - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
loadAllNeurocartaPhenotypes() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

load all the valueUri and value of phenotype present in Neurocarta
loadAllNeurocartaPhenotypes() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
loadAllNeurocartaPhenotypes() - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
loadAllNeurocartaPhenotypes() - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: find all phenotypes in Neurocarta, this was requested by AspireBD
loadAllNeurocartaPhenotypes() - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
loadAllNeurocartaPhenotypes() - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
loadAllPhenotypesAsTree(EvidenceFilter) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Same as loadAllPhenotypesByTree(EvidenceFilter), but does not flatten out the tree.
loadAllPhenotypesAsTree(EvidenceFilter) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
loadAllPhenotypesByTree(Long, boolean, Collection<Long>) - Method in class ubic.gemma.web.controller.PhenotypeController
loadAllPhenotypesByTree(EvidenceFilter) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Loads all phenotypes in the database and counts their occurrence using the database It builds the tree using parents of terms, and will return 3 trees representing Disease, HP and MP
loadAllPhenotypesByTree(EvidenceFilter) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
loadAllPhenotypesUri() - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
loadAllPhenotypesUri() - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl: load all valueURI of Phenotype in the database
loadAllSessionGroups() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX
loadAllTaxaWithGenes() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
loadAllTaxaWithGenes() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
loadAllUsedPhenotypeUris() - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
loadAllUsedPhenotypeUris() - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
loadAllUserAndSessionGroups() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX
loadAllUserOwnedAndSessionGroups() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX
loadAllValueObjects() - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
loadAllValueObjects() - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
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.expression.arrayDesign.CuratableService
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.ExternalDatabaseService
loadAllWithAuditTrail() - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
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
loadAndThawLiteOrFail(Long, Function<String, T>, 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, T>, String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
loadAndThawLiteOrFail(Long, Function<String, T>, 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, T>, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadAndThawOrFail(Long, Function<String, T>, 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.
loadAndThawOrFail(Long, Function<String, T>, String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadArrayDesignsForShowAll(Long[]) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
loadArrayDesignsForShowAll(Long[]) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
loadArrayDesignsSummary() - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
loadArrayDesignsSummary() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
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
loadBioAssaySet(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
loadBioAssaySet(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadBioAssaySet(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load a BioAssaySet by ID which can be either a ExpressionExperiment or a ExpressionExperimentSubSet.
loadBioAssaySet(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
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.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.ExpressionExperimentService
loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadByDescription(String) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
loadByDescription(String) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
loadByDescription(String) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
loadByDescription(String) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
loadByName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
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
loadContrastDetailsForResults(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao
loadContrastDetailsForResults(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl: Key method for getting contrasts associated with results.
loadContrastDetailsForResults(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
loadContrastDetailsForResults(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
loadCountsForDataSummaryTable() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX method to get data for database summary table, returned as a JSON object the slow part here is loading each new or updated object in whatsNewService.retrieveReport() -> fetch()
loadDatabase(Persister, Collection<?>) - Static method in class ubic.gemma.core.loader.util.ParserAndLoaderTools: User the loader to persist the collection.
loadDetailedExpressionExperiments(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX - for display in tables.
loadDetailsValueObjects(Collection<Long>, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Special method for front-end access.
loadDetailsValueObjects(Collection<Long>, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadDetailsValueObjects(Collection<Long>, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadDetailsValueObjects(Collection<Long>, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadDetailsValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Like ExpressionExperimentDao.loadDetailsValueObjects(Collection, Taxon, Sort, int, int), but returning a list.
loadDetailsValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadDetailsValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadDetailsValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadDetailsValueObjectsByIdsWithCache(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
loadDetailsValueObjectsByIdsWithCache(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadDetailsValueObjectsByIdsWithCache(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadDetailsValueObjectsByIdsWithCache(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadDetailsValueObjectsByIdsWithCache(Collection<Long>, 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<Long>, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
loadDetailsValueObjectsWithCache(Collection<Long>, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadDetailsValueObjectsWithCache(Collection<Long>, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loader() - Method in class ubic.gemma.core.util.Pointcuts: Methods that load (read) from the persistent store
LoadEvidenceForClassifier - Class in ubic.gemma.core.loader.association.phenotype: Retrieve information used for classifying Phenocarta evidence quality.
LoadEvidenceForClassifier() - Constructor for class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
loadEvidenceWithExternalDatabaseName(String, int, int) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

use if we want to reimport data from a specific external Database
loadEvidenceWithExternalDatabaseName(String, int, int) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

returns an DifferentialExpressionEvidence for a geneDifferentialExpressionMetaAnalysisId if one exists (used to find the threshold and phenotypes for a GeneDifferentialExpressionMetaAnalysis)
loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long, int) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long, int) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long, int) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long, int) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
loadEvidenceWithoutExternalDatabaseName() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.
loadEvidenceWithoutExternalDatabaseName() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
loadExperimentsForPlatform(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX get experiments that used a given platform.
LoadExpressionDataCli - Class in ubic.gemma.core.apps: Simple command line to load expression experiments, either singly or in batches defined on the command line or in a file.
LoadExpressionDataCli() - Constructor for class ubic.gemma.core.apps.LoadExpressionDataCli
loadExpressionExperimentDetails(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX; Populate all the details.
loadExpressionExperiments(List<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX - for display in tables.
loadExpressionExperimentsWithQcIssues() - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX; get a collection of experiments that have had samples removed due to outliers TODO: and experiment that have possible batch effects detected
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
loadFromPubmedID(String) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
loadFromPubmedID(String) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
loadFromSoftFile(String, String, boolean, boolean, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService: Load from a SOFT file.
loadFromSoftFile(String, String, boolean, boolean, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
loadFullMatrix(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService: Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.
loadFullMatrix(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
loadFullyPopulatedValueObject(Long) - Method in interface ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneServiceImpl
loadGeneDetails(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
loadGeneEvidence(Long, boolean, Collection<Long>, Long, String[]) - Method in class ubic.gemma.web.controller.genome.gene.GeneController: AJAX used to show gene info in the phenotype tab FIXME Why is the taxonId a parameter, since we have the gene ID?
loadGenePhenotypes(Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
loadGenePhenotypes(Long) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
loadGenePhenotypes(Long) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
loadGroupAuthorities(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
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
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.expression.arrayDesign.CuratableService
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.ExpressionExperimentService
loadIdsWithCache(Filters, Sort) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueDao: Deprecated.
loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl: Deprecated.
loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>) - 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<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl: Deprecated.
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.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.ExpressionExperimentService
loadLackingTags() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadMicroRNAs(Taxon) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
loadMicroRNAs(Taxon) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
loadMpsNames() - Method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize
loadMultiple(Collection<Long>) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
loadMultiple(Collection<Long>) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
loadMyGeneSets() - Method in interface ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneSetServiceImpl
loadMyGeneSets(Taxon) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
loadMyGeneSets(Taxon) - Method in class ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneSetService
loadMySharedGeneSets(Taxon) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
loadNeurocartaStatistics() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

find statistics on evidence used in neurocarta
loadNeurocartaStatistics() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
loadOrFail(Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
loadOrFail(Long) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Long) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Convenience for running BaseReadOnlyService.load(Long) and checking if the result is null.
loadOrFail(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
loadOrFail(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
loadOrFail(Long, Function<String, T>) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Long, Function<String, T>) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Load an entity or fail with the supplied exception; the message is generated automatically.
loadOrFail(Long, Function<String, T>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
loadOrFail(Long, Function<String, T>) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
loadOrFail(Long, Function<String, T>, String) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Long, Function<String, T>, String) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Load an entity or fail with the supplied exception and message.
loadOrFail(Long, Function<String, T>, String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
loadOrFail(Long, Function<String, T>, String) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
loadOrFail(Long, Supplier<T>) - Method in class ubic.gemma.persistence.service.AbstractService
loadOrFail(Long, Supplier<T>) - Method in interface ubic.gemma.persistence.service.BaseReadOnlyService: Load an entity or fail with the supplied exception.
loadOrFail(Long, Supplier<T>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
loadOrFail(Long, Supplier<T>) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
loadPvalueDistribution(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao
loadPvalueDistribution(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
loadPvalueDistribution(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
loadPvalueDistribution(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
loadQuantitationTypes(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX - for display in tables
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(Collection<Long>) - Method in class ubic.gemma.persistence.service.AbstractDao
loadReference(Collection<Long>) - Method in interface ubic.gemma.persistence.service.BaseDao: Load references for all the given IDs.
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
loadResult(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
loadResult(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
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) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao: Load a DifferentialExpressionAnalysisResult to Gene multi-map.
loadResultToGenesMap(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
LoadSimpleExpressionDataCli - Class in ubic.gemma.core.apps: Command Line tools for loading the expression experiment in flat files
LoadSimpleExpressionDataCli() - Constructor for class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
loadStatisticsOnAllEvidence(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
loadStatisticsOnAllEvidence(String) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
loadStatisticsOnAllEvidence(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
loadStatisticsOnAllEvidence(String) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
loadStatisticsOnExternalDatabases(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
loadStatisticsOnExternalDatabases(String) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
loadStatisticsOnExternalDatabases(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
loadStatisticsOnExternalDatabases(String) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
loadStatisticsOnManualCuration(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
loadStatisticsOnManualCuration(String) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
loadStatisticsOnManualCuration(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
loadStatisticsOnManualCuration(String) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
loadStatusSummaries(Long, List<Long>, Integer, Integer, Boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX.
loadThawed(Collection<Long>) - Method in interface ubic.gemma.core.genome.gene.service.GeneService: Load with objects already thawed.
loadThawed(Collection<Long>) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
loadThawed(Collection<Long>) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
loadThawed(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
loadThawedLiter(Collection<Long>) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
loadThawedLiter(Collection<Long>) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
loadThawedLiter(Collection<Long>) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
loadThawedLiter(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
loadUser(HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController: AJAX entry point.
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.expression.arrayDesign.CuratableService
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(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(SearchResult<T>) - Method in interface ubic.gemma.core.search.SearchService: Convert a SearchResult to its VO flavour.
loadValueObject(SearchResult<T>) - Method in class ubic.gemma.core.search.SearchServiceImpl
loadValueObject(ExperimentalEvidence) - Method in class ubic.gemma.persistence.service.association.phenotype.ExperimentalEvidenceDaoImpl
loadValueObject(BibliographicReference) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
loadValueObject(GeneSet) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
loadValueObject(GeneSet) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
loadValueObject(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObjectById(Long) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
loadValueObjectById(Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
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.expression.arrayDesign.CuratableService
loadValueObjectById(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
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.core.genome.gene.service.GeneSetService
loadValueObjectByIdLite(Long) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
loadValueObjectByIdLite(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
loadValueObjectByIdLite(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObjects(Collection<C>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
loadValueObjects(Collection<Long>, boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
loadValueObjects(Collection<Long>, boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
loadValueObjects(Collection<O>) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadValueObjects(Collection<O>) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao: The default implementation calls AbstractVoEnabledDao.loadValueObject(Identifiable) for each entity and filters out nulls.
loadValueObjects(Collection<O>) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledService
loadValueObjects(Collection<O>) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledDao: Load value objects corresponding to entities
loadValueObjects(Collection<O>) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledService: Loads value objects for all given entities.
loadValueObjects(Collection<SearchResult<?>>) - Method in interface ubic.gemma.core.search.SearchService: Convert a collection of SearchResult to their VO flavours.
loadValueObjects(Collection<SearchResult<?>>) - Method in class ubic.gemma.core.search.SearchServiceImpl
loadValueObjects(Collection<BioAssay>, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
loadValueObjects(Collection<BioAssay>, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
loadValueObjects(Collection<BioAssay>, Map<Long, ArrayDesignValueObject>, boolean) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
loadValueObjects(Collection<BioAssay>, Map<Long, ArrayDesignValueObject>, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl: Method that allows specification of FactorValueBasicValueObject in the bioMaterialVOs
loadValueObjects(Collection<GeneSet>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
loadValueObjects(Collection<GeneSet>) - 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.expression.arrayDesign.CuratableService
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.expression.arrayDesign.CuratableService
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
loadValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
loadValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService: Ids of member genes will be filled in
loadValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
loadValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
loadValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao
loadValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledService
loadValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.BaseVoEnabledService: Load value objects by a given collection of IDs.
loadValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
loadValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
loadValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
loadValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObjectsByIds(List<Long>, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Variant of CuratableService.loadValueObjectsByIds(Collection) that preserve its input order.
loadValueObjectsByIds(List<Long>, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadValueObjectsByIdsLite(Collection<Long>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
loadValueObjectsByIdsLite(Collection<Long>) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
loadValueObjectsByIdsLite(Collection<Long>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
loadValueObjectsByIdsLite(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
loadValueObjectsByIdsLiter(Collection<Long>) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
loadValueObjectsByIdsLiter(Collection<Long>) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
loadValueObjectsByIdsWithRelationsAndCache(List<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Load VOs for the given dataset IDs and initialize their relations like CuratableService.load(Filters, Sort).
loadValueObjectsByIdsWithRelationsAndCache(List<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadValueObjectsForEE(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
loadValueObjectsForEE(Long) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
loadValueObjectsForEE(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.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) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
loadValueObjectsForGene(Gene, int, int) - 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.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.ExpressionExperimentService
loadValueObjectsWithCache(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadValueObjectsWithExpressionExperiment(Collection<QuantitationType>, ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
loadValueObjectsWithExpressionExperiment(Collection<QuantitationType>, ExpressionExperiment) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl: Load QuantitationTypeValueObject in the context of an associated expression experiment.
loadValueObjectsWithExpressionExperiment(Collection<QuantitationType>, ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
loadValueObjectsWithExpressionExperiment(Collection<QuantitationType>, 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) - 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) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
loadValueObjectWithResults(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
loadValueObjectWithResults(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
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, 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.ExpressionExperimentService
loadWithCharacteristics(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
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) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Load a FactorValue with an initialized experimental factor or fail.
loadWithExperimentalFactorOrFail(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
loadWithExperimentalFactors(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDao
loadWithExperimentalFactors(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl
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.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.ExternalDatabaseService
loadWithExternalDatabases(Long) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl
loadWithMeanVarianceRelation(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadWithMeanVarianceRelation(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
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.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.ExpressionExperimentService
loadWithPrimaryPublication(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
loadWithRelationsAndCache(List<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao: Load datasets by IDs with the same relation as CachedFilteringDao.loadWithCache(Filters, Sort).
loadWithRelationsAndCache(List<Long>) - 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
loadWithResultId(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
loadWithResultId(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl
loadWithResultsAndContrasts(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao
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
LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExperimentAnnotationEndpoint: The local name of the expected request/response.
LOCAL_NAME - Static variable in class ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint: The local name of the expected Request/Response.
LOCAL_NAME - Static variable in class ubic.gemma.web.services.Gene2GOdescriptionEndpoint: The local name of the expected request/response.
LOCAL_NAME - Static variable in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint: The local name of the expected request/response.
LOCAL_NAME - Static variable in class ubic.gemma.web.services.GeneNameEndpoint: The local name of the expected Request/Response.
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
LocalFile - Class in ubic.gemma.model.common.description: Not a persistent entity
LocalFile() - Constructor for class ubic.gemma.model.common.description.LocalFile
LocalFile.Factory - Class in ubic.gemma.model.common.description
LocalSeriesFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher: A fetcher that only looks locally for "family" files (GPLXXX_family, GSEXXX_family).
LocalSeriesFetcher(String) - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.LocalSeriesFetcher
locateArrayDesign(String) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
locateExpressionExperiment(String) - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
locatePrimaryReference(ExpressionExperiment) - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder
log - Static variable in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
log - Static variable in class ubic.gemma.core.externalDb.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.util.biomart.BiomartEnsemblNcbiObjectGenerator
log - Static variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
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.util.AbstractCLI
log - Static variable in class ubic.gemma.persistence.persister.AbstractPersister: Shared logger for all persisters.
log - Static variable in class ubic.gemma.persistence.service.AbstractDao
log - Static variable in class ubic.gemma.persistence.service.AbstractService
log - Static variable in class ubic.gemma.rest.TaxaWebService
log - Variable in class ubic.gemma.web.controller.BaseController
log - Static variable in class ubic.gemma.web.controller.BaseFormController: Deprecated.
log - Static variable in class ubic.gemma.web.controller.ControllerUtils
log - Static variable in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController
log - Static variable in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
LOG10 - ubic.gemma.model.common.quantitationtype.ScaleType
log10ratio - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
LOG1P - ubic.gemma.model.common.quantitationtype.ScaleType: Data is log-transformed as per ln X + 1
LOG2 - ubic.gemma.model.common.quantitationtype.ScaleType
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.
log2Ratio - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
Log4jConfigurer - Class in ubic.gemma.core.logging.log4j: Implementation of LoggingConfigurer for Log4j.
Log4jConfigurer() - Constructor for class ubic.gemma.core.logging.log4j.Log4jConfigurer
LOGBASEUNKNOWN - ubic.gemma.model.common.quantitationtype.ScaleType
logERatio - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
logException(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper: Indicate if the given exception should be logged.
logException(Throwable) - Method in class ubic.gemma.rest.providers.UnhandledExceptionMapper
logException(WebApplicationException) - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapper
logException(AuthenticationException) - Method in class ubic.gemma.rest.providers.AuthenticationExceptionMapper
loggedIn() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
logger - Static variable in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.
LoggingConfigurer - Interface in ubic.gemma.core.logging: Simple interface for configuring logging levels.
logIds(String, Collection<OntologyTerm>) - Method in class ubic.gemma.core.ontology.GoMetricImpl
loginCheck() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController: AJAX DWR
logRatio - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
logTransformMatrix(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil: Log-transform the values in the matrix (base 2).
LONG - ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType
LONG - ubic.gemma.model.common.quantitationtype.PrimitiveType
lowVarianceFilter(ExpressionDataDoubleMatrix, int) - Static method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter: Remove rows that have a low variance, below the stated quantile
LuceneHighlighter - Interface in ubic.gemma.core.search.lucene: Highlighter with additional capabilities for Lucene.
LuceneParseSearchException - Exception in ubic.gemma.core.search.lucene
LuceneParseSearchException(String, String, ParseException) - Constructor for exception ubic.gemma.core.search.lucene.LuceneParseSearchException
LuceneParseSearchException(String, String, ParseException, LuceneParseSearchException) - Constructor for exception ubic.gemma.core.search.lucene.LuceneParseSearchException
LuceneParseSearchException(String, ParseException) - Constructor for exception 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

M

MailEngine - Interface in ubic.gemma.persistence.util
MailEngineImpl - Class in ubic.gemma.persistence.util
MailEngineImpl() - Constructor for class ubic.gemma.persistence.util.MailEngineImpl
MailUtils - Interface in ubic.gemma.core.util
MailUtilsImpl - Class in ubic.gemma.core.util
MailUtilsImpl() - Constructor for class ubic.gemma.core.util.MailUtilsImpl
main(String[]) - Static method in class ubic.gemma.core.apps.GemmaCLI
main(String[]) - Static method in class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser: Deprecated.
MaintenanceModeController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Performs actions required when we wish to indicate that the system is undergoing maintenance and many not behave normally.
MaintenanceModeController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
makeDataMatrix(ObjectMatrix<String, String, Object>, DoubleMatrix<CompositeSequence, BioMaterial>) - Static method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer: Convert the data into a string-keyed matrix.
makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long, SortedSet<CharacteristicValueObject>, Double) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

creates the DifferentialExpressionEvidences using an DiffExpressionMetaAnalysis
makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long, SortedSet<CharacteristicValueObject>, Double) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long, SortedSet<CharacteristicValueObject>, Double) - Method in class ubic.gemma.web.controller.PhenotypeController
makeEvidence(EvidenceValueObject<? extends PhenotypeAssociation>) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Links an Evidence to a Gene
makeEvidence(EvidenceValueObject<? extends PhenotypeAssociation>) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
MakeExperimentPrivateCli - Class in ubic.gemma.core.apps
MakeExperimentPrivateCli() - Constructor for class ubic.gemma.core.apps.MakeExperimentPrivateCli
MakeExperimentsPublicCli - Class in ubic.gemma.core.apps: Make data sets public.
MakeExperimentsPublicCli() - Constructor for class ubic.gemma.core.apps.MakeExperimentsPublicCli
makeGroupReadable(EntityDelegator<? extends Securable>, String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
makeGroupReadable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
makeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
makeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
makePrivate(EntityDelegator<? extends Securable>) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
makePrivate(EntityDelegator<? extends Securable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
MakePrivateEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
MakePrivateEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.MakePrivateEvent
makePublic(EntityDelegator<? extends Securable>) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
makePublic(EntityDelegator<? extends Securable>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
MakePublicEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
MakePublicEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.MakePublicEvent
makeTitle(String, String) - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl: Form title (will be experiment name) and ensure is valid length
MalformedArgException - Exception in ubic.gemma.rest.util: Specialized error for malformed Arg The recommended HTTP status for this exception is 400 Bad Request.
MalformedArgException(String) - Constructor for exception ubic.gemma.rest.util.MalformedArgException
MalformedArgException(String, Throwable) - Constructor for exception ubic.gemma.rest.util.MalformedArgException
MalformedArgException(Throwable) - Constructor for exception ubic.gemma.rest.util.MalformedArgException
MalformedArgExceptionMapper - Class in ubic.gemma.rest.providers
MalformedArgExceptionMapper() - Constructor for class ubic.gemma.rest.providers.MalformedArgExceptionMapper
MANUAL_CURATION - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
MANUAL_CURATION_FILE_LOCATION - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
ManualAnnotationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
ManualAnnotationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ManualAnnotationEvent
manualAuthenticationService - Variable in class ubic.gemma.web.services.AbstractGemmaEndpoint
map(Function<? super O, ? extends S>) - Method in class ubic.gemma.persistence.util.Slice
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.
markAsMissing(Collection<BioAssay>) - 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<BioAssay>) - Method in class ubic.gemma.core.analysis.service.OutlierFlaggingServiceImpl
markAsNeedsAttention(FactorValue, String) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService: Mark a given factor value as needs attention.
markAsNeedsAttention(FactorValue, String) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
markFactorValuesAsNeedsAttention(Long[], String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
markOutlier(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
maskMatrix(ExpressionDataDoubleMatrix, ExpressionDataBooleanMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil: Use the mask matrix to turn some values in a matrix to NaN.
MASS - ubic.gemma.model.common.measurement.MeasurementKind
match(TaskCommand) - Method in interface ubic.gemma.core.job.executor.common.TaskCommandToTaskMatcher
match(TaskCommand) - Method in class ubic.gemma.core.job.executor.common.TaskCommandToTaskMatcherImpl
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_SHORT_NAME_SCORE - Static variable in class ubic.gemma.core.search.source.DatabaseSearchSource
matchBioAssayToCelFileName(Map<String, BioAssay>, String) - Static method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize
matches(TypeDescriptor, TypeDescriptor) - Method in class ubic.gemma.persistence.util.ServiceBasedEntityConverter
matches(TypeDescriptor, TypeDescriptor) - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverter
MatrixRowPairAnalysis - Interface in ubic.gemma.core.analysis.expression.coexpression.links
MatrixWriter - Class in ubic.gemma.core.datastructure.matrix
MatrixWriter() - Constructor for class ubic.gemma.core.datastructure.matrix.MatrixWriter
max - ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod
MAX - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
MAX_CLAUSES - Static variable in class ubic.gemma.rest.util.args.FilterArg: Maximum number of clauses that can appear in a filter expression.
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_MINUTES - 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_RESULTS - Static variable in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint: The maximum number of coexpression results to return per input gene; a value of zero will return all possible results (ie.
MAX_RUNTIME_MINUTES - Static variable in class ubic.gemma.core.job.TaskCommand
MAX_SEARCH_RESULTS - Static variable in class ubic.gemma.rest.SearchWebService: Maximum number of search results.
MAX_WARNINGS - Static variable in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
maxAge() - Method in annotation type ubic.gemma.rest.annotations.CacheControl
MAXIMUM - Static variable in class ubic.gemma.rest.util.args.LimitArg: This is the default maximum used for LimitArg.getValue().
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
mean - ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod
MEAN - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
MeanVarianceRelation - Class in ubic.gemma.model.expression.bioAssayData
MeanVarianceRelation() - Constructor for class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation: No-arg constructor added to satisfy javabean contract
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
measuredRegion(StopWatch) - Static method in class ubic.gemma.core.util.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
MeasurementKind - Enum in ubic.gemma.model.common.measurement
measurementOf - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Inverse of TGFVO.hasMeasurement.
MeasurementType - Enum in ubic.gemma.model.common.measurement
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 - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
MedianComparator - 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
MediaTypeUtils - Class in ubic.gemma.rest.util: Utilities for MediaType.
MediaTypeUtils() - Constructor for class ubic.gemma.rest.util.MediaTypeUtils
MedicalSubjectHeading - Class in ubic.gemma.model.common.description
MedicalSubjectHeading() - Constructor for class ubic.gemma.model.common.description.MedicalSubjectHeading
MedicalSubjectHeading.Factory - Class in ubic.gemma.model.common.description
merge(ArrayDesign, Collection<ArrayDesign>, String, String, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeService: Merge array designs based on their sequence content.
merge(ArrayDesign, Collection<ArrayDesign>, String, String, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceImpl
mergeVectors(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.VectorMergingService
mergeVectors(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.VectorMergingServiceImpl
MeshTermFetcherCli - Class in ubic.gemma.core.apps: Deprecated.
should not be part of Gemma main code
MeshTermFetcherCli() - Constructor for class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
message - Variable in class ubic.gemma.web.remote.JsonReaderResponse
MessageUtil - Interface in ubic.gemma.web.util: Provides methods for putting messages to the user in the session.
MessageUtilImpl - Class in ubic.gemma.web.util
MessageUtilImpl() - Constructor for class ubic.gemma.web.util.MessageUtilImpl
metabolism - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
METADATA - ubic.gemma.core.apps.GemmaCLI.CommandGroup
MetaFile - Class in ubic.gemma.web.controller.expression.experiment: Wrapper for metadata file information for the frontend
MeterRegistryCliConfigurer - Class in ubic.gemma.core.metrics: This configurer adds two tags: environment='cli' and user to the given meter registry.
MeterRegistryCliConfigurer(MeterRegistry) - Constructor for class ubic.gemma.core.metrics.MeterRegistryCliConfigurer
MeterRegistryEhcacheConfigurer - Class in ubic.gemma.core.metrics: Add metrics from each available Ehcache in the given CacheManager to the supplied meter registry.
MeterRegistryEhcacheConfigurer(MeterRegistry, CacheManager) - Constructor for class ubic.gemma.core.metrics.MeterRegistryEhcacheConfigurer
MeterRegistryWebConfigurer - Class in ubic.gemma.web.metrics: Configured the environment='web' tag to the provided registry.
MeterRegistryWebConfigurer(MeterRegistry) - Constructor for class ubic.gemma.web.metrics.MeterRegistryWebConfigurer
methylationArraybased - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
methylationByGenomeTiling - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
MetricsApplicationEventListener - Class in ubic.gemma.rest.providers
MetricsApplicationEventListener() - Constructor for class ubic.gemma.rest.providers.MetricsApplicationEventListener
MICROARRAY - Static variable in enum ubic.gemma.model.expression.arrayDesign.TechnologyType: Enumeration of microarray platforms.
MIDDLE - ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod
Migration() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.Migration
MigrationFailedException(FactorValueMigratorService.Migration, Throwable) - Constructor for exception ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException
MigrationResult() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationResult
MIN - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
MIN_PARSED_LINES_FOR_UPDATE - Static variable in interface ubic.gemma.core.loader.util.parser.LineParser
MIN_PASSWORD_LENGTH - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController
MinifierPostProcessor - Class in ubic.gemma.web.util: JAWR postprocessor to remove console.log and debugger breakpoint statements.
MinifierPostProcessor() - Constructor for class ubic.gemma.web.util.MinifierPostProcessor
MINIMUM_ROWS_TO_BOTHER - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig: Fewer rows than this, and we bail.
MINIMUM_SAMPLE - Static variable in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig: How many samples a dataset has to have before we consider analyzing it.
MISC - ubic.gemma.core.apps.GemmaCLI.CommandGroup
MISCRNA - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
missCount() - Method in class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics
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 - ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
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.
modeNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
modifier() - Method in class ubic.gemma.core.util.Pointcuts: CRUD-like method that modifies the database (i.e.
MOLECULAR_FUNCTION - ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect
MondoOntologyService - Class in ubic.gemma.core.ontology.providers: MONDO ontology.
MondoOntologyService() - Constructor for class ubic.gemma.core.ontology.providers.MondoOntologyService
monitor(MeterRegistry, Ehcache, Iterable<Tag>) - Static method in class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics: Record metrics on an EhCache cache.
monitor(MeterRegistry, Ehcache, String...) - Static method in class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics: Record metrics on an EhCache cache.
MonitoredDiskFileItem - Class in ubic.gemma.web.util.upload: Commons FileItem that uses a MonitoredOutputStream
MonitoredDiskFileItem(String, String, boolean, String, int, File, OutputStreamListener) - Constructor for class ubic.gemma.web.util.upload.MonitoredDiskFileItem
MonitoredDiskFileItemFactory - Class in ubic.gemma.web.util.upload
MonitoredDiskFileItemFactory(int, File, OutputStreamListener) - Constructor for class ubic.gemma.web.util.upload.MonitoredDiskFileItemFactory
MonitoredDiskFileItemFactory(OutputStreamListener) - Constructor for class ubic.gemma.web.util.upload.MonitoredDiskFileItemFactory
MonitoredOutputStream - Class in ubic.gemma.web.util.upload: OutputStream that puts information on how many bytes have been read into a OutputStreamListener.
MonitoredOutputStream(OutputStream, OutputStreamListener) - Constructor for class ubic.gemma.web.util.upload.MonitoredOutputStream
MOUSE - ubic.gemma.core.apps.ShellDelegatingBlat.BlattableGenome
MouseCoexpressionSupportDetailsImpl - Class in ubic.gemma.model.analysis.expression.coexpression
MouseCoexpressionSupportDetailsImpl() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.MouseCoexpressionSupportDetailsImpl
MouseCoexpressionSupportDetailsImpl(Long, Long, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.MouseCoexpressionSupportDetailsImpl
MouseCoexpressionSupportDetailsImpl(Gene, Gene, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.MouseCoexpressionSupportDetailsImpl
MouseExperimentCoexpressionLinkImpl - Class in ubic.gemma.model.association.coexpression
MouseExperimentCoexpressionLinkImpl() - Constructor for class ubic.gemma.model.association.coexpression.MouseExperimentCoexpressionLinkImpl
MouseExperimentCoexpressionLinkImpl(BioAssaySet, Long, Long, Long) - Constructor for class ubic.gemma.model.association.coexpression.MouseExperimentCoexpressionLinkImpl
MouseGeneCoExpression - Class in ubic.gemma.model.association.coexpression
MouseGeneCoExpression() - Constructor for class ubic.gemma.model.association.coexpression.MouseGeneCoExpression
MouseGeneCoExpression.Factory - Class in ubic.gemma.model.association.coexpression
MouseGeneCoExpressionImpl - Class in ubic.gemma.model.association.coexpression
MouseGeneCoExpressionImpl() - Constructor for class ubic.gemma.model.association.coexpression.MouseGeneCoExpressionImpl
MPSS - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
MPSS - ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
mRNA - ubic.gemma.model.genome.biosequence.SequenceType
MS - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
Multifunctionality - Class in ubic.gemma.model.genome.gene
Multifunctionality() - Constructor for class ubic.gemma.model.genome.gene.Multifunctionality: No-arg constructor added to satisfy javabean contract
MULTIFUNCTIONALITY - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
Multifunctionality.Factory - Class in ubic.gemma.model.genome.gene
MultifunctionalityCli - Class in ubic.gemma.core.apps
MultifunctionalityCli() - Constructor for class ubic.gemma.core.apps.MultifunctionalityCli
mungeFileName(String) - Static method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl: Remove file separators (e.g., "/") from the file names.
MUTLQC_REPORT - ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType
MySQL57InnoDBDialect - Class in ubic.gemma.persistence.hibernate
MySQL57InnoDBDialect() - Constructor for class ubic.gemma.persistence.hibernate.MySQL57InnoDBDialect

N

name - Variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
nameForR(ExperimentalFactor) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
nameForR(FactorValue, boolean) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
NAMESPACE_URI - Static variable in class ubic.gemma.web.services.AbstractGemmaEndpoint: Namespace of both request and response.
NAS - ubic.gemma.model.association.GOEvidenceCode
NCBI_GENE_ID_URI_PREFIX - Static variable in class ubic.gemma.core.search.source.DatabaseSearchSource
NCBIGene2Accession - Class in ubic.gemma.core.loader.genome.gene.ncbi.model: See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README
NCBIGene2Accession() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
NcbiGene2AccessionParser - Class in ubic.gemma.core.loader.genome.gene.ncbi: Class to parse the NCBI gene2accession files.
NcbiGene2AccessionParser() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
NCBIGene2GOAssociationLoader - Class in ubic.gemma.core.loader.association
NCBIGene2GOAssociationLoader() - Constructor for class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
NCBIGene2GOAssociationLoaderCLI - Class in ubic.gemma.core.apps: Load GO -> gene associations from NCBI.
NCBIGene2GOAssociationLoaderCLI() - Constructor for class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
NCBIGene2GOAssociationParser - Class in ubic.gemma.core.loader.association: This parses GO annotations from NCBI.
NCBIGene2GOAssociationParser(Collection<Taxon>) - 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<Taxon>) - 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 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 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
NcbiGeneLoader(Persister) - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
NcbiGeneLoaderCLI - Class in ubic.gemma.core.apps: Command line interface to gene parsing and loading
NcbiGeneLoaderCLI() - Constructor for class ubic.gemma.core.apps.NcbiGeneLoaderCLI
NCBIUtil - Class in ubic.gemma.core.loader.genome.gene.ncbi
NCBIUtil() - Constructor for class ubic.gemma.core.loader.genome.gene.ncbi.NCBIUtil
NCRNA - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
ND - ubic.gemma.model.association.GOEvidenceCode
NeedsAttentionEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Indicates that previous validation is being invalidated
NeedsAttentionEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionEvent: No-arg constructor added to satisfy javabean contract
NEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
NEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
NEQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
netDataSourceUtil - Variable in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
NetDatasourceUtil - Class in ubic.gemma.core.util: Helper methods to get FTP connection.
NetDatasourceUtil() - Constructor for class ubic.gemma.core.util.NetDatasourceUtil
newFileUpload(HttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver: Create a factory for disk-based file items with a listener we can check for progress.
newInstance() - Static method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution.Factory
newInstance() - Static method in class ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.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.diff.PvalueDistribution.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.analysis.expression.pca.ProbeLoading.Factory
newInstance() - Static method in class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence.Factory: Deprecated.
newInstance() - Static method in class ubic.gemma.model.association.phenotype.ExperimentalEvidence.Factory: Deprecated.
newInstance() - Static method in class ubic.gemma.model.association.phenotype.GenericEvidence.Factory: Deprecated.
newInstance() - Static method in class ubic.gemma.model.association.phenotype.GenericExperiment.Factory: Deprecated.
newInstance() - Static method in class ubic.gemma.model.association.phenotype.LiteratureEvidence.Factory: Deprecated.
newInstance() - Static method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication.Factory: Deprecated.
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.User.Factory
newInstance() - Static method in class ubic.gemma.model.common.auditAndSecurity.UserGroup.Factory
newInstance() - Static method in class ubic.gemma.model.common.auditAndSecurity.UserQuery.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.LocalFile.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.ExpressionExperimentSubSet.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.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(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, Long, Long) - Static method in class ubic.gemma.model.association.coexpression.HumanGeneCoExpression.Factory
newInstance(Double, Long, Long) - Static method in class ubic.gemma.model.association.coexpression.MouseGeneCoExpression.Factory
newInstance(Double, Long, Long) - Static method in class ubic.gemma.model.association.coexpression.OtherGeneCoExpression.Factory
newInstance(Double, Long, Long) - Static method in class ubic.gemma.model.association.coexpression.RatGeneCoExpression.Factory
newInstance(Double, Gene) - Static method in class ubic.gemma.model.genome.gene.GeneSetMember.Factory
newInstance(Integer, byte[]) - 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.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.gene.GeneAlias.Factory
newInstance(String) - Static method in class ubic.gemma.model.genome.Taxon.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, String, String, GOEvidenceCode) - Static method in class ubic.gemma.model.common.description.Characteristic.Factory
newInstance(String, String, String, ExternalDatabase) - Static method in class ubic.gemma.model.common.description.DatabaseEntry.Factory
newInstance(String, String, Date, Integer, SearchSettings) - Static method in class ubic.gemma.model.common.auditAndSecurity.UserQuery.Factory
newInstance(String, String, List<BioAssay>) - Static method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension.Factory
newInstance(String, Date) - Static method in class ubic.gemma.model.common.auditAndSecurity.UserQuery.Factory
newInstance(String, DatabaseType) - Static method in class ubic.gemma.model.common.description.ExternalDatabase.Factory
newInstance(String, ArrayDesign) - Static method in class ubic.gemma.model.expression.designElement.CompositeSequence.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.genome.biosequence.BioSequence.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(Set<ExperimentalFactor>, Integer, Integer, FactorValue, Set<DifferentialExpressionAnalysisResult>, DifferentialExpressionAnalysis, PvalueDistribution, Set<HitListSize>) - Static method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet.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(ExperimentalFactor) - Static method in class ubic.gemma.model.expression.experiment.FactorValue.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) - Static method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree.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
NewsItem - Class in ubic.gemma.web.feed
NewsItem() - Constructor for class ubic.gemma.web.feed.NewsItem
newThread(Runnable) - Method in class ubic.gemma.core.util.SimpleThreadFactory
NO_BATCH_EFFECT_SUCCESS - ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that there is no batch effect.
NO_BATCH_INFO - 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
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.
nonCodingRNAProfilingArraybased - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
nonCodingRNAProfilingBySequencing - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
none - ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.NormalizationMethod
none - ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.SingularThreshold
noNeedToRun(Auditable, Class<? extends AuditEventType>) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
NonPersistentNonOrderedCoexpLink - Class in ubic.gemma.persistence.service.association.coexpression: Wrapper object used to track and eliminate duplicates.
NonPersistentNonOrderedCoexpLink(Long, Long, boolean) - Constructor for class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
NonPersistentNonOrderedCoexpLink(Gene2GeneCoexpression) - Constructor for class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
NonPersistentNonOrderedCoexpLink(Gene, Gene, boolean) - Constructor for class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
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
normalize(DoubleMatrix<R, C>) - Method in class ubic.gemma.core.analysis.preprocess.normalize.QuantileNormalizer
normalizeByValue(Characteristic) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao: Normalize a characteristic by value.
normalizeByValue(Characteristic) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
NoRowsLeftAfterFilteringException - Exception in ubic.gemma.core.analysis.preprocess.filter: This is a special kind of preprocessing exception that occurs when filtering the expression data matrix result in no rows left.
NoRowsLeftAfterFilteringException(ExpressionExperiment, String) - Constructor for exception ubic.gemma.core.analysis.preprocess.filter.NoRowsLeftAfterFilteringException
notEq - ubic.gemma.persistence.util.Filter.Operator
NotFoundExceptionMapper - Class in ubic.gemma.rest.providers: This mapper ensures that raised NotFoundException throughout the API contain well-formed ResponseErrorObject entity.
NotFoundExceptionMapper() - Constructor for class ubic.gemma.rest.providers.NotFoundExceptionMapper
NotTroubledStatusFlagEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: This event type resets the trouble flag of curation details of a curatable object.
NotTroubledStatusFlagEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent: No-arg constructor added to satisfy javabean contract
NR - ubic.gemma.model.association.GOEvidenceCode
NS - Static variable in class ubic.gemma.core.ontology.jena.TGFVO: Namespace used by TGFVO.
nuclearRNA - ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
NULL_BIOSEQUENCE - Static variable in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService: Used to identify design elements that have no sequence associated with them.
nullMatrix() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis: Flag the correlation matrix as un-fillable.
nullSafeGet(ResultSet, String[], SessionImplementor, Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
nullSafeGet(ResultSet, String[], SessionImplementor, Object) - Method in class ubic.gemma.persistence.hibernate.BatchEffectType
nullSafeSet(PreparedStatement, Object, int, SessionImplementor) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
NUM_BINS - Static variable in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
numAllCompositeSequenceWithBioSequences() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numAllCompositeSequenceWithBioSequences() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numAllCompositeSequenceWithBioSequences() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Function to return a count of all compositeSequences with bioSequence associations
numAllCompositeSequenceWithBioSequences() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numAllCompositeSequenceWithBioSequences(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numAllCompositeSequenceWithBioSequences(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numAllCompositeSequenceWithBioSequences(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Function to return the count of all composite sequences with biosequences, given a list of array design Ids
numAllCompositeSequenceWithBioSequences(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numAllCompositeSequenceWithBlatResults() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numAllCompositeSequenceWithBlatResults() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numAllCompositeSequenceWithBlatResults() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Function to return all composite sequences with blat results
numAllCompositeSequenceWithBlatResults() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numAllCompositeSequenceWithBlatResults(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numAllCompositeSequenceWithBlatResults(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numAllCompositeSequenceWithBlatResults(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Function to return the count of all composite sequences with blat results, given a list of array design Ids
numAllCompositeSequenceWithBlatResults(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numAllCompositeSequenceWithGenes() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numAllCompositeSequenceWithGenes() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numAllCompositeSequenceWithGenes() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Function to return a count of all composite sequences with associated genes.
numAllCompositeSequenceWithGenes() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numAllCompositeSequenceWithGenes(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numAllCompositeSequenceWithGenes(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numAllCompositeSequenceWithGenes(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Function to return the count of all composite sequences with genes, given a list of array design Ids
numAllCompositeSequenceWithGenes(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numAllGenes() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numAllGenes() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numAllGenes() - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Returns a count of the number of genes associated with all arrayDesigns
numAllGenes() - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numAllGenes(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numAllGenes(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numAllGenes(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Returns the number of unique Genes associated with the collection of ArrayDesign ids.
numAllGenes(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numberOfBioAssays - Variable in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
numBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: returns the number of bioSequences associated with this ArrayDesign id
numBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: returns the number of BlatResults (BioSequence2GeneProduct) entries associated with this ArrayDesign id.
numBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numCached() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
numCached() - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
numCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numCompositeSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numCompositeSequenceWithBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numCompositeSequenceWithBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numCompositeSequenceWithBioSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
numCompositeSequenceWithBioSequences(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numCompositeSequenceWithBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numCompositeSequenceWithBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numCompositeSequenceWithBlatResults(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
numCompositeSequenceWithBlatResults(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numCompositeSequenceWithGenes(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numCompositeSequenceWithGenes(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numCompositeSequenceWithGenes(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
numCompositeSequenceWithGenes(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numExperiments(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
numExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
numFactors(ExpressionExperiment) - Static method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils
numGenes(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
numGenes(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
numGenes(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService: Returns the number of unique Genes associated with this ArrayDesign id
numGenes(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl

O

OBJECT_ALIAS - Static variable in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
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.bioAssay.BioAssayDao
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
objectIsUser(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
objectIsUserGroup(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
objectMapper() - Method in class ubic.gemma.rest.util.JacksonConfig: Mapper used to generate JSON payloads from the REST API.
ObjectMapperResolver - Class in ubic.gemma.rest.providers
ObjectMapperResolver() - Constructor for class ubic.gemma.rest.providers.ObjectMapperResolver
objectsPersistedUpdate(int, int, String) - Static method in class ubic.gemma.core.loader.util.ParserAndLoaderTools
objectToSQLString(Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
OFFICIAL - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus
OffsetArg - Class in ubic.gemma.rest.util.args: Argument used to represent an offset.
OLIGO - ubic.gemma.model.genome.biosequence.SequenceType: Represents a (synthetic) oligonucleotide.
oligonucleotideBeads - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
OmimDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
OmimDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
onApplicationEvent(ContextRefreshedEvent) - Method in class ubic.gemma.core.util.BeanInitializationTimeMonitor
onComplete() - Method in interface ubic.gemma.core.job.executor.common.ExecutingTask.TaskLifecycleHandler: On completion, regardless of failure.
ONECOLOR - ubic.gemma.model.expression.arrayDesign.TechnologyType: Indicates this platform uses one channel and measurements are non-ratiometric (e.g.
onError(RetryContext, RetryCallback<T>, Throwable) - Method in class ubic.gemma.persistence.retry.RetryLogger
onEvent(ApplicationEvent) - Method in class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
onEvent(ApplicationEvent) - Method in class ubic.gemma.rest.providers.MetricsApplicationEventListener
onEvent(ApplicationEvent) - Method in class ubic.gemma.rest.providers.RequestExceptionEventListener
onEvent(RequestEvent) - Method in class ubic.gemma.rest.providers.AnalyticsRequestEventListener
onEvent(RequestEvent) - Method in class ubic.gemma.rest.providers.RequestExceptionLogger
onFailure(Exception) - Method in interface ubic.gemma.core.job.executor.common.ExecutingTask.TaskLifecycleHandler: On failure.
onProgress(String) - Method in interface ubic.gemma.core.job.executor.common.ExecutingTask.TaskLifecycleHandler: When progress is made on the task.
onProgressUpdate(String) - Method in interface ubic.gemma.core.job.executor.common.ProgressUpdateAppender.ProgressUpdateCallback
onRequest(RequestEvent) - Method in class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
onRequest(RequestEvent) - Method in class ubic.gemma.rest.providers.MetricsApplicationEventListener
onRequest(RequestEvent) - Method in class ubic.gemma.rest.providers.RequestExceptionEventListener
onStart() - Method in interface ubic.gemma.core.job.executor.common.ExecutingTask.TaskLifecycleHandler: Whenever the task execution begins.
onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
onSubmit(HttpServletRequest, PubMedSearchCommand, BindingResult, SessionStatus) - Method in interface ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
onSubmit(HttpServletRequest, PubMedSearchCommand, BindingResult, SessionStatus) - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerImpl
onSuccess() - Method in interface ubic.gemma.core.job.executor.common.ExecutingTask.TaskLifecycleHandler: On successful completion.
ONTOLOGY - ubic.gemma.model.common.description.DatabaseType
OntologyController - Class in ubic.gemma.web.controller: Provide minimal support for exposing Gemma ontology.
OntologyController() - Constructor for class ubic.gemma.web.controller.OntologyController
OntologyHighlighter - Interface in ubic.gemma.core.search: Highlighter specialized for ontology terms.
OntologyIndividualSimple - Class in ubic.gemma.core.ontology
OntologyIndividualSimple(String, String, OntologyTermSimple) - Constructor for class ubic.gemma.core.ontology.OntologyIndividualSimple
OntologyPropertySimple - Class in ubic.gemma.core.ontology: Simple in-memory implementation of OntologyProperty.
OntologyPropertySimple(String, String) - Constructor for class ubic.gemma.core.ontology.OntologyPropertySimple
OntologySearchSource - Class in ubic.gemma.core.search.source
OntologySearchSource() - Constructor for class ubic.gemma.core.search.source.OntologySearchSource
OntologyService - Interface in ubic.gemma.core.ontology
OntologyServiceFactory<T extends OntologyService> - Class in ubic.gemma.core.ontology.providers: Factory bean for baseCode's OntologyService.
OntologyServiceFactory(Class<T>) - Constructor for class ubic.gemma.core.ontology.providers.OntologyServiceFactory
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
OntologyStatement() - Constructor for class ubic.gemma.core.ontology.FactorValueOntologyService.OntologyStatement
OntologyTermValueObject(OntologyTerm, Set<DatasetsWebService.OntologyTermValueObject>) - Constructor for class ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
OntologyUtils - Class in ubic.gemma.core.ontology: Utilities for working with ontologies.
OntologyUtils() - Constructor for class ubic.gemma.core.ontology.OntologyUtils
openAndParse(InputStream) - Static method in class ubic.gemma.core.util.XMLUtils
OpenApiUtils - Class in ubic.gemma.rest.util: Utilities for interacting with OpenAPI at runtime.
OpenApiUtils() - Constructor for class ubic.gemma.rest.util.OpenApiUtils
operator() - Method in class ubic.gemma.rest.util.args.FilterArgParser
operator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
operator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
OperatorContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
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<T>) - Static method in class ubic.gemma.persistence.util.QueryUtils: Optimize a collection of Identifiable entities.
optimizeParameterList(Collection<T>) - 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<T>, Filter.Operator, Collection<T>) - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder: Add a sub-clause explicitly.
or(String, String, Class<T>, Filter.Operator, Collection<T>, String) - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder
or(String, String, Class<T>, Filter.Operator, T) - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder: Add a sub-clause explicitly.
or(String, String, Class<T>, 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.
orderByExperimentalDesign(List<BioMaterial>, Collection<ExperimentalFactor>) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
orderByExperimentalDesign(List<BioMaterial>, Collection<ExperimentalFactor>, ExperimentalFactor) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
orderByExperimentalDesign(DoubleMatrix<R, BioAssay>) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
orderByExperimentalDesign(DoubleMatrix<R, BioAssay>, ExperimentalFactor) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
orderByExperimentalDesign(ExpressionDataMatrix<?>) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
orderByExperimentalDesign(ExpressionDataMatrix<?>, ExperimentalFactor) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
OrderVectorsByDesignCli - Class in ubic.gemma.core.apps: Use to change the order of the values to match the experimental design.
OrderVectorsByDesignCli() - Constructor for class ubic.gemma.core.apps.OrderVectorsByDesignCli
ORF - ubic.gemma.model.genome.biosequence.SequenceType
organismPart - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
OSTTEST - ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType
other - ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
other - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
other - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
other - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
Other - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
OTHER - ubic.gemma.core.loader.expression.geo.model.GeoSample.LibraryStrategy
OTHER - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
OTHER - ubic.gemma.model.association.GOEvidenceCode: Unsupported/unknown GO evidence code are mapped to this value.
OTHER - ubic.gemma.model.common.description.DatabaseType
OTHER - ubic.gemma.model.common.measurement.MeasurementKind
OTHER - ubic.gemma.model.common.quantitationtype.ScaleType
OTHER - ubic.gemma.model.common.quantitationtype.StandardQuantitationType
OTHER - ubic.gemma.model.expression.arrayDesign.TechnologyType: We don't know
OTHER - ubic.gemma.model.genome.biosequence.SequenceType
OtherCoexpressionSupportDetailsImpl - Class in ubic.gemma.model.analysis.expression.coexpression
OtherCoexpressionSupportDetailsImpl() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.OtherCoexpressionSupportDetailsImpl
OtherCoexpressionSupportDetailsImpl(Long, Long, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.OtherCoexpressionSupportDetailsImpl
OtherCoexpressionSupportDetailsImpl(Gene, Gene, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.OtherCoexpressionSupportDetailsImpl
OtherExperimentCoexpressionLinkImpl - Class in ubic.gemma.model.association.coexpression
OtherExperimentCoexpressionLinkImpl() - Constructor for class ubic.gemma.model.association.coexpression.OtherExperimentCoexpressionLinkImpl
OtherExperimentCoexpressionLinkImpl(BioAssaySet, Long, Long, Long) - Constructor for class ubic.gemma.model.association.coexpression.OtherExperimentCoexpressionLinkImpl
OtherGeneCoExpression - Class in ubic.gemma.model.association.coexpression
OtherGeneCoExpression() - Constructor for class ubic.gemma.model.association.coexpression.OtherGeneCoExpression
OtherGeneCoExpression.Factory - Class in ubic.gemma.model.association.coexpression
OtherGeneCoExpressionImpl - Class in ubic.gemma.model.association.coexpression
OtherGeneCoExpressionImpl() - Constructor for class ubic.gemma.model.association.coexpression.OtherGeneCoExpressionImpl
OutlierAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
OutlierAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.OutlierAnalysisEvent: No-arg constructor added to satisfy javabean contract
OutlierDetails - Class in ubic.gemma.core.analysis.preprocess: Container for details about a proposed outlier
OutlierDetails(BioAssay) - 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() - Constructor for class ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceImpl
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
OutliersNotFoundAnalysisEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
OutliersNotFoundAnalysisEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.OutliersNotFoundAnalysisEvent
OutputStreamListener - Interface in ubic.gemma.web.util.upload
OWA - ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType

P

pad(List<T>, T, int) - Static method in class ubic.gemma.core.util.ListUtils: Pad a collection with the given element.
padToNextPowerOfTwo(List<T>, T) - Static method in class ubic.gemma.core.util.ListUtils: Pad a collection to the next power of 2 with the given element.
paginate(Slice<T>, String[]) - Static method in class ubic.gemma.rest.util.Responder: Produce a PaginatedResponseDataObject for a given unfiltered Slice.
paginate(Slice<T>, Filters, String[]) - Static method in class ubic.gemma.rest.util.Responder: Produce a FilteredAndPaginatedResponseDataObject for a given Slice
paginate(Responder.FilterMethod<T>, Filters, String[], Sort, int, int) - Static method in class ubic.gemma.rest.util.Responder: Paginate using an arbitrary filtering method.
PaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util: Represents paginated results with offset and limit.
PaginatedResponseDataObject(Slice<T>, String[]) - Constructor for class ubic.gemma.rest.util.PaginatedResponseDataObject
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<NcbiGeneData>, Map<String, NCBIGeneInfo>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
parse(InputStream) - Method in class ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParser
parse(InputStream) - 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 interface ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService
parse(InputStream) - Method in class ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl
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, BlockingQueue<String>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
parse(InputStream, BlockingQueue<T>) - 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<NcbiGeneData>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser
parse(InputStream, BlockingQueue<Gene2GOAssociation>) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
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<String>) - Static method in class ubic.gemma.persistence.util.Filter
parse(String, String, Class<?>, Filter.Operator, Collection<String>, 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_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
parseGenePixDateTime(String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
parseGenericCCHeader(DataInputStream) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractor
parseISO8601(String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
parseLongFormat(String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
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.ArrayDesignParser: Deprecated.
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 - Variable in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
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) - 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(SearchSettings, QueryParser) - 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 in ubic.gemma.core.search: An exception that indicate that the search query could not be parsed.
ParseSearchException(String, String, Throwable) - Constructor for exception ubic.gemma.core.search.ParseSearchException
ParseSearchException(String, String, Throwable, ParseSearchException) - Constructor for exception ubic.gemma.core.search.ParseSearchException
ParseSearchException(String, Throwable) - Constructor for exception ubic.gemma.core.search.ParseSearchException
parseStandardFormat(String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor
parseStringInputStream(String) - Static method in class ubic.gemma.core.loader.entrez.EutilFetch
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.
ParsingStreamConsumer<T> - Class in ubic.gemma.core.util.concurrent: See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html
ParsingStreamConsumer(Parser<T>, InputStream) - Constructor for class ubic.gemma.core.util.concurrent.ParsingStreamConsumer
PATH - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
PatoOntologyService - Class in ubic.gemma.core.ontology.providers
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
pcaFactors(Long, OutputStream) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
pcaScree(Long, OutputStream) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
PearsonMetrics - Class in ubic.gemma.core.analysis.expression.coexpression.links: A correlation analysis for a given data set, designed for selection of values based on criteria set by the user.
PearsonMetrics(ExpressionDataDoubleMatrix) - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics
PearsonMetrics(ExpressionDataDoubleMatrix, double) - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics
percent - ubic.gemma.core.ontology.GoMetric.Metric
PERCENT - ubic.gemma.model.common.quantitationtype.ScaleType: Constrained to be a value between 0 and 100.
PERCENT1 - ubic.gemma.model.common.quantitationtype.ScaleType: Constrained to be a value between 0 and 1.
performMigration(FactorValueMigratorService.Migration, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService: Perform the given migration.
performMigration(FactorValueMigratorService.Migration, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorServiceImpl: Deprecated.
performMigrationOfRemainingFactorValues(Set<Long>, boolean, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService: Migrate all remaining factor values that have not been migrated yet.
performMigrationOfRemainingFactorValues(Set<Long>, boolean, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorServiceImpl: Deprecated.
performMigrationOfRemainingOldStyleCharacteristics(Long, Set<Long>, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService: Migrate all the old-style characteristics of a given factor value to subject-only statements.
performMigrationOfRemainingOldStyleCharacteristics(Long, Set<Long>, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorServiceImpl: Deprecated.
performMultipleMigrations(List<FactorValueMigratorService.Migration>, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService: Perform multiple migrations in a single transaction.
performMultipleMigrations(List<FactorValueMigratorService.Migration>, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorServiceImpl: Deprecated.
PermissionChangeEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Represents a change in permissions
PermissionChangeEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.PermissionChangeEvent
persist(Object) - Method in class ubic.gemma.persistence.persister.AbstractPersister
persist(Object) - Method in interface ubic.gemma.persistence.persister.Persister: Persist a single object.
persist(Collection<?>) - Method in class ubic.gemma.persistence.persister.AbstractPersister
persist(Collection<?>) - Method in interface ubic.gemma.persistence.persister.Persister: Persist all the objects in a collection.
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<RawExpressionDataVector>) - Method in interface ubic.gemma.core.analysis.preprocess.TwoChannelMissingValueHelperService
persist(ExpressionExperiment, ArrayDesign) - Method in interface ubic.gemma.core.loader.expression.ExperimentPlatformSwitchHelperService
persist(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in class ubic.gemma.persistence.persister.ExpressionPersister
persist(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in interface ubic.gemma.persistence.persister.PersisterHelper
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.
persistAuditTrail(AuditTrail) - Method in class ubic.gemma.persistence.persister.CommonPersister
persistBioSequence(BioSequence, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.GenomePersister
persistContact(Contact) - Method in class ubic.gemma.persistence.persister.CommonPersister
Persister - Interface in ubic.gemma.persistence.persister: Interface defining the ability to create domain objects in bulk or singly.
persisterHelper - Variable in class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
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
persistExpressionExperiment(ExpressionExperiment, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.ExpressionPersister
persistExternalDatabase(ExternalDatabase, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.CommonPersister
persistGene(Gene, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.GenomePersister
persistMerging(ArrayDesign, ArrayDesign, Collection<ArrayDesign>, boolean, Collection<CompositeSequence>) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperService: Finalize the assembly and persistence of the merged array design.
persistMerging(ArrayDesign, ArrayDesign, Collection<ArrayDesign>, boolean, Collection<CompositeSequence>) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperServiceImpl
persistOrUpdate(Object) - Method in class ubic.gemma.persistence.persister.AbstractPersister
persistOrUpdate(Object) - Method in interface ubic.gemma.persistence.persister.Persister: Persist or update a single object.
persistProtocol(Protocol) - Method in class ubic.gemma.persistence.persister.CommonPersister
persistQuantitationType(QuantitationType, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.CommonPersister
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, AbstractPersister.Caches) - Method in class ubic.gemma.persistence.persister.GenomePersister
persistUnit(Unit) - Method in class ubic.gemma.persistence.persister.CommonPersister
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.
PHENOCARTA_EXPORT - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
PHENOCARTA_HOME_FOLDER_PATH - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
PHENOCARTA_NAME - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
phenotype - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
PHENOTYPE - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
PHENOTYPE_CATEGORY_URI - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
PhenotypeAssociation - Class in ubic.gemma.model.association.phenotype: Deprecated.
PhenotypeAssociation() - Constructor for class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.

No-arg constructor added to satisfy javabean contract
PhenotypeAssociationConstants - Class in ubic.gemma.core.association.phenotype: Deprecated.
PhenotypeAssociationConstants() - Constructor for class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
PhenotypeAssociationDao - Interface in ubic.gemma.persistence.service.association.phenotype
PhenotypeAssociationDaoImpl - Class in ubic.gemma.persistence.service.association.phenotype: deals with all basic queries used by Neurocarta
PhenotypeAssociationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
PhenotypeAssociationManagerService - Interface in ubic.gemma.core.association.phenotype: Deprecated.
PhenotypeAssociationManagerServiceImpl - Class in ubic.gemma.core.association.phenotype: Deprecated.
PhenotypeAssociationManagerServiceImpl() - Constructor for class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
PhenotypeAssociationPublication - Class in ubic.gemma.model.association.phenotype: Deprecated.
PhenotypeAssociationPublication() - Constructor for class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication: Deprecated.
PhenotypeAssociationPublication.Factory - Class in ubic.gemma.model.association.phenotype: Deprecated.
phenotypeAssociations2BibliographicPhenotypesValueObjects(Collection<PhenotypeAssociation>) - Static method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
PhenotypeAssociationService - Interface in ubic.gemma.persistence.service.association.phenotype.service
PhenotypeAssociationServiceImpl - Class in ubic.gemma.persistence.service.association.phenotype.service: Service responsible for low level operations, used by PhenotypeAssociationManagerServiceImpl
PhenotypeAssociationServiceImpl(PhenotypeAssociationDao) - Constructor for class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
PhenotypeAssoManagerServiceHelper - Interface in ubic.gemma.core.association.phenotype: Deprecated.
PhenotypeAssoManagerServiceHelperImpl - Class in ubic.gemma.core.association.phenotype: Deprecated.
PhenotypeAssoManagerServiceHelperImpl(BibliographicReferenceService, CharacteristicService, DatabaseEntryDao, ExternalDatabaseService, GeneDiffExMetaAnalysisService, GeneService, PhenotypeAssoOntologyHelper, Persister, PhenotypeAssociationService, QuantitationTypeService) - Constructor for class ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelperImpl: Deprecated.
PhenotypeAssoOntologyHelper - Interface in ubic.gemma.core.association.phenotype: Deprecated.
PhenotypeAssoOntologyHelperImpl - Class in ubic.gemma.core.association.phenotype: Deprecated.
PhenotypeAssoOntologyHelperImpl(OntologyService, MondoOntologyService, MammalianPhenotypeOntologyService, HumanPhenotypeOntologyService) - Constructor for class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl: Deprecated.
PhenotypeAssPubValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
PhenotypeAssPubValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
PhenotypeAssPubValueObject(PhenotypeAssociationPublication) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
PhenotypeController - Class in ubic.gemma.web.controller: Controller for phenotype
PhenotypeController() - Constructor for class ubic.gemma.web.controller.PhenotypeController
PhenotypeGroupValueObject - Class in ubic.gemma.core.genome.gene
PhenotypeGroupValueObject() - Constructor for class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
PhenotypeGroupValueObject(String, String, Long, String, Collection<Long>, String, String, String) - Constructor for class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject: Method to create a display object from scratch
PhenotypeMappingType - Class in ubic.gemma.model.association.phenotype: Deprecated.
PhenotypeMappingType() - Constructor for class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
PHENOTYPES - ubic.gemma.core.apps.GemmaCLI.CommandGroup
PhenotypeValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
PhenotypeValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
PhenotypeValueObject(String, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
PhenotypeWebService - Class in ubic.gemma.rest: Deprecated.
PhenotypeWebService() - Constructor for class ubic.gemma.rest.PhenotypeWebService: Deprecated.

Required by spring
PhenotypeWebService(PhenotypeAssociationManagerService) - Constructor for class ubic.gemma.rest.PhenotypeWebService: Deprecated.

Constructor for service autowiring
PhysicalLocation - Class in ubic.gemma.model.genome
PhysicalLocation() - Constructor for class ubic.gemma.model.genome.PhysicalLocation: No-arg constructor added to satisfy javabean contract
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
PLATFORM - ubic.gemma.core.apps.GemmaCLI.CommandGroup
PlatformArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for dataset (ExpressionExperiment) API.
PlatformArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.PlatformArg
PlatformArgService - Class in ubic.gemma.rest.util.args
PlatformArgService(ArrayDesignService, ExpressionExperimentService, CompositeSequenceService) - Constructor for class ubic.gemma.rest.util.args.PlatformArgService
PlatformArrayArg - Class in ubic.gemma.rest.util.args
platformFetcher - Variable in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
PlatformFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher: Fetch GEO "GPLXXX_family.soft.gz" files
PlatformFetcher() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.PlatformFetcher
PlatformIdArg - Class in ubic.gemma.rest.util.args: Long argument type for platform API, referencing the platform ID.
PlatformStringArg - Class in ubic.gemma.rest.util.args: String argument type for platform API, referencing the Platform short name.
PlatformsWebService - Class in ubic.gemma.rest: RESTful interface for platforms.
PlatformsWebService() - Constructor for class ubic.gemma.rest.PlatformsWebService: Required by spring
PlatformsWebService(GeneService, ArrayDesignService, CompositeSequenceService, ArrayDesignAnnotationService, PlatformArgService, CompositeSequenceArgService) - Constructor for class ubic.gemma.rest.PlatformsWebService: Constructor for service autowiring
plot(String) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBat: Make diagnostic plots.
plotExperimentalDesign(ExpressionExperiment) - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl: Test method for now, shows how this can be used.
Pointcuts - Class in ubic.gemma.core.util: General-purpose pointcuts to recognize CRUD operations etc.
Pointcuts() - Constructor for class ubic.gemma.core.util.Pointcuts
polyARNA - ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
PolymerType - Enum in ubic.gemma.model.genome.biosequence
populateBMFMap(Map<ExperimentalFactor, Map<Long, Double>>, BioMaterial) - Static method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl: Retrieve relationships between factors, biomaterials and factor values.
populateEventInformation(Collection<ExpressionExperimentDetailsValueObject>) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService
populateEventInformation(Collection<ExpressionExperimentDetailsValueObject>) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl: Fills in event and security information from the database.
populateFactorValuesFromBASet(BioAssaySet, ExperimentalFactor, Collection<FactorValue>) - Static method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
populateMapSet(Map<T, Set<S>>, T, S) - Static method in class ubic.gemma.persistence.util.EntityUtils: Checks if the given map already contains a Set for the given key, and if it does, adds the given has code to it.
populateModifiedValues(EvidenceValueObject<? extends PhenotypeAssociation>, PhenotypeAssociation) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelper: Deprecated.

load evidence from the database and populate it with the updated information
populateModifiedValues(EvidenceValueObject<? extends PhenotypeAssociation>, PhenotypeAssociation) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelperImpl: Deprecated.
populateReportInformation(Collection<ExpressionExperimentDetailsValueObject>) - 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<ExpressionExperimentDetailsValueObject>) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
population - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
postProcessAfterInitialization(Object, String) - Method in class ubic.gemma.core.util.BeanInitializationTimeMonitor
postProcessBeforeInitialization(Object, String) - Method in class ubic.gemma.core.util.BeanInitializationTimeMonitor
postProcessBundle(BundleProcessingStatus, StringBuffer) - Method in class ubic.gemma.web.util.MinifierPostProcessor
postProcessValueObjects(List<ArrayDesignValueObject>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
postProcessValueObjects(List<ExpressionExperimentValueObject>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
postProcessValueObjects(List<GeneValueObject>) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
postProcessValueObjects(List<VO>) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao: Post-process VOs in bulk.
ppUtil - Variable in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
prepare(ExpressionExperiment) - Method in class ubic.gemma.persistence.persister.ExpressionPersister
prepare(ExpressionExperiment) - Method in interface ubic.gemma.persistence.persister.PersisterHelper
prepare(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService
prepare(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
prepare(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.ExpressionExperimentPrePersistService: Call this before calling the persister.
prepare(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.ExpressionExperimentPrePersistServiceImpl
prepare(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in interface ubic.gemma.persistence.service.ExpressionExperimentPrePersistService
prepare(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in class ubic.gemma.persistence.service.ExpressionExperimentPrePersistServiceImpl
prepareContext(ApplicationContext) - Static method in class ubic.gemma.persistence.util.SpringContextUtil: Prepare a given context for prime time.
prepareDatabaseQuery(String, boolean) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils
prepareDatabaseQuery(SearchSettings) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Escape the query for a database match.
prepareDatabaseQuery(SearchSettings, boolean) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Obtain a query suitable for a database match.
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
prepareTermUriQuery(String) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils
prepareTermUriQuery(SearchSettings) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils
PreprocessController - Class in ubic.gemma.web.controller.analysis.preprocess: A controller to pre-process expression data (including updating diagnostics)
PreprocessController() - Constructor for class ubic.gemma.web.controller.analysis.preprocess.PreprocessController
PreprocessExperimentTask - Interface in ubic.gemma.core.tasks.analysis.expression: A "processed expression data vector create" task
PreprocessingException - Exception in ubic.gemma.core.analysis.preprocess: Allows us to catch preprocessing errors and handle them correctly.
PreprocessingException(ExpressionExperiment, String) - Constructor for exception ubic.gemma.core.analysis.preprocess.PreprocessingException
PreprocessingException(ExpressionExperiment, Throwable) - Constructor for exception ubic.gemma.core.analysis.preprocess.PreprocessingException
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 - ubic.gemma.model.common.quantitationtype.StandardQuantitationType
PRIMARY - Static variable in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
PrimitiveType - Enum in ubic.gemma.model.common.quantitationtype
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
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
printResult(CompositeSequence, Collection<BlatAssociation>) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService: Print results to STDOUT
printResult(CompositeSequence, Collection<BlatAssociation>) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
Probe2GeneEndpoint - Class in ubic.gemma.web.services: Used for determining what genes a probe assays for.
Probe2GeneEndpoint() - Constructor for class ubic.gemma.web.services.Probe2GeneEndpoint
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: No-arg constructor added to satisfy javabean contract
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_BATCH_INFO_FAILURE - 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(ExpressionExperiment, FilterConfig, LinkAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisService: Run a link analysis on an experiment, and persist the results if the configuration says to.
process(ExpressionExperiment, FilterConfig, LinkAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceImpl
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[], 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[], String, Taxon, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, InputStream, String[], String, Taxon, boolean, FastaCmd) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
processArrayDesign(ArrayDesign, InputStream, String[], 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
processArrayDesign(ArrayDesign, String[], boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, String[], 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[], String, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
processArrayDesign(ArrayDesign, String[], String, boolean, FastaCmd) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Provided primarily for testing.
processArrayDesign(ArrayDesign, String[], String, boolean, FastaCmd) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl
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, 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, 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<BlatResult>) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService
processArrayDesign(ArrayDesign, Taxon, Collection<BlatResult>) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
processBlatResults(GoldenPathSequenceAnalysis, Collection<BlatResult>) - 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<BlatResult>) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
processBlatResults(GoldenPathSequenceAnalysis, Collection<BlatResult>, 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<BlatResult>, 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
processDataSet(GeoSeries, String) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator: Process a data set and add it to the series
processDiagnostics(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.PreprocessorService: Create or update the sample correlation, PCA and M-V data.
processDiagnostics(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl
ProcessedDataComputeCLI - Class in ubic.gemma.core.apps: Prepare the "processed" expression data vectors, and can also do batch correction.
ProcessedDataComputeCLI() - Constructor for class ubic.gemma.core.apps.ProcessedDataComputeCLI
ProcessedDataVectorCache - Interface in ubic.gemma.persistence.service.expression.bioAssayData: Cache of data vectors
ProcessedDataVectorCacheImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData: Configures the cache for data vectors.
ProcessedDataVectorCacheImpl() - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl
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
ProcessedExpressionDataVectorDao - Interface in ubic.gemma.persistence.service.expression.bioAssayData
ProcessedExpressionDataVectorDao.RankMethod - Enum in ubic.gemma.persistence.service.expression.bioAssayData
ProcessedExpressionDataVectorDaoImpl - Class in ubic.gemma.persistence.service.expression.bioAssayData
ProcessedExpressionDataVectorDaoImpl(SessionFactory, ProcessedDataVectorCache) - Constructor for class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
processedExpressionDataVectorService - Variable in class ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService
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
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
processErrors(HttpServletRequest, HttpServletResponse, Object, BindException, String) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.

Convenience method to get the user object from the session
processFormSubmission(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.

Default behavior for FormControllers - redirect to the successView when the cancel button has been pressed.
processFormSubmission(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
processFormSubmission(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
processFormSubmission(HttpServletRequest, HttpServletResponse, SearchSettings, BindException) - Method in interface ubic.gemma.web.controller.GeneralSearchController
processFormSubmission(HttpServletRequest, HttpServletResponse, SearchSettings, BindException) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl
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<String[]>) - Method in interface ubic.gemma.core.analysis.sequence.ProbeMapper
processGbIds(GoldenPathSequenceAnalysis, Collection<String[]>) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
processGeneList() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI: Main entry point to service class which reads a gene file and persists the genes in that file.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli: See 'configure' for how the other options are handled.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.BlacklistCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI: This method is called at the end of processCommandLine
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.GeeqCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.GeoGrabberCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.IndexGemmaCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.LinkAnalysisCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.MultifunctionalityCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.PubMedLoaderCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ReplaceDataCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.SplitExperimentCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.TaxonLoaderCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.UpdateEE2CCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.UpdatePubMedCli
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
processOptions(CommandLine) - Method in class ubic.gemma.core.util.AbstractCLI: Process command line options.
processPhenotypeAssociationForm(EvidenceValueObject<?>) - Method in class ubic.gemma.web.controller.PhenotypeController
processPsl(InputStream, Taxon) - Method in interface ubic.gemma.core.apps.Blat
processPsl(InputStream, Taxon) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
processRepeatMaskerOutput(Collection<BioSequence>, String) - 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<BioSequence>, ProbeMapperConfig) - Method in interface ubic.gemma.core.analysis.sequence.ProbeMapper: Given a collection of sequences, blat them against the selected genome.
processSequences(GoldenPathSequenceAnalysis, Collection<BioSequence>, ProbeMapperConfig) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperImpl
processSingleAccession(String, String[], String, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService: Update a single sequence in the system.
processSingleAccession(String, String[], String, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl: Update a single sequence in the system.
processStandardOptions(CommandLine) - Method in class ubic.gemma.core.util.AbstractAuthenticatedCLI: You must override this method to process any options you added.
processStandardOptions(CommandLine) - Method in class ubic.gemma.core.util.AbstractCLI: Somewhat annoying: This causes subclasses to be unable to safely use 'h', 'p', 'u' and 'P' etc.
processVectors(Taxon, Collection<ProcessedExpressionDataVector>, FilterConfig, LinkAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisService: Used when the input is data vectors from another source, instead of from a DB-bound expressionExperiment.
processVectors(Taxon, Collection<ProcessedExpressionDataVector>, FilterConfig, LinkAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceImpl
PRODUCTION - Static variable in class ubic.gemma.persistence.util.EnvironmentProfiles
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
ProgressStatusService - Interface in ubic.gemma.web.job.progress: These methods are exposed to front-end.
ProgressStatusServiceImpl - Class in ubic.gemma.web.job.progress: This class exposes methods for AJAX calls.
ProgressStatusServiceImpl() - Constructor for class ubic.gemma.web.job.progress.ProgressStatusServiceImpl
ProgressUpdateAppender - Class in ubic.gemma.core.job.executor.common: This appender is used by remote tasks to send progress notifications to the webapp.
ProgressUpdateAppender() - Constructor for class ubic.gemma.core.job.executor.common.ProgressUpdateAppender
ProgressUpdateAppender.ProgressUpdateCallback - Interface in ubic.gemma.core.job.executor.common: Callback used to emit progress updates.
ProgressUpdateAppender.ProgressUpdateContext - Class in ubic.gemma.core.job.executor.common: Represents a context under which progress update logs are intercepted the ProgressUpdateAppender.ProgressUpdateCallback is invoked.
ProgressUpdateContext(ProgressUpdateAppender.ProgressUpdateCallback) - Constructor for class ubic.gemma.core.job.executor.common.ProgressUpdateAppender.ProgressUpdateContext
promptConfirmationOrAbort(String) - Method in class ubic.gemma.core.util.AbstractCLI: Prompt the user for a confirmation or raise an exception to abort the AbstractCLI.doWork() method.
PROPERTY - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
PROPERTY - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
PROPERTY() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
PROPERTY() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
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
propertySourcesPlaceholderConfigurer() - Static method in class ubic.gemma.persistence.util.SettingsConfig: Allow for substitution placeholders with values from the settings.
protein - ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
protein - ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
PROTEIN - ubic.gemma.model.common.description.DatabaseType
PROTEIN - ubic.gemma.model.genome.biosequence.PolymerType
PROTEINCODING - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
proteinExpressionArraybased - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
proteinExpressionMSBased - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
protocol - 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
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
PSEUDO - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
pub - ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode
PubMedLoaderCli - Class in ubic.gemma.core.apps: Load PubMed files from XML files -- not used routinely!
PubMedLoaderCli() - Constructor for class ubic.gemma.core.apps.PubMedLoaderCli
PubMedQueryController - Interface in ubic.gemma.web.controller.common.description.bibref: Note: do not use parameterized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
PubMedQueryControllerImpl - Class in ubic.gemma.web.controller.common.description.bibref: Allow users to search for and view PubMed abstracts from NCBI, or from Gemma.
PubMedQueryControllerImpl() - Constructor for class ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerImpl
PubMedSearch - Class in ubic.gemma.core.loader.entrez.pubmed: Search PubMed for terms, retrieve document records.
PubMedSearch() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch
PubMedSearchCommand - Class in ubic.gemma.web.controller.common.description.bibref: Supports seaching of pubmed references
PubMedSearchCommand(String) - Constructor for class ubic.gemma.web.controller.common.description.bibref.PubMedSearchCommand
PubMedSearcher - Class in ubic.gemma.core.loader.entrez.pubmed: Simple application to perform pubmed searches from a list of terms, and persist the results in the database.
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
PubMedXMLFetcher - Class in ubic.gemma.core.loader.entrez.pubmed: Class that can retrieve pubmed records (in XML format) via HTTP.
PubMedXMLFetcher() - Constructor for class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcher
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<Reporter>) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
putCount() - Method in class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics
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
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

Q

QTM - ubic.gemma.model.association.GOEvidenceCode: Quantitative Trait Measurement (RGD code)
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
QuantitationMismatchException - Exception in ubic.gemma.core.datastructure.matrix: Exception raised when an ExpressionDataMatrix does not meet the expectations set by a given QuantitationType.
QuantitationMismatchException(QuantitationType, String) - Constructor for exception ubic.gemma.core.datastructure.matrix.QuantitationMismatchException
QuantitationMismatchPreprocessingException - Exception in ubic.gemma.core.analysis.preprocess
QuantitationMismatchPreprocessingException(ExpressionExperiment, QuantitationMismatchException) - Constructor for exception ubic.gemma.core.analysis.preprocess.QuantitationMismatchPreprocessingException
QuantitationType - Class in ubic.gemma.model.common.quantitationtype
QuantitationType() - Constructor for class ubic.gemma.model.common.quantitationtype.QuantitationType: No-arg constructor added to satisfy javabean contract
QuantitationType.Factory - Class in ubic.gemma.model.common.quantitationtype
QuantitationTypeArg<T> - Class in ubic.gemma.rest.util.args
QuantitationTypeArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.QuantitationTypeArg
QuantitationTypeArgService - Class in ubic.gemma.rest.util.args
QuantitationTypeArgService(QuantitationTypeService) - Constructor for class ubic.gemma.rest.util.args.QuantitationTypeArgService
QuantitationTypeByIdArg - Class in ubic.gemma.rest.util.args
QuantitationTypeByNameArg - Class in ubic.gemma.rest.util.args
QuantitationTypeConversionException - Exception in ubic.gemma.core.datastructure.matrix: Base class for representing problematic QuantitationType conversion.
QuantitationTypeConversionException(String) - Constructor for exception ubic.gemma.core.datastructure.matrix.QuantitationTypeConversionException
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
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
QuantitationTypePropertyEditor - Class in ubic.gemma.web.propertyeditor
QuantitationTypePropertyEditor(Collection<QuantitationType>) - Constructor for class ubic.gemma.web.propertyeditor.QuantitationTypePropertyEditor
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
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<? extends DesignElementDataVector>) - Constructor for class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject: Create a QuantitationType VO in the context of an associated experiment.
QUANTITATIVE - ubic.gemma.model.common.quantitationtype.GeneralType
QUANTITY - ubic.gemma.model.common.measurement.MeasurementKind
QueriedAndFilteredAndPaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util
QueriedAndFilteredAndPaginatedResponseDataObject(Slice<T>, String, Filters, String[]) - Constructor for class ubic.gemma.rest.util.QueriedAndFilteredAndPaginatedResponseDataObject
QueriedAndFilteredResponseDataObject<T> - Class in ubic.gemma.rest.util
QueriedAndFilteredResponseDataObject(List<T>, String, Filters, String[], Sort) - Constructor for class ubic.gemma.rest.util.QueriedAndFilteredResponseDataObject
queryAndCache(Gene) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
queryAndCache(Gene) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
queryAndFilter(List<T>, String, Filters, String[], Sort) - Static method in class ubic.gemma.rest.util.Responder
queryAndPaginate(Slice<T>, String, Filters, String[]) - Static method in class ubic.gemma.rest.util.Responder
QueryArg - Class in ubic.gemma.rest.util.args
QueryUtils - Class in ubic.gemma.persistence.util: Utilities for Query.
QueryUtils() - Constructor for class ubic.gemma.persistence.util.QueryUtils
QUEUED - ubic.gemma.core.job.SubmittedTask.Status
QueuingParser<T> - Interface in ubic.gemma.core.loader.util: Defines a class that produces object that can be consumed by other classes.
quote(String) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils: Quote the given Lucene query to be used for an exact match.
QUOTED_STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
QUOTED_STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
QUOTED_STRING() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext

R

R - ubic.gemma.model.common.auditAndSecurity.AuditAction: Read
RANGE - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
RANK - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
RankComputationEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: For backwards compatibility only.
RankComputationEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent
RAT - ubic.gemma.core.apps.ShellDelegatingBlat.BlattableGenome
RatCoexpressionSupportDetailsImpl - Class in ubic.gemma.model.analysis.expression.coexpression
RatCoexpressionSupportDetailsImpl() - Constructor for class ubic.gemma.model.analysis.expression.coexpression.RatCoexpressionSupportDetailsImpl
RatCoexpressionSupportDetailsImpl(Long, Long, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.RatCoexpressionSupportDetailsImpl
RatCoexpressionSupportDetailsImpl(Gene, Gene, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.RatCoexpressionSupportDetailsImpl
RatExperimentCoexpressionLinkImpl - Class in ubic.gemma.model.association.coexpression
RatExperimentCoexpressionLinkImpl() - Constructor for class ubic.gemma.model.association.coexpression.RatExperimentCoexpressionLinkImpl
RatExperimentCoexpressionLinkImpl(BioAssaySet, Long, Long, Long) - Constructor for class ubic.gemma.model.association.coexpression.RatExperimentCoexpressionLinkImpl
RatGeneCoExpression - Class in ubic.gemma.model.association.coexpression
RatGeneCoExpression() - Constructor for class ubic.gemma.model.association.coexpression.RatGeneCoExpression
RatGeneCoExpression.Factory - Class in ubic.gemma.model.association.coexpression
RatGeneCoExpressionImpl - Class in ubic.gemma.model.association.coexpression
RatGeneCoExpressionImpl() - Constructor for class ubic.gemma.model.association.coexpression.RatGeneCoExpressionImpl
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
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
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 - Variable in class ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService
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
RCA - ubic.gemma.model.association.GOEvidenceCode
READ - Static variable in enum ubic.gemma.model.common.auditAndSecurity.AuditAction: Aliases, for readability.
readAnnotationFile(ArrayDesign) - Static method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl
readAnnotationFileAsString(ArrayDesign) - Static method in class ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl: 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.
readListFileToStrings(String) - Static method in class ubic.gemma.core.util.FileUtils: may be tab-delimited, only first column used, commented (#) lines are ignored.
readReport(InputStream) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint: Looks to parse a previously generated xml report that was saved to disk.
readReport(String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint: uses the default path of gemmaData/datafile/xml/ to look for reports.
readReport(String, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
reauthenticate(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
recalculateBatchConfound(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
recalculateBatchEffect(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
recalculateBatchInfo() - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: Recalculates the batch effect and batch confound information for datasets that have been updated in the last 24 hours.
recalculateBatchInfo() - 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
ReCaptcha - Class in ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
ReCaptcha(String) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
ReCaptchaException - Exception in ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
ReCaptchaException(String) - Constructor for exception ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException
ReCaptchaException(String, Throwable) - Constructor for exception ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException
ReCaptchaResponse - Class in ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
ReCaptchaResponse(boolean, String) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaResponse
reclaimRequestAttributes(HttpServletRequest) - Static method in class ubic.gemma.web.util.RequestUtil: Returns request attributes from session to request
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
records - Variable in class ubic.gemma.web.remote.JsonReaderResponse
redo(Long, Long) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController: AJAX entry point to redo an analysis.
redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, boolean) - Method in interface ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService: Redo
redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl
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
referenceData(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
referenceData(HttpServletRequest) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
referenceData(HttpServletRequest) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl
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.core.annotation.reference.BibliographicReferenceService
refresh(String) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
refreshStats(Long, Long) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController
REFSEQ - ubic.gemma.model.genome.biosequence.SequenceType
registerAlias(String, String, Class<?>, String, int) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
registerAlias(String, String, Class<?>, String, int, boolean) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer: Register an alias for a property.
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.
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
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
reinitializeOntologyIndices() - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController: AJAX Note that this completely scraps the indices, and runs asynchronously.
RelationshipPersister - Class in ubic.gemma.persistence.persister: Persist objects like Gene2GOAssociation.
RelationshipPersister() - Constructor for class ubic.gemma.persistence.persister.RelationshipPersister
release() - Method in class ubic.gemma.web.taglib.ConstantsTag: Release all allocated resources.
release() - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
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
RELEVANT - Static variable in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
remoteBaseDir - Variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
remove(C) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
remove(Long) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Removes an evidence
remove(Long) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
remove(Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
remove(Long) - Method in class ubic.gemma.persistence.service.AbstractDao
remove(Long) - Method in class ubic.gemma.persistence.service.AbstractService
remove(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
remove(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
remove(Long) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
remove(Long) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
remove(Long) - Method in interface ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
remove(Long) - Method in class ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl
remove(Long) - Method in interface ubic.gemma.persistence.service.BaseDao: Remove a persistent instance based on its ID.
remove(Long) - Method in interface ubic.gemma.persistence.service.BaseImmutableService: Removes the entity with given ID from the persistent storage.
remove(Long) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
remove(Long) - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolService
remove(Long) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
remove(Long) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService: Removes the entity with given ID from the persistent storage.
remove(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
remove(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl
remove(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
remove(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
remove(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
remove(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
remove(Long) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
remove(Long, Long) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController: AJAX entry point to remove an analysis given by the ID
remove(Object) - Method in class ubic.gemma.persistence.util.Slice: Deprecated.
remove(Collection<? extends BioAssaySet>) - Method in interface ubic.gemma.persistence.service.expression.experiment.BioAssaySetService
remove(Collection<? extends BioAssaySet>) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
remove(Collection<Long>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache: Bulk remove from cache.
remove(Collection<Long>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
remove(Collection<O>) - Method in class ubic.gemma.persistence.service.AbstractService
remove(Collection<O>) - Method in interface ubic.gemma.persistence.service.BaseImmutableService: Removes all the given entities from persistent storage.
remove(Collection<T>) - Method in class ubic.gemma.persistence.service.AbstractDao
remove(Collection<T>) - Method in interface ubic.gemma.persistence.service.BaseDao
remove(Collection<CoexpressionAnalysis>) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
remove(Collection<DifferentialExpressionAnalysis>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
remove(Collection<ExternalDatabase>) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
remove(Collection<QuantitationType>) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
remove(Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
remove(Collection<ExperimentalFactor>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
remove(Collection<ExperimentalFactor>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl
remove(Collection<ExpressionExperiment>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
remove(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
remove(Collection<ExpressionExperimentSubSet>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl
remove(Collection<FactorValue>) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
remove(Collection<DatabaseBackedGeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Given a valid gene group will remove it from db (if the user has permissons to do so).
remove(Collection<GeneProduct>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
remove(Collection<GeneProduct>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
remove(Collection<GeneSet>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
remove(Collection<GeneSet>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
remove(Collection<AnnotationAssociation>) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
remove(Collection<Taxon>) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
remove(O) - Method in class ubic.gemma.persistence.service.AbstractService
remove(O) - Method in interface ubic.gemma.persistence.service.BaseImmutableService: Removes the given entity from the persistent storage.
remove(T) - Method in class ubic.gemma.persistence.service.AbstractDao
remove(T) - Method in interface ubic.gemma.persistence.service.analysis.AnalysisService
remove(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Remove a persistent instance
remove(CoexpressionAnalysis) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
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(ExpressionExperimentSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
remove(PhenotypeAssociation) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
remove(PhenotypeAssociation) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
remove(Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.ContactService
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.core.annotation.reference.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(Protocol) - Method in interface ubic.gemma.persistence.service.common.protocol.ProtocolService
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(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
remove(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
remove(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
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(BioAssaySet) - Method in interface ubic.gemma.persistence.service.expression.experiment.BioAssaySetService
remove(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
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(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 interface ubic.gemma.persistence.service.expression.experiment.FactorValueService
remove(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
remove(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
remove(Gene) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
remove(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
remove(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
remove(GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
remove(GeneSet) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
remove(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
remove(AnnotationAssociation) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
remove(BlatAssociation) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
remove(BlatResult) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService
remove(Taxon) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
remove(EntityDelegator<ArrayDesign>) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
remove(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
removeAll() - Method in interface ubic.gemma.core.genome.gene.service.GeneService
removeAll() - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
removeAll() - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
removeAll() - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
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.association.phenotype.PhenotypeAssociationDao
removeAll() - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
removeAll() - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
removeAll() - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
removeAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDao
removeAll() - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl
removeAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityService: Remove all blacklisted platforms and experiments.
removeAll() - Method in class ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityServiceImpl
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.GeneDao
removeAll() - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
removeAllEvidenceFromMetaAnalysis(Long) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Removes all the evidence that came from a specific metaAnalysis
removeAllEvidenceFromMetaAnalysis(Long) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
removeAllEvidenceFromMetaAnalysis(Long) - Method in class ubic.gemma.web.controller.PhenotypeController
removeAttribute(String) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
removeAttribute(String, int) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
removeAuthority(UserGroup, String) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao
removeAuthority(UserGroup, String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
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
removeBiomaterialTag(Characteristic, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
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
removeByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDao: Remove the given audit trails by IDs.
removeByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDaoImpl
removeCharacteristic(BioMaterial, Characteristic) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Remove the given characteristic from the given biomaterial
removeCharacteristic(BioMaterial, Characteristic) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
removeCharacteristics(Collection<AnnotationValueObject>) - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController
removeDuplicates(Collection<BlatResult>) - Static method in class ubic.gemma.core.analysis.sequence.ProbeMapUtils: Prune a set of results that have the same coordinates and query.
removeEntity(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
removeEntity(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
removeExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager
removeExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
removeExperimentTag(Collection<Long>, Long) - Method in class ubic.gemma.web.controller.expression.experiment.AnnotationController
removeForExperiment(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
removeForExperiment(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
removeForExperiment(BioAssaySet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
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(BioAssaySet) - Method in interface ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService: Removes all analyses for the given experiment
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
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<ExperimentalFactor>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
removeForExperimentalFactors(Collection<ExperimentalFactor>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
removeGeneSet(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager
removeGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
removeGroupAuthority(UserGroup, String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
removeGroupAuthority(String, GrantedAuthority) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
removeGroupReadable(EntityDelegator<? extends Securable>, String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
removeGroupReadable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
removeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
removeGroupWriteable(EntityDelegator<? extends Securable>, String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
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).
removeMetaAnalysis(Long) - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
removeOutliers(ExpressionDataDoubleMatrix, ExpressionExperiment) - Static method in class ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl: Remove outlier samples from the data matrix, based on outliers that were flagged in the experiment (not just candidate outliers)
removePhenotypeAssociation(Long) - Method in class ubic.gemma.web.controller.PhenotypeController
removePhenotypePublication(PhenotypeAssociationPublication) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao: remove a PhenotypeAssociationPublication
removePhenotypePublication(PhenotypeAssociationPublication) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
removePhenotypePublication(PhenotypeAssociationPublication) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
removePhenotypePublication(PhenotypeAssociationPublication) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
removePrimaryPublication(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Remove the primary publication for the given expression experiment (by id).
removeProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
removeProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl
removeProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
removeProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
removeRootTerms(Collection<AnnotationValueObject>) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
removeRootTerms(Collection<AnnotationValueObject>) - 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<GeoSample>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries: Clean up samples we have decided are ineligible (i.e., non transcriptomic)
removeSessionGroups(Collection<SessionBoundGeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: Deprecated.
removeSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Given a valid experiment group will remove it from the session.
removeSet(GemmaSessionBackedValueObject) - Method in class ubic.gemma.web.persistence.AbstractSetListContainer
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
removeUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Given valid experiment groups will remove them from the session or the database appropriately.
removeUserAndSessionGroups(Collection<GeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Given valid gene groups will remove them from the session or the database appropriately.
removeUserFromGroup(User, UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
removeUserFromGroup(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
removeUsersFromGroup(String[], String) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
removeUsersFromGroup(String[], String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
renameFile(File, File) - Static method in class ubic.gemma.persistence.util.EntityUtils
renameGroup(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
render(List<Object>) - Method in class ubic.gemma.web.view.JSONTableRenderer
render(Map<String, ?>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.view.JSONView
renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.view.TextView
renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.view.XmlView
reorder(List<BioAssayValueObject>) - 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
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<BioSequence>) - 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
RepeatScan() - Constructor for class ubic.gemma.core.analysis.sequence.RepeatScan
replace(Object, Object, Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
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<String, String>) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
replaceData(ExpressionExperiment, ArrayDesign, QuantitationType, DoubleMatrix<String, String>) - Method in class ubic.gemma.core.loader.expression.DataUpdaterImpl: Replace the data associated with the experiment (or add it if there is none).
ReplaceDataCli - Class in ubic.gemma.core.apps: Replace data in an existing data set.
ReplaceDataCli() - Constructor for class ubic.gemma.core.apps.ReplaceDataCli
replaceProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService: Replace the processed vectors of a EE with the given vectors.
replaceProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
replaceRawVectors(ExpressionExperiment, Collection<RawExpressionDataVector>) - 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.
replaceRawVectors(ExpressionExperiment, Collection<RawExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
REPORT_BATCH_SIZE - Static variable in class ubic.gemma.persistence.persister.AbstractPersister: Size if batch to report when persisting multiple entities with AbstractPersister.doPersist(Collection, Caches).
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.Factory - Class in ubic.gemma.core.loader.expression.arrayDesign
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 - ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode
REQUEST - Static variable in class ubic.gemma.web.services.AbstractGemmaEndpoint
RequestAttributesBasedClientIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Strategy that retrieves and store client IDs in the RequestAttributes.
RequestAttributesBasedClientIdRetrievalStrategy() - Constructor for class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy
requestCancellation() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
requestCancellation() - Method in interface ubic.gemma.core.job.SubmittedTask: Send cancellation request.
RequestExceptionEventListener - Class in ubic.gemma.rest.providers: Listen and dispatch ApplicationEvent.
RequestExceptionEventListener() - Constructor for class ubic.gemma.rest.providers.RequestExceptionEventListener
RequestExceptionLogger - Class in ubic.gemma.rest.providers: Log request exceptions.
RequestExceptionLogger() - Constructor for class ubic.gemma.rest.providers.RequestExceptionLogger
RequestHeaderBasedClientIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Strategy that retrieves the client ID in a request header.
RequestHeaderBasedClientIdRetrievalStrategy() - Constructor for class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy
RequestUtil - Class in ubic.gemma.web.util: RequestUtil utility class
RequestUtil() - Constructor for class ubic.gemma.web.util.RequestUtil
requireLogin() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
requireLogin() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
requireLogin() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
requireLogin() - Method in class ubic.gemma.core.apps.BlacklistCli
requireLogin() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
requireLogin() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
requireLogin() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
requireLogin() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
requireLogin() - Method in class ubic.gemma.core.util.AbstractAuthenticatedCLI: Indicate if the command requires authentication.
requiresLayout() - Method in class ubic.gemma.core.job.executor.common.ProgressUpdateAppender
requiresLayout() - Method in class ubic.gemma.web.logging.SlackAppender
resetHibernateStatus() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
resetPassword(String, String, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController: Resets the password to a random alphanumeric (of length MIN_PASSWORD_LENGTH).
resetStats() - Method in interface ubic.gemma.web.util.HibernateMonitor: Clear all statistics.
resetStats() - Method in class ubic.gemma.web.util.HibernateMonitorImpl
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 - ubic.gemma.core.ontology.GoMetric.Metric
resolve(AnnotatedType, ModelConverterContext, Iterator<ModelConverter>) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver
resolveAllowableValues(Annotated, Annotation[], Schema) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver: Resolves allowed values for the SearchWebService.search(QueryArg, TaxonArg, PlatformArg, List, LimitArg, ExcludeArg) resultTypes argument.
resolveDescription(Annotated, Annotation[], Schema) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver
resolveException(HttpServletRequest, HttpServletResponse, Object, Exception) - Method in class ubic.gemma.web.util.UnhandledExceptionResolver
resolveExtensions(Annotated, Annotation[], Schema) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver
resolveMultipart(HttpServletRequest) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver
respond(T) - Static method in class ubic.gemma.rest.util.Responder: Produce a ResponseDataObject that wraps the given argument.
Responder - Class in ubic.gemma.rest.util: Handles setting of the response status code and composing a proper payload structure.
Responder() - Constructor for class ubic.gemma.rest.util.Responder
Responder.FilterMethod<T> - Interface in ubic.gemma.rest.util: A functional interface matching the signature of a paginating service method.
RESPONSE - Static variable in class ubic.gemma.web.services.AbstractGemmaEndpoint
ResponseDataObject<T> - Class in ubic.gemma.rest.util: Wrapper for a non-error response payload compliant with the Google JSON style-guide
ResponseDataObject(T) - Constructor for class ubic.gemma.rest.util.ResponseDataObject
ResponseErrorObject - Class in ubic.gemma.rest.util: Wrapper for an error response payload compliant with the Google JSON style-guide
ResponseErrorObject(WellComposedErrorBody, OpenAPI) - Constructor for class ubic.gemma.rest.util.ResponseErrorObject
RestapidocsIndexRewriteFilter - Class in ubic.gemma.rest.servlet: Rewrites the path to the index file.
RestapidocsIndexRewriteFilter() - Constructor for class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilter
RestAuthEntryPoint - Class in ubic.gemma.rest.security: Implementation of AuthenticationEntryPoint for the RESTful API to handle authentication.
RestAuthEntryPoint(ObjectMapper) - Constructor for class ubic.gemma.rest.security.RestAuthEntryPoint
RESULT_TYPES_SCHEMA_NAME - Static variable in class ubic.gemma.rest.SearchWebService: Name used in the OpenAPI schema to identify result types as per SearchWebService.search(QueryArg, TaxonArg, PlatformArg, List, LimitArg, ExcludeArg)'s fourth argument.
retainHavingEvent(Collection<? extends Auditable>, Class<? extends AuditEventType>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao
retainHavingEvent(Collection<? extends Auditable>, Class<? extends AuditEventType>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
retainHavingEvent(Collection<? extends Auditable>, Class<? extends AuditEventType>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
retainHavingEvent(Collection<? extends Auditable>, Class<? extends AuditEventType>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
retainLackingEvent(Collection<? extends Auditable>, Class<? extends AuditEventType>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao
retainLackingEvent(Collection<? extends Auditable>, Class<? extends AuditEventType>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl
retainLackingEvent(Collection<? extends Auditable>, Class<? extends AuditEventType>) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
retainLackingEvent(Collection<? extends Auditable>, Class<? extends AuditEventType>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl
retrieveByHTTP(int) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcher
retrieveByHTTP(Collection<Integer>) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcher
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
retrieveSummaryObjects(Collection<Long>) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService: retrieves a collection of cached value objects containing summary information
retrieveSummaryObjects(Collection<Long>) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl
retrieveSvd(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper
retrieveSvd(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl: Get the SVD information for experiment with id given.
Retryable - Annotation Type in ubic.gemma.persistence.retry: Indicate that the method should be retried on failure.
retryableMethod() - Method in class ubic.gemma.core.util.Pointcuts: A method that can be retried, public and annotated with Retryable.
retryableOrTransactionalServiceMethod() - Method in class ubic.gemma.core.util.Pointcuts: A retryable or transactional service method.
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
returnedClass() - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
reverseComplement(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
RgdDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
RgdDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
RIGHT - 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.
RNA - ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
RNA - ubic.gemma.model.genome.biosequence.PolymerType
RNASEQ - ubic.gemma.core.loader.expression.geo.model.GeoSample.LibraryStrategy
RNASeqBatchInfoCli - Class in ubic.gemma.core.apps: Deprecated.
this should not be necessary and the regular batch population tool can be used instead.
RNASeqBatchInfoCli() - Constructor for class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
RNASeqDataAddCli - Class in ubic.gemma.core.apps: Designed to add count and/or RPKM data to a data set that has only meta-data.
RNASeqDataAddCli() - Constructor for class ubic.gemma.core.apps.RNASeqDataAddCli
RootWebService - Class in ubic.gemma.rest: Handles calls to the root API url and user info api
RootWebService() - Constructor for class ubic.gemma.rest.RootWebService
RootWebService.ApiInfoValueObject - Class in ubic.gemma.rest
RootWebService.UserValueObject - Class in ubic.gemma.rest
RowLevelFilter - Class in ubic.gemma.core.analysis.preprocess.filter
RowLevelFilter() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter
RowLevelFilter.Method - Enum in ubic.gemma.core.analysis.preprocess.filter
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
rows() - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
rows() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
rows() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
rows() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
rows() - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
rows() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
rowStatistics() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
rowStatistics() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics: Calculate mean and sumsqsqrt for each row
rowStatistics() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics: Calculate mean and sumsqsqrt for each row -- using the ranks of course!
RowsWithSequencesFilter - Class in ubic.gemma.core.analysis.preprocess.filter: Remove rows that have no BioSequence associated with the row.
RowsWithSequencesFilter() - Constructor for class ubic.gemma.core.analysis.preprocess.filter.RowsWithSequencesFilter
RRNA - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
RssFeedController - Class in ubic.gemma.web.controller.common.rss
RssFeedController() - Constructor for class ubic.gemma.web.controller.common.rss.RssFeedController
RTPCR - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
RULE_clause - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_collection - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_collectionOperator - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_disjunction - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_filter - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_operator - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_scalar - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_subClause - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
ruleNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
ruleNames - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
run() - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBat
run() - Method in class ubic.gemma.core.util.concurrent.GenericStreamConsumer
run() - Method in class ubic.gemma.core.util.concurrent.ParsingStreamConsumer
run(boolean) - Method in class ubic.gemma.core.analysis.preprocess.batcheffects.ComBat
run(Long) - Method in class ubic.gemma.web.controller.analysis.expression.coexpression.links.LinkAnalysisController
run(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.BatchInfoFetchController
run(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.PreprocessController: Update the processed data vectors as well as diagnostics
run(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.SvdController: AJAX entry point.
run(Long) - Method in class ubic.gemma.web.controller.analysis.preprocess.TwoChannelMissingValueController: AJAX entry point.
run(Long) - Method in class ubic.gemma.web.controller.analysis.sequence.ArrayDesignRepeatScanController: AJAX entry point.
run(Long) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController: AJAX entry point when running completely automatically.
run(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignProbeMapperController: AJAX entry point.
run(Long) - Method in class ubic.gemma.web.controller.ExpressionExperimentReportGenerationController
run(ExpressionExperiment, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.AbstractDifferentialExpressionAnalyzer
run(ExpressionExperiment, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer
run(ExpressionExperiment, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
run(ExpressionExperiment, ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.AbstractDifferentialExpressionAnalyzer
run(ExpressionExperiment, ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer: Allows entry of modified data matrices into the workflow.
run(ExpressionExperiment, ExpressionDataDoubleMatrix, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
run(ExpressionExperimentSubSet, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer: Note that normally when we run a subset analysis, the subsetting is done internally, so we pass in the expression experiment, not the subset.
run(ExpressionExperimentSubSet, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer
runAll() - Method in interface ubic.gemma.core.analysis.report.DatabaseViewGenerator
runAll() - Method in class ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl
runAll() - Method in class ubic.gemma.web.controller.ExpressionExperimentReportGenerationController
runAll(Integer) - Method in interface ubic.gemma.core.analysis.report.DatabaseViewGenerator
runAll(Integer) - Method in class ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl
runCustom(Long, Collection<Long>, boolean, Long) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController: Perform a customized DEA based on user input on web interface.
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
runGeeq(Long, String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
RUNNING - ubic.gemma.core.job.SubmittedTask.Status

S

SAGE - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SAGE - ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
SAGENlaIII - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SAGERsaI - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SAGESau3A - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
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(BioAssaySet, SampleCoexpressionMatrix, SampleCoexpressionMatrix) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis
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
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(BioAssayDimension, byte[]) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
SampleCoexpressionRelatedPreprocessingException - Exception 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 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
sampleInfoMatrix(List<ExperimentalFactor>, List<BioMaterial>, Map<ExperimentalFactor, FactorValue>) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils
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
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
sampleTypeSet(String, String) - Method in class ubic.gemma.core.loader.expression.geo.GeoFamilyParser
SARST - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SARST - ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
save(C) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
save(Collection<C>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
save(Collection<O>) - Method in class ubic.gemma.persistence.service.AbstractService
save(Collection<O>) - Method in interface ubic.gemma.persistence.service.BaseService
save(Collection<T>) - Method in class ubic.gemma.persistence.service.AbstractDao
save(Collection<T>) - Method in interface ubic.gemma.persistence.service.BaseDao: Save all the given entities in the persistent storage.
save(Collection<GeneSet>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
save(O) - Method in class ubic.gemma.persistence.service.AbstractService
save(O) - Method in interface ubic.gemma.persistence.service.BaseService
save(T) - Method in class ubic.gemma.persistence.service.AbstractDao
save(T) - Method in interface ubic.gemma.persistence.service.BaseDao: Create or update an entity whether it is transient.
save(GeneSet) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
saveLinksToDb(LinkAnalysis) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersister: Persist links to the database.
saveLinksToDb(LinkAnalysis) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersisterImpl
saveMessage(HttpServletRequest, String) - Method in class ubic.gemma.web.controller.BaseController
saveMessage(HttpServletRequest, String) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.
saveMessage(HttpServletRequest, String) - Method in interface ubic.gemma.web.util.MessageUtil: Put a message into the session.
saveMessage(HttpServletRequest, String) - Method in class ubic.gemma.web.util.MessageUtilImpl
saveMessage(HttpServletRequest, String, Object[], String) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.
saveMessage(HttpServletRequest, String, Object[], String) - Method in interface ubic.gemma.web.util.MessageUtil: Put a message into the session.
saveMessage(HttpServletRequest, String, Object[], String) - Method in class ubic.gemma.web.util.MessageUtilImpl
saveMessage(HttpServletRequest, String, Object, String) - Method in class ubic.gemma.web.controller.BaseController
saveMessage(HttpServletRequest, String, Object, String) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.
saveMessage(HttpServletRequest, String, Object, String) - Method in interface ubic.gemma.web.util.MessageUtil: Put a message into the session.
saveMessage(HttpServletRequest, String, Object, String) - Method in class ubic.gemma.web.util.MessageUtilImpl
saveMessage(HttpServletRequest, String, String) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.
saveMessage(HttpServletRequest, String, String) - Method in interface ubic.gemma.web.util.MessageUtil: Put a message into the session.
saveMessage(HttpServletRequest, String, String) - Method in class ubic.gemma.web.util.MessageUtilImpl
saveMessage(HttpSession, String) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.
saveMessage(HttpSession, String) - Method in interface ubic.gemma.web.util.MessageUtil: Put a message into the session.
saveMessage(HttpSession, String) - Method in class ubic.gemma.web.util.MessageUtilImpl
saver() - Method in class ubic.gemma.core.util.Pointcuts: This is a specially behaved method that create transient entities or save persistent one.
saveResultSets(Collection<Long>, String, String) - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
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
saveUser(UserValueObject) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.UserListController: Save or create the user.
saveUser(UserValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserListControllerImpl
scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser
scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
scalar(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
ScalarContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
scalarDivideMatrix(ExpressionDataDoubleMatrix, double) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil: Divide all values by the dividend
ScaleType - Enum in ubic.gemma.model.common.quantitationtype
ScaleTypeConverter - Class in ubic.gemma.web.remote
ScaleTypeConverter() - Constructor for class ubic.gemma.web.remote.ScaleTypeConverter
ScanDateExtractor - Interface in ubic.gemma.core.analysis.preprocess.batcheffects: Generic interface for classes that extract scan dates from raw data files.
scheduleDiffExpSearchTask(Long, ExpressionExperimentSetValueObject, GeneSetValueObject) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionSearchController: AJAX - method used for main display metaheatmap.
scope - Variable in class ubic.gemma.web.taglib.ConstantsTag: The scope to be put the variable in.
score() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult: Based on the JKSrc method in psl.c, but without double-penalizing for mismatches.
scoreResults(Collection<BlatAssociation>) - 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.
ScoreValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
ScoreValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject
ScoreValueObject(Double, String, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject
SCRNA - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
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.core.annotation.reference.BibliographicReferenceService
search(String) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
search(String, String) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
search(SearchSettings) - Method in interface ubic.gemma.core.search.SearchService: The results are sorted in order of decreasing score, organized by class.
search(SearchSettings) - Method in class ubic.gemma.core.search.SearchServiceImpl
search(SearchSettingsValueObject) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
search(SearchSettingsValueObject) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
search(SearchSettingsValueObject) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
search(SearchSettingsValueObject) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
search(QueryArg, TaxonArg<?>, PlatformArg<?>, List<String>, LimitArg, ExcludeArg<SearchResult<?>>) - Method in class ubic.gemma.rest.SearchWebService: Search everything subject to taxon and platform constraints.
searchAndRetrieveByHTTP(Collection<String>) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch: Search based on terms
searchAndRetrieveIdByHTTP(Collection<String>) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearch
searchAndRetrieveIdsByHTTP(String) - 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.
searchAndRetrieveIdsByHTTP(Collection<String>) - 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.
searchAnnotations(StringArrayArg) - Method in class ubic.gemma.rest.AnnotationsWebService: Does a search for annotation tags based on the given string.
searchAnnotationsByPathQuery(StringArrayArg) - Method in class ubic.gemma.rest.AnnotationsWebService
searchArrayDesign(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
searchArrayDesign(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchArrayDesign(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource: A general search for array designs.
searchArrayDesign(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchBibliographicReference(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
searchBibliographicReference(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchBibliographicReference(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchBibRefs(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
searchBibRefs(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
searchBioSequence(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
searchBioSequence(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchBioSequence(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource: A database search for biosequences.
searchBioSequence(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>) - Method in interface ubic.gemma.core.search.SearchSource: Deprecated.
use SearchSource.searchBioSequence(SearchSettings) (SearchSettings)} instead
searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>) - Method in class ubic.gemma.core.search.source.CompositeSearchSource: Deprecated.
searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchBlacklistedEntities(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
searchBlacklistedEntities(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchBlacklistedEntities(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchCompositeSequence(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
searchCompositeSequence(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchCompositeSequence(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchCompositeSequence(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchCompositeSequenceAndGene(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource: Deprecated.
use SearchSource.searchCompositeSequence(SearchSettings) instead
searchCompositeSequenceAndGene(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource: Deprecated.
searchCompositeSequenceAndGene(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource: Search the DB for composite sequences and the genes that are matched to them.
searchDatasets(StringArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.AnnotationsWebService: Does a search for datasets containing characteristics matching the given string.
searchDatasetsByQueryInPath(StringArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.AnnotationsWebService
SearchException - Exception in ubic.gemma.core.search: Exception raised by the SearchService when the search could not be performed.
SearchException(String, Throwable) - Constructor for exception ubic.gemma.core.search.SearchException
SearchException(Throwable) - Constructor for exception ubic.gemma.core.search.SearchException
searchExperimentsAndExperimentGroups(String, Long) - Method in interface ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchService: does not include session bound sets
searchExperimentsAndExperimentGroups(String, Long) - Method in class ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchServiceImpl
searchExperimentsAndExperimentGroups(String, Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX (used by experimentAndExperimentGroupCombo.js)
searchExperimentSet(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
searchExperimentSet(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchExperimentSet(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchExperimentSet(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchExpressionExperiment(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
searchExpressionExperiment(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchExpressionExperiment(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource: Does search on exact string by: id, name and short name.
searchExpressionExperiment(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchExpressionExperiment(SearchSettings) - Method in class ubic.gemma.core.search.source.OntologySearchSource: Search via characteristics i.e.
searchExpressionExperiments(String) - Method in interface ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchService
searchExpressionExperiments(String) - Method in class ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchServiceImpl
searchExpressionExperiments(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX (used by ExperimentCombo.js)
searchExpressionExperiments(String, Long) - Method in interface ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchService
searchExpressionExperiments(String, Long) - Method in class ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchServiceImpl
searchExpressionExperiments(List<String>) - Method in interface ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchService
searchExpressionExperiments(List<String>) - Method in class ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchServiceImpl
searchGene(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
searchGene(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchGene(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource: Search the DB for genes that exactly match the given search string searches geneProducts, gene and bioSequence tables
searchGene(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchGenes(String, Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneCoreService: Search for genes (by name or symbol)
searchGenes(String, Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
searchGenes(String, Long) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl: Search for genes (by name or symbol)
searchGenes(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX (used by GeneCombo.js)
searchGenesAndGeneGroups(String, Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneSearchService
searchGenesAndGeneGroups(String, Long) - Method in class ubic.gemma.core.genome.gene.service.GeneSearchServiceImpl
searchGenesAndGeneGroups(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX (used by GeneAndGeneGroupCombo.js)
searchGeneSet(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
searchGeneSet(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
searchGeneSet(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
searchGeneSet(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
searchGenesWithNCBIId(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX (used by Phenocarta)
searchGeoRecords(String, int, int, boolean) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowserService
searchGeoRecords(String, int, int, boolean) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
searchInDatabaseForPhenotype(String, int) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

For a given search string find all Ontology terms related, and then count their gene occurrence by taxon, including ontology children terms
searchInDatabaseForPhenotype(String, int) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
searchMultipleGenes(String, Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneSearchService: Search for multiple genes at once.
searchMultipleGenes(String, Long) - Method in class ubic.gemma.core.genome.gene.service.GeneSearchServiceImpl
searchMultipleGenes(String, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX Search for multiple genes at once.
searchMultipleGenesGetMap(Collection<String>, Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneSearchService: Search for multiple genes at once.
searchMultipleGenesGetMap(Collection<String>, Long) - Method in class ubic.gemma.core.genome.gene.service.GeneSearchServiceImpl
searchMultipleGenesGetMap(Collection<String>, Long) - Method in class ubic.gemma.web.controller.genome.gene.GenePickerController: AJAX Search for multiple genes at once.
searchOntologyForPhenotypes(String, Long) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Giving a phenotype searchQuery, returns a selection choice to the user
searchOntologyForPhenotypes(String, Long) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
searchOntologyForPhenotypes(String, Long) - Method in class ubic.gemma.web.controller.PhenotypeController: Returns all phenotypes satisfied the given search criteria.
SearchResult<T extends Identifiable> - Class in ubic.gemma.core.search: Represents an individual search result.
SearchResult() - Constructor for class ubic.gemma.core.search.SearchResult
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 extends Identifiable> - Class in ubic.gemma.core.search: This is a special kind of set designed for holding SearchResult.
SearchResultSet(SearchSettings) - Constructor for class ubic.gemma.core.search.SearchResultSet
SearchResultSet(SearchSettings, int) - Constructor for class ubic.gemma.core.search.SearchResultSet
SearchResultsResponseDataObject(List<SearchWebService.SearchResultValueObject<?>>, SearchWebService.SearchSettingsValueObject) - Constructor for class ubic.gemma.rest.SearchWebService.SearchResultsResponseDataObject
SearchResultValueObject(SearchResult<T>) - Constructor for class ubic.gemma.rest.SearchWebService.SearchResultValueObject
SearchResultValueObject(SearchResult<T>) - Constructor for class ubic.gemma.web.controller.GeneralSearchController.SearchResultValueObject
SearchService - Interface in ubic.gemma.core.search
SearchService.SearchResultMap - Interface in ubic.gemma.core.search
SearchServiceImpl - Class in ubic.gemma.core.search: This service is used for performing searches using free text or exact matches to items in the database.
SearchServiceImpl() - Constructor for class ubic.gemma.core.search.SearchServiceImpl
SearchSettings - Class in ubic.gemma.model.common.search: Configuration options for searching.
SearchSettings() - Constructor for class ubic.gemma.model.common.search.SearchSettings
SearchSettings.SearchMode - Enum in ubic.gemma.model.common.search
SearchSettingsValueObject - Class in ubic.gemma.model.common.search: author: anton date: 18/03/13
SearchSettingsValueObject() - Constructor for class ubic.gemma.model.common.search.SearchSettingsValueObject
SearchSettingsValueObject(SearchSettings) - Constructor for class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
SearchSource - Interface in ubic.gemma.core.search: Search source that provides SearchResult from a search engine.
searchTaxonDatasets(TaxonArg<?>, StringArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.AnnotationsWebService: Same as AnnotationsWebService.searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
searchTaxonDatasetsByQueryInPath(TaxonArg<?>, StringArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.AnnotationsWebService
SearchWebService - Class in ubic.gemma.rest: Provides search capabilities to the RESTful API.
SearchWebService() - Constructor for class ubic.gemma.rest.SearchWebService
SearchWebService.SearchResultsResponseDataObject - Class in ubic.gemma.rest
SearchWebService.SearchResultValueObject<T extends IdentifiableValueObject<?>> - Class in ubic.gemma.rest: Representation of SearchResult for the RESTful API.
SearchWebService.SearchSettingsValueObject - Class in ubic.gemma.rest: Represents search settings for the RESTful API.
SecureMethodInvokingJobDetailFactoryBean - Class in ubic.gemma.web.scheduler: Specialization of Spring task-running support so task threads have secure context (without using MODE_GLOBAL!).
SecureMethodInvokingJobDetailFactoryBean() - Constructor for class ubic.gemma.web.scheduler.SecureMethodInvokingJobDetailFactoryBean
SecurityController - Interface in ubic.gemma.web.controller.common.auditAndSecurity: Note: do not use parameterized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
SecurityControllerImpl - Class in ubic.gemma.web.controller.common.auditAndSecurity: Manages data-level security (ie.
SecurityControllerImpl() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
SecurityInfoValueObject - Class in ubic.gemma.web.controller.common.auditAndSecurity: Carries extensive security information about an entity.
SecurityInfoValueObject() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
SecurityInfoValueObject(Securable) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
send(SimpleMailMessage) - Method in class ubic.gemma.core.util.DummyMailSender
send(SimpleMailMessage[]) - Method in class ubic.gemma.core.util.DummyMailSender
sendAdminMessage(String, String) - Method in interface ubic.gemma.persistence.util.MailEngine: Send an email message to the administrator.
sendAdminMessage(String, String) - Method in class ubic.gemma.persistence.util.MailEngineImpl: Sends a message to the gemma administrator as defined in the Gemma.properties file
sendConfirmationEmail(HttpServletRequest, String, String, String, Map<String, Object>, String) - Method in class ubic.gemma.web.controller.BaseController
sendEvent(String, String...) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider: Publish an event without specifying a date.
sendEvent(String, Date, String...) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider: Publish an event with additional parameters expressed as a sequence of keys and values.
sendEvent(String, Date, Map<String, String>) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider: Publish an event.
sendEvent(String, Date, Map<String, String>) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
sendMessage(String, String, String) - Method in interface ubic.gemma.persistence.util.MailEngine: Send a text email message.
sendMessage(String, String, String) - Method in class ubic.gemma.persistence.util.MailEngineImpl
sendMessage(String, String, String, Map<String, Object>) - Method in interface ubic.gemma.persistence.util.MailEngine: Send a templated email message.
sendMessage(String, String, String, Map<String, Object>) - Method in class ubic.gemma.persistence.util.MailEngineImpl
sendTaskCompletedNotificationEmail(EmailNotificationContext, TaskResult) - Method in interface ubic.gemma.core.util.MailUtils
sendTaskCompletedNotificationEmail(EmailNotificationContext, TaskResult) - Method in class ubic.gemma.core.util.MailUtilsImpl
SEQUENCE - ubic.gemma.model.common.description.DatabaseType
SequenceBinUtils - Class in ubic.gemma.persistence.util: 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.persistence.util.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
SequenceSimilaritySearchResult - Class in ubic.gemma.model.genome.sequenceAnalysis
SequenceSimilaritySearchResult() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult: No-arg constructor added to satisfy javabean contract
SequenceType - Enum in ubic.gemma.model.genome.biosequence
SequenceTypePropertyEditor - Class in ubic.gemma.web.propertyeditor
SequenceTypePropertyEditor() - Constructor for class ubic.gemma.web.propertyeditor.SequenceTypePropertyEditor
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 - ubic.gemma.model.expression.arrayDesign.TechnologyType: Indicate the platform is based on sequencing (e.g.
serialize(FactorValueBasicValueObject, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer
serialize(FactorValueValueObject, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer
seriesFetcher - Variable in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
SeriesFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher
SeriesFetcher() - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.SeriesFetcher
service - Variable in class ubic.gemma.rest.util.args.AbstractEntityArgService
ServiceBasedEntityConverter<O extends Identifiable> - Class in ubic.gemma.persistence.util: Performs conversion by identifier and collection of identifier for a BaseReadOnlyService.
ServiceBasedEntityConverter(BaseReadOnlyService<? extends O>, Class<O>) - Constructor for class ubic.gemma.persistence.util.ServiceBasedEntityConverter
ServiceBasedValueObjectConverter<O extends Identifiable,VO extends IdentifiableValueObject<O>> - 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<O, ? extends VO>, Class<O>, Class<VO>) - Constructor for class ubic.gemma.persistence.util.ServiceBasedValueObjectConverter
serviceMethod() - Method in class ubic.gemma.core.util.Pointcuts: A public method defined in a service.
ServiceUnavailableException - Exception in ubic.gemma.web.util
ServiceUnavailableException(String) - Constructor for exception ubic.gemma.web.util.ServiceUnavailableException
ServletMetricsFilter - Class in ubic.gemma.web.metrics.binder.servlet: Metrics for servlet requests.
ServletMetricsFilter() - Constructor for class ubic.gemma.web.metrics.binder.servlet.ServletMetricsFilter
ServletUtils - Class in ubic.gemma.rest.util
ServletUtils() - Constructor for class ubic.gemma.rest.util.ServletUtils
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.core.genome.gene
SessionBoundGeneSetValueObject() - Constructor for class ubic.gemma.core.genome.gene.SessionBoundGeneSetValueObject: default constructor to satisfy java bean contract
sessionCreated(HttpSessionEvent) - Method in class ubic.gemma.web.listener.UserCounterListener
sessionDestroyed(HttpSessionEvent) - Method in class ubic.gemma.web.listener.UserCounterListener
SessionListManager - Interface in ubic.gemma.web.persistence
SessionListManagerImpl - Class in ubic.gemma.web.persistence
SessionListManagerImpl() - Constructor for class ubic.gemma.web.persistence.SessionListManagerImpl
set(int, int, Boolean) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
set(int, int, Double) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
set(int, int, Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
set(int, int, Object) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
set(int, int, String) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
set(int, int, T) - Method in interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix: Set a value in the matrix, by index
set(CompositeSequence, BioAssay, Double) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
set_id(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
set_id(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
set_is_leaf(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
set_parent(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
setAbaGeneImageUrl(Collection<String>) - Method in class ubic.gemma.core.image.ABALinkOutValueObject
setAbaGeneUrl(String) - Method in class ubic.gemma.core.image.ABALinkOutValueObject
setAbsentPresentCalls(ExpressionDataBooleanMatrix) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter: Supply a separate matrix of booleans.
setAbsoluteValue(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setAbstractText(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setAbstractText(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setAccessDenied(boolean) - Method in class ubic.gemma.model.BaseValueObject
setAccessDenied(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setAccession(String) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setAccession(String) - Method in class ubic.gemma.model.common.description.DatabaseEntry
setAccession(String) - Method in class ubic.gemma.model.expression.BlacklistedValueObject
setAccession(String) - Method in class ubic.gemma.web.controller.common.description.bibref.PubMedSearchCommand
setAccession(DatabaseEntry) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setAccession(DatabaseEntry) - Method in class ubic.gemma.model.expression.experiment.BioAssaySet
setAccession(DatabaseEntryValueObject) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setAccessions(Collection<NCBIGene2Accession>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
setAccessions(Set<DatabaseEntry>) - Method in class ubic.gemma.model.genome.gene.GeneProduct
setAccessions(Set<DatabaseEntry>) - Method in class ubic.gemma.model.genome.Gene
setAccessionVersion(String) - Method in class ubic.gemma.model.common.description.DatabaseEntry
setAccToDatasetOrPlatformMap(Map<String, String>) - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
setAccToTitleMap(Map<String, String>) - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
setAction(String) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setActiveExperiments(Collection<BioAssaySet>) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setAdditionalPropertyUris(Set<String>) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Set the URIs used for inferring additional properties.
setAdditionalTaxa(Collection<Taxon>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt: Method to format taxon list for display.
setAddress(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setAdminUser(Boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setAdvertisedNumberOfDesignElements(Integer) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setAfterDistinctValueCut(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setAfterInitialFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setAfterLowExpressionCut(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setAfterLowVarianceCut(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setAfterMinPresentFilter(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setAfterZeroVarianceCut(int) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setAggressiveQtRemoval(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setAlias(String) - Method in class ubic.gemma.model.genome.gene.GeneAlias
setAliases(Set<GeneAlias>) - Method in class ubic.gemma.model.genome.Gene
setAll(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand: Indexing of probes and BioSequences sometimes bails because of the size of the index created.
setAll(Boolean) - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
setAllCharacteristics(Set<Characteristic>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setAllowArrayExpressDesign(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setAllowCredentials(boolean) - Method in class ubic.gemma.rest.servlet.CorsFilter: Indicate if the credentials (i.e.
setAllowedHeaders(String) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the allowed headers by a CORS request.
setAllowedMethods(String) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the allowed methods by a CORS request.
setAllowedOrigins(String) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the allowed origins of a CORS request.
setAllowModification(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setAllowPositionalArguments(boolean) - Method in class ubic.gemma.core.util.AbstractCLI: Allow positional arguments to be specified.
setAllowPredictedGenes(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
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
setAllParentsAnnotationLink(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
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
setAlternateNames(Collection<String>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setAlternateNames(Set<AlternateName>) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setAlternative(ArrayDesignValueObject) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
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.IncludedResultSetInfoValueObject
setAnalysisId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setAnalysisNotRun(boolean) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setAnalysisObj(CoexpressionAnalysis) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
setAnalysisType(DifferentialExpressionAnalyzerServiceImpl.AnalysisType) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setAnalysisType(DifferentialExpressionAnalyzerServiceImpl.AnalysisType) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
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.
setAnnotation(String) - Method in class ubic.gemma.persistence.model.Gene2CsStatus
setAnnotations(Set<Characteristic>) - Method in class ubic.gemma.model.common.description.BibliographicReference: Deprecated.
setAnnotations(Set<Characteristic>) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor: Deprecated.
setAnnotationValueObjects(Collection<AnnotationValueObject>) - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
setApplicationContext(ApplicationContext) - Method in class ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl
setApplicationContext(ApplicationContext) - Method in class ubic.gemma.core.metrics.MeterRegistryCliConfigurer
setArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
setArrayDesign(ArrayDesign) - Method in class ubic.gemma.model.expression.designElement.CompositeSequence
setArrayDesign(ArrayDesign) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
setArrayDesign(ArrayDesign) - Method in class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
setArrayDesign(ArrayDesignValueObject) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setArrayDesign(ArrayDesignValueObject) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
setArrayDesignId(Long) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setArrayDesignIds(Collection<Long>) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setArrayDesignMatchesDataFile(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setArrayDesignMismatchProblemMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setArrayDesignName(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setArrayDesignName(String) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setArrayDesignName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setArrayDesigns(Collection<ArrayDesign>) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setArrayDesigns(Collection<ArrayDesignValueObject>) - 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.
setArrayDesignService(ArrayDesignService) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
setArrayDesignService(ArrayDesignService) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
setArrayDesignService(ArrayDesignService) - Method in class ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint: Sets the "business service" to delegate to.
setArrayDesignService(ArrayDesignService) - Method in class ubic.gemma.web.services.Probe2GeneEndpoint
setArrayDesignShortName(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setArrayDesignUsed(ArrayDesign) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setArrayExpress(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setArrayName(String) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setAsNonSignficant(Long, Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject: Mark data as available, but not significant (so details will be missing).
setAssociationType(Characteristic) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setAsText(String) - Method in class ubic.gemma.web.propertyeditor.ArrayDesignPropertyEditor
setAsText(String) - Method in class ubic.gemma.web.propertyeditor.QuantitationTypePropertyEditor
setAsText(String) - Method in class ubic.gemma.web.propertyeditor.SequenceTypePropertyEditor
setAsText(String) - Method in class ubic.gemma.web.propertyeditor.TaxonPropertyEditor: Allow us to convert from either an id or the scientific name.
setAttribute(String) - Method in class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy: Set the attribute to retrieve to obtain the client ID.
setAttribute(String, Object) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
setAttribute(String, Object, int) - Method in class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
setAuditTrail(AuditTrail) - Method in class ubic.gemma.model.common.AbstractAuditable
setAuditTrail(AuditTrail) - Method in interface ubic.gemma.model.common.Auditable
setAuditTrail(AuditTrail) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setAuditTrailService(AuditTrailService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
setAuthorities(Set<GroupAuthority>) - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup
setAuthority(String) - Method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority
setAuthority(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
setAuthorList(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setAuthorList(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setAutoLoad(boolean) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Enable loading of ontologies on startup.
setAutoRunFrequencyHours(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
setAvailableGroups(Collection<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setAvoidDownload(boolean) - Method in class ubic.gemma.core.loader.util.fetcher.FtpFetcher
setBaselineFactorValue(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setBaselineFactorValueId(Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setBaseLineFactorValues(Map<ExperimentalFactor, FactorValue>) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setBaselineGroup(FactorValue) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setBaselineGroup(FactorValueBasicValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
setBatchConfound(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setBatchCorrected(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
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
setBatchEffectStatistics(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setBatchFetchEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setBeanFactory(BeanFactory) - Method in class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
setBibliographicPhenotypes(Collection<BibliographicPhenotypesValueObject>) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setBibliographicReferenceService(BibliographicReferenceService) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
setBin(Integer) - Method in class ubic.gemma.model.genome.PhysicalLocation
setBin(Integer) - Method in class ubic.gemma.model.genome.PhysicalLocationValueObject
setBinCounts(byte[]) - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution
setBinCounts(byte[]) - 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.DesignElementDataVector
setBioAssayDimension(BioAssayDimensionValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
setBioAssayIds(Collection<Long>) - Method in class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
setBioAssays(Collection<BioAssayValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
setBioAssays(Collection<BioAssayValueObject>) - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
setBioAssays(List<BioAssay>) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension
setBioAssays(Set<BioAssay>) - Method in class ubic.gemma.model.expression.experiment.BioAssaySet
setBioAssayService(BioAssayService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
setBioAssaysUsedIn(Set<BioAssay>) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
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
setBioMaterialIds(Long[]) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
setBioMaterialProvider(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setBioMaterialService(BioMaterialService) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
setBioMaterialService(BioMaterialService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
setBioProcessAnnotationLink(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setBioSequence(BioSequence) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setBioSequence2GeneProduct(Set<BioSequence2GeneProduct>) - 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
setBlatResult(BlatResult) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
setBlatResult(BlatResultValueObject) - Method in class ubic.gemma.core.analysis.sequence.GeneMappingSummary
setBlatResults(Collection<BlatResult>) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
setBlatScoreThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setBlatScoreThreshold(double) - Method in interface ubic.gemma.core.apps.Blat
setBlatScoreThreshold(double) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
setBlockCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setBlockCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
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.web.feed.NewsItem
setBytes(byte[]) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
setBytesRead(long) - Method in class ubic.gemma.web.util.upload.UploadInfo
setCacheMonitor(CacheMonitor) - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
setCanEdit(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
setCatalogNumbers(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setCategory(String) - Method in class ubic.gemma.model.common.description.Characteristic
setCategory(Characteristic) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setCategoryUri(String) - Method in class ubic.gemma.model.common.description.Characteristic
setCdfCut(double) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setChannel(String) - Method in class ubic.gemma.web.logging.SlackAppender
setChannelCount(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setChannelNumber(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setChannels(List<GeoChannel>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setCharacteristic(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setCharacteristics(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setCharacteristics(Set<Characteristic>) - Method in class ubic.gemma.model.analysis.Investigation
setCharacteristics(Set<Characteristic>) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setCharacteristics(Set<Characteristic>) - Method in class ubic.gemma.model.genome.gene.GeneSet
setCharacteristics(Set<Statement>) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setCheckCorrelationDistribution(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setCheckForBatchEffect(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setCheckForOutliers(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setChemicals(Set<Compound>) - Method in class ubic.gemma.model.common.description.BibliographicReference
setChildren(List<String>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject: Not used directly in java, allow constructor to manage.
setChildren(TreeSet<TreeCharacteristicValueObject>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
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(BibliographicReference) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication: Deprecated.
setCitation(BibliographicReference) - Method in class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
setCitation(CitationValueObject) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setCitationValueObject(CitationValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
setCity(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setClassDelegatingFor(String) - Method in class ubic.gemma.web.remote.EntityDelegator
setClassName(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setClassName(String) - Method in class ubic.gemma.web.taglib.ConstantsTag
setClientIdRetrievalStrategy(ClientIdRetrievalStrategy) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Set the strategy used to retrieve client IDs.
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
setCoexGeneSymbol(String) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
setCoexpCorrelationDistribution(CoexpCorrelationDistribution) - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis
setCoexpNodeDegree(GeneCoexpressionNodeDegreeValueObject) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
setCoexpressionMatrix(byte[]) - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
setCol(Integer) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
setColor(String) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setColorString(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setCommonName(String) - Method in class ubic.gemma.model.genome.Taxon
setCommonName(String) - Method in class ubic.gemma.model.genome.TaxonValueObject
setCompassOn(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
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.core.analysis.sequence.GeneMappingSummary
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<CompositeSequence>) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setCompositeSequenceService(CompositeSequenceService) - Method in class ubic.gemma.web.services.ExperimentDEDVEndpoint
setCompositeSequenceService(CompositeSequenceService) - Method in class ubic.gemma.web.services.Gene2ProbeEndpoint
setCompositeSequenceService(CompositeSequenceService) - Method in class ubic.gemma.web.services.Probe2GeneEndpoint: Sets the "business service" to delegate to.
setConfirmNewPassword(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setContact(GeoContact) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setContactName(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setContainQueryPhenotype(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setContainsMyData(Boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setContrasts(Set<ContrastResult>) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setContrasts(ContrastsValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setContrastsFactorValues(Map<Long, String>) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setContributer(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setContributers(Collection<GeoContact>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setCookie(HttpServletResponse, String, String, String) - Static method in class ubic.gemma.web.util.RequestUtil
setCorrectedPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setCorrectedPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setCorrectedPValueBin(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setCorrelationCacheThreshold(double) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setCorrespondingExperiments(Collection<Long>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setCorrMatIssues(byte) - Method in class ubic.gemma.model.expression.experiment.Geeq
setCorrP(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setCount(int) - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
setCountry(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
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
setCurationNote(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setCurationNote(String) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setCurrentGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setCurrentGroup(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setCurrentGroupCanRead(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setCurrentGroupCanWrite(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setCurrentUserCanwrite(Boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setCurrentUserHasWritePermission(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
setCurrentUserIsOwner(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
setCurrentUserOwns(Boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setData(byte[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setData(double[]) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setDatabaseEntry(DatabaseEntry) - Method in class ubic.gemma.web.taglib.DatabaseEntryTag
setDatabaseEntryValueObject(DatabaseEntryValueObject) - Method in class ubic.gemma.web.taglib.DatabaseEntryTag
setDatabaseSupplier(Contact) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setDataFileFormatProblemMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setDataFileIsValidFormat(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setDataMatrix(ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
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
setDatasetFetcher(Fetcher) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
setDatasetId(Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setDatasetLink(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setDatasetName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setDataSets(Collection<GeoDataset>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setDatasetsAvailable(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
setDatasetShortName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setDatasetsTested(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
setDatasetType(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setDate(Date) - Method in class ubic.gemma.core.analysis.report.AuditableObject
setDate(Date) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setDate(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setDate(Date) - Method in class ubic.gemma.web.feed.NewsItem
setDateArrayDesignLastUpdated(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDateBatchFetch(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDateCached(Date) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDateCorrelations(Map<Integer, Double>) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
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
setDbPhenotype(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
setDbPhenotype(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
setDebug(boolean) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Enable the debug mode.
setDedvId(Long) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setDefaultSymbol(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
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
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.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.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.common.AbstractDescribable
setDescription(String) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setDescription(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setDescription(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setDescription(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
setDescription(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setDescription(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setDescriptionInvalidSymbol(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setDesignElement(CompositeSequence) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
setDesignElement(CompositeSequence) - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
setDesignElement(CompositeSequenceValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
setDesignProvider(Contact) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setDetail(String) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setDetectedQualityScore(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setDetectedSuitabilityScore(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
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)
setDifferentialExpressionAnalyses(Collection<DifferentialExpressionAnalysisValueObject>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setDifferentialExpressionResultService(DifferentialExpressionResultService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint
setDiffExpressionEvidence(DiffExpressionEvidenceValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setDir(String) - Method in class ubic.gemma.web.remote.ListBatchCommand
setDirection(Direction) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setDirection(Direction) - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
setDirty(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setDirty(boolean) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
setDiscontinuedId(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
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
setDone(boolean) - Method in class ubic.gemma.core.job.progress.ProgressData
setDoSampleMatching(boolean) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
setDummy(boolean) - Method in class ubic.gemma.model.genome.gene.GeneProduct
setDuplicateMap(Map<CompositeSequence, Set<Gene>>) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
setDuplicateMap(Map<CompositeSequence, Set<Gene>>) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
setEdit(String) - Method in class ubic.gemma.web.taglib.expression.experiment.AssayViewTag
setEditable(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
setEditor(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setEe(Long) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: The id of the EE to display QC info
setEeCountPerTaxon(Map<Taxon, Long>) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setEeId(Long) - Method in class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
setEeId(Long) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setEeIds(Collection<Long>) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setEeIds(Collection<Long>) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
setEeManagerId(String) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setEeQuery(String) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setEeQuery(String) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
setEeSetId(Long) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setEeSetId(Long) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
setEeSetName(String) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setEeSetName(String) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
setEevo(ExpressionExperimentDetailsValueObject) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setEEwithPvalue(ExpressionExperimentDetailsValueObject, Double) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setEfId(Long) - Method in class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand
setEigenValues(Set<Eigenvalue>) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setEigenVectors(Set<Eigenvector>) - 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.model.common.auditAndSecurity.Contact
setEmail(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setEmail(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setEmailAlert(boolean) - Method in class ubic.gemma.core.job.TaskCommand
setEnableAuthorities(boolean) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
setEnabled(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
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
setEnabled(Boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
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
setEnsemblPeptideId(String) - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
setEnsemblTranscriptId(String) - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
setEntityClazz(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setEntityDescription(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setEntityId(Long) - Method in class ubic.gemma.core.job.TaskCommand
setEntityId(Long) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setEntityName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setEntityShortName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setError(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
setError(Exception) - Method in class ubic.gemma.persistence.model.Gene2CsStatus
setErrorCategory(String) - Method in class ubic.gemma.web.util.UnhandledExceptionResolver: Set the name of the logger to use for reporting unhandled exceptions.
setErrorFound(boolean) - Method in class ubic.gemma.model.BaseValueObject
setErrorMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
setErrorState(String) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
setErrorView(String) - Method in class ubic.gemma.web.util.UnhandledExceptionResolver: Set the view to use for reporting unhandled exception.
setEvents(List<AuditEvent>) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
setEventType(AuditEventType) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setEvidence(Collection<EvidenceValueObject<? extends PhenotypeAssociation>>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject: Deprecated.
setEvidenceCode(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setEvidenceCode(GOEvidenceCode) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setEvidenceCode(GOEvidenceCode) - Method in class ubic.gemma.model.common.description.Characteristic
setEvidenceId(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
setEvidenceNotFound(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setEvidenceSecurityValueObject(EvidenceSecurityValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setEvidenceSource(DatabaseEntry) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setEvidenceSource(EvidenceSourceValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setException(Exception) - Method in class ubic.gemma.core.job.TaskResult
setException(Exception) - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
setExcludePattern(String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher
setExons(Set<PhysicalLocation>) - Method in class ubic.gemma.model.genome.gene.GeneProduct: Only used for transient instances, we do not store exon locations in the database.
setExperiment(Investigation) - Method in class ubic.gemma.model.association.phenotype.ExperimentalEvidence: Deprecated.
setExperiment(BioAssaySet) - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
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
setExperimentalDesignId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setExperimentalDesignName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setExperimentalFactor(ExperimentalFactor) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setExperimentalFactors(Collection<ExperimentalFactorValueObject>) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
setExperimentalFactors(Collection<ExperimentalFactorValueObject>) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setExperimentalFactors(Set<ExperimentalFactor>) - Method in class ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet
setExperimentalFactors(Set<ExperimentalFactor>) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setExperimentAnalyzed(BioAssaySet) - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis
setExperimentCharacteristics(Collection<CharacteristicValueObject>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject: Deprecated.
setExperimentId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject
setExperiments(Collection<ExpressionExperimentValueObject>) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setExperiments(Set<BioAssaySet>) - Method in class ubic.gemma.model.analysis.expression.ExpressionExperimentSet
setExperimentType(GeoDataset.ExperimentType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setExpressionDataMatrixService(ExpressionDataMatrixService) - Method in class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer
setExpressionDataMatrixService(ExpressionDataMatrixService) - Method in interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer: this is needed so we can alter this in tests
setExpressionDataMatrixService(ExpressionDataMatrixService) - Method in class ubic.gemma.web.services.DEDVRankEndpoint
setExpressionDataMatrixService(ExpressionDataMatrixService) - Method in class ubic.gemma.web.services.ExperimentDEDVEndpoint
setExpressionExperiment(BioAssaySet) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
setExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
setExpressionExperiment(ExpressionExperimentValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setExpressionExperiment(ExpressionExperimentValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
setExpressionExperiment(ExpressionExperimentValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
setExpressionExperimentId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setExpressionExperimentId(Long) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setExpressionExperimentIds(Collection<Long>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl
setExpressionExperimentService(ExpressionExperimentService) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ArrayDesignUsedEndpoint: Sets the "business service" to delegate to.
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.DEDVRankEndpoint
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentAnnotationEndpoint: Sets the "business service" to delegate to.
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentDEDVEndpoint: Sets the "business service" to delegate to.
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint: Sets the "business service" to delegate to.
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentIdEndpoint: Sets the "business service" to delegate to.
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentNameEndpoint: Sets the "business service" to delegate to.
setExpressionExperimentService(ExpressionExperimentService) - Method in class ubic.gemma.web.services.ExperimentNumSamplesEndpoint: Sets the "business service" to delegate to.
setExpressionExperimentSets(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setExpressionExperimentSetService(ExpressionExperimentSetService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint
setExpressionExperimentSetService(ExpressionExperimentSetService) - Method in class ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint: Sets the "business service" to delegate to.
setExpressionExperimentSetService(ExpressionExperimentSetService) - Method in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint
setExpressionExperimentValueObjectHelper(ExpressionExperimentSetValueObjectHelper) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
setExternalAccession(DatabaseEntry) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setExternalAccession(DatabaseEntry) - Method in class ubic.gemma.model.expression.BlacklistedEntity
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.expression.BlacklistedValueObject
setExternalDatabase(ExternalDatabaseValueObject) - Method in class ubic.gemma.model.genome.TaxonValueObject
setExternalDatabaseIds(Collection<Long>) - Method in class ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
setExternalDatabases(Set<ExternalDatabase>) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setExternalDatabaseService(ExternalDatabaseService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
setExternalReference(DatabaseEntry) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setExternalReferences(Set<DatabaseEntry>) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setExternalUrl(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSourceValueObject
setExtractProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setExtraMissingValueIndicators(Collection<Double>) - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
setFactor(Integer) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setFactorCategory(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setFactorCorrelations(Map<Integer, Map<Long, Double>>) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
setFactorDescription(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setFactorId(Long) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setFactorName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setFactorNames(LinkedHashMap<String, LinkedHashMap<String, String>>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setFactorProfiles(Collection<FactorProfile>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setFactors(Collection<ExperimentalFactor>) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setFactors(Collection<ExperimentalFactorValueObject>) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo
setFactors(List<String>) - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
setFactorsToInclude(Collection<ExperimentalFactor>) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setFactorsToInclude(List<ExperimentalFactor>) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setFactorValue(FactorValue) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setFactorValueMap(Map<String, String>) - Method in class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject
setFactorValues(List<List<String>>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setFactorValues(Set<FactorValue>) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setFactorValues(Set<FactorValue>) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setFactorValueService(FactorValueService) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
setFactorValuesToNames(List<LinkedHashMap<String, String[]>>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setFailed(boolean) - Method in class ubic.gemma.core.job.progress.ProgressData
setFailedMessage(String) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setFastqHeaders(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setFastWarningThresholdMillis(int) - Method in class ubic.gemma.core.search.source.CompositeSearchSource: Threshold in milliseconds for a warning to be logged when searching with SearchSettings.SearchMode.FAST.
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
setFile(byte[]) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
setFile(FileUpload) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
setFileIndex(int) - Method in class ubic.gemma.web.util.upload.UploadInfo
setFilter(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
setFilter(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setFirstGene(Long) - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
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
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.
setForceRewrite(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setFormat(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setForwardingURL(String) - Method in class ubic.gemma.core.job.progress.ProgressData
setFoundGene(GeneValueObject) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setFoundGeneNodeDegree(Integer) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setFoundGeneNodeDegreeRank(Double) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setFractionRepeats(Double) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setFractionRepeats(Double) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setFromCache(boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
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
setFwe(double) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setGeeq(Geeq) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setGene(Gene) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setGene(Gene) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
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
setGene2GOAssociationService(Gene2GOAssociationService) - Method in interface ubic.gemma.core.ontology.GoMetric
setGene2GOAssociationService(Gene2GOAssociationService) - Method in class ubic.gemma.core.ontology.GoMetricImpl
setGeneCoexpressionSearchService(GeneCoexpressionSearchService) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint
setGeneCoexpressionSearchService(GeneCoexpressionSearchService) - Method in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint
setGeneCoexpressionService(GeneCoexpressionSearchService) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint
setGeneDifferentialExpressionMetaAnalysisId(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setGeneDifferentialExpressionMetaAnalysisResult(GeneDifferentialExpressionMetaAnalysisResult) - Method in class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence: Deprecated.
setGeneDifferentialExpressionMetaAnalysisResultId(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setGeneDifferentialExpressionMetaAnalysisSummaryValueObject(GeneDifferentialExpressionMetaAnalysisSummaryValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setGeneId(long) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
setGeneId(Integer) - Method in class ubic.gemma.core.image.aba.AbaGene
setGeneId(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressedGenes
setGeneId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setGeneId(Long) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
setGeneId(Long) - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
setGeneId(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
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<Long>) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setGeneIds(Collection<Long>) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
setGeneIds(Collection<Long>) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setGeneInfo(NCBIGeneInfo) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
setGeneMappingSummaries(Collection<GeneMappingSummary>) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
setGeneName(String) - Method in class ubic.gemma.core.image.aba.AbaGene
setGeneName(String) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
setGeneName(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
setGeneNCBI(Integer) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
setGeneNCBI(Integer) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setGeneOfficialName(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setGeneOfficialSymbol(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setGeneOntologyService(GeneOntologyService) - Method in interface ubic.gemma.core.ontology.GoMetric
setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.core.ontology.GoMetricImpl
setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.web.services.Gene2GOdescriptionEndpoint: Sets the "business service" to delegate to.
setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.web.services.Gene2GoTermEndpoint: Sets the "business service" to delegate to.
setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.web.services.GeneOverlapEndpoint: Sets the "business service" to delegate to.
setGeneOntologyService(GeneOntologyService) - Method in class ubic.gemma.web.services.GoTerm2GeneEndpoint: Sets the "business service" to delegate to.
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<GeneProductValueObject, GeneValueObject>) - Method in class ubic.gemma.core.analysis.sequence.GeneMappingSummary
setGeneProducts(Collection<GeneProduct>) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
setGeneProducts(Map<Long, GeneProductValueObject>) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setGeneralType(GeneralType) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setGeneralType(GeneralType) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setGenes(Collection<Long>) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
setGenes(Collection<GeneValueObject>) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setGenes(Collection<Gene>) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
setGenes(Map<Long, GeneValueObject>) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
setGeneService(GeneService) - Method in class ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService
setGeneService(GeneService) - Method in class ubic.gemma.web.services.DEDVRankEndpoint: Sets the "business service" to delegate to.
setGeneService(GeneService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint
setGeneService(GeneService) - Method in class ubic.gemma.web.services.Gene2GOdescriptionEndpoint
setGeneService(GeneService) - Method in class ubic.gemma.web.services.Gene2GoTermEndpoint
setGeneService(GeneService) - Method in class ubic.gemma.web.services.Gene2ProbeEndpoint
setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneByNCBIIdEndpoint: Sets the "business service" to delegate to.
setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint
setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint
setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneDetailsByGeneIDEndpoint: Sets the "business service" to delegate to.
setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneIDbyTaxonEndpoint: Sets the "business service" to delegate to.
setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneIdEndpoint: Sets the "business service" to delegate to.
setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneNameEndpoint: Sets the "business service" to delegate to.
setGeneService(GeneService) - Method in class ubic.gemma.web.services.GeneOverlapEndpoint
setGeneSetId(Long) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setGeneSymbol(String) - Method in class ubic.gemma.core.image.aba.AbaGene
setGeneSymbol(String) - Method in class ubic.gemma.core.image.ABALinkOutValueObject
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
setGeneUrl(String) - Method in class ubic.gemma.core.image.aba.AbaGene
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 class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService
setGeoDomainObjectGenerator(GeoDomainObjectGenerator) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService
setGoId(String) - Method in class ubic.gemma.core.genome.gene.GOGroupValueObject
setGroupMembers(Set<User>) - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup
setGroupName(String) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
setGroupName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
setGroups(Set<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setGroups(Set<UserGroup>) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setGroupsThatCanRead(Collection<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setGroupsThatCanWrite(Collection<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setGrowthProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setHasBatchInformation(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasBothIntensities(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasCoexpressionAnalysis(Boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasCorrDist(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setHasCorrMat(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setHasDifferentialExpressionAnalysis(Boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasEitherIntensity(Boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasMeanVariance(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setHasMultiplePreferredQuantitationTypes(Boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasMultipleTechnologyTypes(Boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setHasNodeDegreeDist(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setHasPCA(boolean) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setHgnc_id(String) - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
setHibernateMonitor(HibernateMonitor) - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
setHighCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter: Set the high threshold for removal.
setHighExpressionCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setHistory(NcbiGeneHistory) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setHitListSizes(Set<HitListSize>) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setHomologeneFile(Resource) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceFactory: Set the resource used for loading Homologene.
setHomologueEvidence(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
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.preprocess.svd.SVDValueObject
setId(Long) - Method in class ubic.gemma.core.analysis.report.AuditableObject
setId(Long) - Method in class ubic.gemma.model.analysis.AnalysisResultSet
setId(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution
setId(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
setId(Long) - Method in class ubic.gemma.model.analysis.expression.coexpression.SupportDetails
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
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.GeneDifferentialExpressionMetaAnalysisResult
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
setId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.PvalueDistribution
setId(Long) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
setId(Long) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
setId(Long) - Method in class ubic.gemma.model.analysis.expression.pca.ProbeLoading
setId(Long) - Method in class ubic.gemma.model.association.BioSequence2GeneProduct
setId(Long) - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
setId(Long) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
setId(Long) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication: Deprecated.
setId(Long) - Method in class ubic.gemma.model.common.AbstractDescribable
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditTrail
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setId(Long) - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
setId(Long) - Method in class ubic.gemma.model.common.description.BibRefAnnotation
setId(Long) - Method in class ubic.gemma.model.common.description.CitationValueObject
setId(Long) - Method in class ubic.gemma.model.common.description.DatabaseEntry
setId(Long) - Method in class ubic.gemma.model.common.description.LocalFile
setId(Long) - Method in class ubic.gemma.model.common.measurement.Measurement
setId(Long) - Method in class ubic.gemma.model.common.measurement.Unit
setId(Long) - Method in class ubic.gemma.model.expression.arrayDesign.AlternateName
setId(Long) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setId(Long) - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
setId(Long) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setId(Long) - Method in interface ubic.gemma.model.GemmaSessionBackedValueObject
setId(Long) - Method in class ubic.gemma.model.genome.ChromosomeLocation
setId(Long) - Method in class ubic.gemma.model.genome.gene.GeneAlias
setId(Long) - Method in class ubic.gemma.model.genome.gene.GeneSetMember
setId(Long) - Method in class ubic.gemma.model.genome.gene.Multifunctionality
setId(Long) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
setId(Long) - Method in class ubic.gemma.model.genome.Taxon
setId(Long) - Method in class ubic.gemma.model.IdentifiableValueObject: Only used by the spring java-beans in jsp files.
setId(Long) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setId(Long) - Method in class ubic.gemma.web.remote.EntityDelegator
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
setIdentity(Double) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setIdentityThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setIgnoreMinimumRowsThreshold(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setIgnoreMinimumSampleThreshold(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setImages(List<Image>) - Method in class ubic.gemma.core.image.aba.ImageSeries
setImageSeries(Collection<ImageSeries>) - Method in class ubic.gemma.core.image.aba.AbaGene
setImageSeriesId(Integer) - Method in class ubic.gemma.core.image.aba.ImageSeries
setImmobilizedCharacteristic(BioSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
setIncludedResultSetsInfo(Collection<IncludedResultSetInfoValueObject>) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
setIncludeInteractions(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setIndex(Integer) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
setIndex(String) - Static method in class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo: Deprecated.
setIndexAD(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexBibRef(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexBioSequence(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexEE(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexExperimentSet(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexGene(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexGeneSet(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexOntologies(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexOntology(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setIndexProbe(boolean) - Method in class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
setInferenceMode(OntologyService.InferenceMode) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Set the inference mode for the ontology.
setInfo(NCBIGeneInfo) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setInGroup(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setInstitute(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setInteractionsToInclude(Collection<Collection<ExperimentalFactor>>) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setInterQueryLink(boolean) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
setIsApproximateLength(Boolean) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setIsBackground(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsBackgroundSubtracted(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
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.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setIsCircular(Boolean) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setIsContinuous(Boolean) - Method in class ubic.gemma.web.controller.visualization.FactorProfile
setIsGenesUsable(boolean) - Method in class ubic.gemma.model.genome.Taxon
setIsGenesUsable(Boolean) - Method in class ubic.gemma.model.genome.TaxonValueObject
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.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setIsNegativeEvidence(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setIsNegativeEvidence(Boolean) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setIsNormalized(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsOutlier(Boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setIsPreferred(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsProbeOmitted(boolean) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
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.ExpressionExperimentValueObject
setIsPublic(boolean) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setIsRatio(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsRatio(Boolean) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setIsRecomputedFromRawData(boolean) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setIsRNASeq(Boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
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.ExpressionExperimentValueObject
setIsShared(boolean) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
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
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
setJobs(Set<JobInfo>) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setJobs(Set<JobInfo>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setKeywords(Set<Keyword>) - Method in class ubic.gemma.model.common.description.BibliographicReference
setKeyWords(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setKindCV(MeasurementKind) - Method in class ubic.gemma.model.common.measurement.Measurement
setLabel(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setLabel(String) - Method in class ubic.gemma.web.util.LabelValue
setLabelProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setLaboratory(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
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
setLastName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.Person: Deprecated.
setLastName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setLastNeedsAttentionEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setLastNeedsAttentionEvent(AuditEventValueObject) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setLastNoteUpdateEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setLastNoteUpdateEvent(AuditEventValueObject) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setLastTroubledEvent(AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
setLastTroubledEvent(AuditEventValueObject) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setLastUpdate(Date) - Method in class ubic.gemma.persistence.model.Gene2CsStatus
setLastUpdated(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setLastUpdated(Date) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
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.description.ExternalDatabase
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
setLastUpdateDate(Date) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
setLastUpdateDifferent(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setLastUsed(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
setLength(Long) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setLength(Long) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setLibraryStrategy(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setLibSource(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setLibStrategy(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setLifecycleHandler(ExecutingTask.TaskLifecycleHandler) - Method in class ubic.gemma.core.job.executor.common.ExecutingTask
setLimit(Integer) - Method in class ubic.gemma.web.remote.ListBatchCommand
setLinkAnalysisEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setLinkCountsNegative(byte[]) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
setLinkCountsPositive(byte[]) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
setLinkId(Long) - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
setLinksFound(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject
setLiteratureSources(Set<BibliographicReference>) - Method in class ubic.gemma.model.genome.gene.GeneSet
setLoadHomologene(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceFactory: Set whether to load homologene or not.
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
setLocalInstallDbName(String) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setLocalName(String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
setLocalPath(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
setLocalURL(URI) - Method in class ubic.gemma.model.common.description.LocalFile
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
setLoggingFrequency(int) - Method in interface ubic.gemma.core.search.IndexerService: Set the logging frequency for reporting progress.
setLoggingFrequency(int) - Method in class ubic.gemma.core.search.IndexerServiceImpl
setLogin(String) - Method in class ubic.gemma.core.util.NetDatasourceUtil
setLogTransform(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setLowCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter: Set the low threshold for removal.
setLowCut(double, boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter
setLowDistinctValueCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setLowerCdfCutUsed(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setLowerTailCut(double) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setLowerTailThreshold(double) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis: Set the threshold, below which correlations are kept (e.g., negative values)
setLowerTailThreshold(double) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
setLowExpressionCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setLowVarianceCut(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setMailEngine(MailEngine) - Method in class ubic.gemma.web.controller.BaseController
setMailEngine(MailEngine) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.
setMakeArchiveFile(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setMakeSampleCorrMatImages(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setManualAuthenticationService(ManualAuthenticationService) - Method in class ubic.gemma.web.scheduler.SecureMethodInvokingJobDetailFactoryBean
setManualAuthenticationService(ManualAuthenticationService) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint
setManualBatchConfoundActive(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualBatchEffectActive(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualHasBatchConfound(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualHasNoBatchEffect(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualHasStrongBatchEffect(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualQualityOverride(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualQualityScore(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualSuitabilityOverride(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
setManualSuitabilityScore(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
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
setMappingType(PhenotypeMappingType) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setMasked(boolean) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
setMaskMissing(boolean) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setMatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setMatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setMaxEdges(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject: Override the value of gemma.cytoscapeweb.maxEdges (or DEFAULT_MAX_EDGES_PER_GRAPH )
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.
setMaximumRepeatFraction(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setMaxNumProbesPerComponent(Integer) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setMaxQueueMinutes(Integer) - Method in class ubic.gemma.core.job.TaskCommand: How long we will allow this task to be queued before giving up.
setMaxResults(Integer) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setMaxRuntime(int) - Method in class ubic.gemma.core.job.TaskCommand
setMaxUploadSize(long) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver: Set the maximum allowed size (in bytes) before uploads are refused.
setMeanLogFoldChange(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setMeanLogFoldChange(Double) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setMeans(byte[]) - 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
setMedianCorrelation(double) - Method in class ubic.gemma.core.analysis.preprocess.OutlierDetails
setMember(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
setMembers(Set<GeneSetMember>) - Method in class ubic.gemma.model.genome.gene.GeneSet
setMergedInto(ArrayDesign) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setMergees(Collection<ArrayDesignValueObject>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setMergees(Set<ArrayDesign>) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setMerger(ArrayDesignValueObject) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setMeshHeadings(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setMeshTerms(Set<MedicalSubjectHeading>) - Method in class ubic.gemma.model.common.description.BibliographicReference
setMessage(String) - Method in class ubic.gemma.web.remote.JsonReaderResponse
setMessages(String) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setMessageSource(MessageSource) - Method in class ubic.gemma.web.controller.BaseController
setMessageUtil(MessageUtil) - Method in class ubic.gemma.web.controller.BaseController
setMessageUtil(MessageUtil) - Method in class ubic.gemma.web.controller.BaseFormController: Deprecated.
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
setMetaPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setMetaPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
setMetaPvalue(Double) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setMetaPvalueRank(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setMetaPvalueRank(Double) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setMetaQvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setMetaQvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
setMetaQvalue(Double) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setMethod(RowLevelFilter.Method) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter: Choose the method that will be used for filtering.
setMetric(String) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setMetricName(String) - Method in class ubic.gemma.web.metrics.binder.servlet.ServletMetricsFilter: Set the name under which servlet metrics are reported.
setMetThreshold(Boolean) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setMightNotHaveDataInFile(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setMigratedToStatement(boolean) - Method in class ubic.gemma.model.common.description.Characteristic: Deprecated.
setMinimumExonOverlapFraction(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setMinNumpresent(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis: Set the number of mutually present values in a pairwise comparison that must be attained before the correlation is stored.
setMinNumpresent(int) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
setMinNumPresent(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
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.
setMinPresentFraction(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig
setMinPresentFraction(double) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter
setMinPvalue(Double) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
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(String, String, HttpServletRequest) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
setModerateStatistics(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setModerateStatistics(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setModifiable(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setModified(boolean) - Method in class ubic.gemma.core.genome.gene.SessionBoundGeneSetValueObject
setModified(boolean) - Method in class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject
setModified(boolean) - Method in interface ubic.gemma.model.GemmaSessionBackedValueObject
setModified(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
setMolecule(GeoChannel.ChannelMolecule) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setMultifunctionality(Multifunctionality) - Method in class ubic.gemma.model.genome.Gene
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.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.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setName(String) - Method in class ubic.gemma.model.common.AbstractDescribable
setName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
setName(String) - Method in class ubic.gemma.model.expression.arrayDesign.AlternateName
setName(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setName(String) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
setName(String) - Method in class ubic.gemma.model.expression.BlacklistedValueObject
setName(String) - Method in class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
setName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setName(String) - Method in class ubic.gemma.model.genome.gene.GeneProductValueObject
setName(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
setName(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
setName(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
setName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setName(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setNameIsFromAuthority(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
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.model.genome.Taxon
setNcbiId(Integer) - Method in class ubic.gemma.model.genome.TaxonValueObject
setNcbiId(String) - Method in class ubic.gemma.core.image.aba.AbaGene
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.expression.experiment.FactorValue
setNeedsAttention(Boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject
setNegSupp(Integer) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
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<Taxon, Collection<Long>>) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setNewObjects(Collection<Auditable>) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setNewPassword(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setNomenclatureStatus(NCBIGeneInfo.NomenclatureStatus) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setNonMatchingProbeNameExamples(Collection<String>) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setNonRepeatNonSpecificSiteCountThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setNonSpecificSiteCountThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setNoParentsAnnotationLink(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setNormalizationDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setNormalizationMethod(LinkAnalysisConfig.NormalizationMethod) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setNormalized(boolean) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setNote(String) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setNoVectors(boolean) - Method in class ubic.gemma.model.expression.experiment.Geeq
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
setNumberMatchingProbes(int) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setNumberOfDataVectors(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setNumberOfElementsAnalyzed(Integer) - Method in class ubic.gemma.model.analysis.SingleExperimentAnalysis
setNumberOfGenes(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
setNumberOfGenesTested(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setNumberOfLinks(Integer) - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis
setNumberOfNonMatchingProbes(int) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
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<List<Integer>>) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
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
setNumberOfSamples(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setNumBins(Integer) - Method in class ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution
setNumBins(Integer) - 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
setNumColumns(int) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setNumComponentsStored(Integer) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setNumDatasetsQueried(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
setNumDatasetsSupporting(Integer) - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression: Warning: wouldn't normally use this.
setNumDatasetsTestedIn(int) - Method in class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn: Used for serializing/marshalling only.
setNumEvidence(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
setNumEvidenceFromSameMetaAnalysis(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setNumExperimentsInScope(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setNumFactors(int) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
setNumFactors(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag: How many factors (including batch etc) are available for PCA display?
setNumGenes(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
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.Multifunctionality
setNumMetThreshold(int) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setNumOutliersRemoved(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setNumPhenotypes(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
setNumPopulatedFactors(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setNumPossibleOutliers(int) - Method in class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
setNumProbes(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setNumPublications(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
setNumResults(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setNumResultSetsIncluded(Integer) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject
setNumRows(int) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
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
setNumTestedIn(Integer) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setNumThreads(int) - Method in interface ubic.gemma.core.search.IndexerService: Set the number of threads to use for indexing entities.
setNumThreads(int) - Method in class ubic.gemma.core.search.IndexerServiceImpl
setNumWithCoexpressionAnalysis(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setNumWithDifferentialExpressionAnalysis(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setObject(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setObjectAlreadyRemoved(boolean) - Method in class ubic.gemma.model.BaseValueObject
setObjectUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setOfficialName(String) - Method in class ubic.gemma.model.genome.Gene
setOfficialSymbol(String) - Method in class ubic.gemma.model.genome.Gene
setOldPassword(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setOldStyleCharacteristics(Set<Characteristic>) - Method in class ubic.gemma.model.expression.experiment.FactorValue: Deprecated.
setOmitNegativeCorrelationLinks(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
setOmitNegativeCorrelationLinks(boolean) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
setOmitNegLinks(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setOntologyService(OntologyService) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
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
setOrganisms(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setOrganisms(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setOrientation(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
setOriginalFileName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setOriginalPhenotype(String) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setOriginalPhenotype(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setOriginalPlatform(ArrayDesign) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay
setOriginalPlatform(ArrayDesignValueObject) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setOriginalPlatforms(Collection<ArrayDesignValueObject>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setOriginalQuery(String) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
setOriginalValue(String) - Method in class ubic.gemma.model.common.description.Characteristic
setOtherIssues(String) - Method in class ubic.gemma.model.expression.experiment.Geeq
setOtherKind(String) - Method in class ubic.gemma.model.common.measurement.Measurement
setOtherParts(Collection<ExpressionExperimentValueObject>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setOtherParts(Set<ExpressionExperiment>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setOtherRelevantPublications(Set<BibliographicReference>) - Method in class ubic.gemma.model.analysis.Investigation
setOutlier(boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setOutputFile(File) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
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(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
setOwner(Contact) - Method in class ubic.gemma.model.analysis.Investigation
setOwner(SidValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setOwnersGroups(Collection<String>) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
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
setParser(NCBIGene2GOAssociationParser) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
setPassword(String) - Method in class ubic.gemma.core.util.NetDatasourceUtil
setPassword(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setPassword(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setPasswordEncoder(PasswordEncoder) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
setPasswordHint(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setPasswordHint(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setPathToDownloadFile(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
setPcaAnalysisEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setPCDateCorrelation(int, double) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
setPCDateCorrelationPval(int, double) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
setPCFactorCorrelation(int, ExperimentalFactor, double) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
setPCFactorCorrelationPval(int, ExperimentalFactor, double) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
setPercent(int) - Method in class ubic.gemma.core.job.progress.ProgressData
setPerformer(String) - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
setPersist(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setPersist(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
setPersisterHelper(Persister) - Method in class ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
setPersisterHelper(Persister) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
setPersisterHelper(Persister) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoader
setPersisterHelper(Persister) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
setPersisterHelper(Persister) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
setPersistJobDetails(Boolean) - Method in class ubic.gemma.core.job.TaskCommand
setPhases(Integer) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setPhenotypeAssociationPublications(Set<PhenotypeAssociationPublication>) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setPhenotypeAssociations(Set<PhenotypeAssociation>) - Method in class ubic.gemma.model.genome.Gene: Deprecated.
setPhenotypeAssPubVO(Set<PhenotypeAssPubValueObject>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setPhenotypeCategory(String) - Method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
setPhenotypeMapping(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setPhenotypeName(String) - Method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
setPhenotypes(Set<Characteristic>) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setPhenotypes(Set<CharacteristicValueObject>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setPhenotypesValues(Set<CharacteristicValueObject>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject
setPhenotypesValueUri(Set<String>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject: Deprecated.
setPhone(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
setPhysicalLocation(PhysicalLocation) - Method in class ubic.gemma.model.genome.ChromosomeFeature
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(ArrayDesign) - Method in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg
setPlatformConstraint(ArrayDesign) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setPlatformData(List<List<String>>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setPlatformFetcher(Fetcher) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
setPlatformId(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setPlatforms(Collection<GeoPlatform>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setPlatformType(GeoDataset.PlatformType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setPlots(List<List<DoublePoint>>) - Method in class ubic.gemma.web.controller.visualization.FactorProfile
setPollingIntervalMillis(long) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Interval at which events are polled and flushed.
setPolymerType(PolymerType) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setPoolName(String) - Method in class ubic.gemma.core.metrics.binder.ThreadPoolTaskExecutorMetrics
setPosSupp(Integer) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
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.expression.experiment.Statement
setPredicateUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setPredictedOutlier(Boolean) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setPreprocessorService(PreprocessorService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
setPreviousClicks(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setPreviousNcbiId(String) - Method in class ubic.gemma.model.genome.ChromosomeFeature
setPrimaryCitation(CitationValueObject) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setPrimaryPublication(BibliographicReference) - Method in class ubic.gemma.model.analysis.Investigation
setPrimaryTaxon(Taxon) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setPrincipal(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
setPrivateGeneCount(long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
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
setProbe(CompositeSequenceValueObject) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setProbeDegreeThreshold(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig: Probe degree threshold: Probes with more than this number of links are ignored.
setProbeId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setProbeId(Long) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setProbeIdsAreImageClones(boolean) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setProbeLoadings(Set<ProbeLoading>) - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
setProbeName(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
setProbeResults(Collection<DifferentialExpressionValueObject>) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setProbeToGeneMap(Map<CompositeSequence, Set<Gene>>) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis: Once set, is unmodifiable.
setProblematicEvidenceIds(Set<Long>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setProcessedDataVectorComputationEventType(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setProcessedExpressionDataVectors(Set<ProcessedExpressionDataVector>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setProcessedExpressionDataVectorService(ProcessedExpressionDataVectorService) - Method in class ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint
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<GeneProduct>) - Method in class ubic.gemma.model.genome.Gene
setProfile(double[]) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setProfiles(Collection<GeneExpressionProfile>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setProperty(String, Object) - Static method in class ubic.gemma.persistence.util.Settings: Deprecated.

Set an environment/application variable programatically.
setProperty(String, Object) - Method in class ubic.gemma.web.util.ConfigurationCookie
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(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.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
setPublicationDate(Date) - Method in class ubic.gemma.model.common.description.BibliographicReference
setPublicationDate(Date) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setPublicGeneCount(long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
setPublicGenesNBCI(HashSet<Integer>) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
setPubliclyReadable(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setPublik(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
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(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
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(Integer) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setPubMedId(String) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
setPubmedIdInvalid(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setPubmedIds(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setPubMedIds(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setPubMedIds(Collection<Integer>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
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.DifferentialExpressionAnalysisResult
setPvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult
setPvalue(Double) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
setPValue(Double) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setPvalueDistribution(PvalueDistribution) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setPValueThreshold(double) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
setPValueThreshold(double) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
setQChtml(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setqScoreBatchConfound(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setqScoreBatchEffect(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setqScoreBatchInfo(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setqScoreOutliers(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setqScorePlatformsTech(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setqScoreReplicates(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setqScoreSampleCorrelationVariance(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setqScoreSampleMeanCorrelation(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setqScoreSampleMedianCorrelation(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setQualifiers(Set<MedicalSubjectHeading>) - Method in class ubic.gemma.model.common.description.MedicalSubjectHeading
setQualityControlDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setQuantitationType(QuantitationType) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
setQuantitationType(QuantitationType) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setQuantitationType(QuantitationTypeValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
setQuantitationTypeDescription(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setQuantitationTypeId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
setQuantitationTypeIsValid(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setQuantitationTypeName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setQuantitationTypeProblemMessage(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setQuantitationTypes(Collection<QuantitationTypeValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
setQuantitationTypes(Set<QuantitationType>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setQuantitationTypeService(QuantitationTypeService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
setQuantitationTypeService(QuantitationTypeService) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
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
setQueryGene(GeneValueObject) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setQueryGeneNodeDegree(Integer) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setQueryGeneNodeDegreeRank(Double) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setQueryGenes(Collection<GeneValueObject>) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
setQueryGenesOnly(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
setQueryGenesOnly(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setQueryGeneSymbol(String) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
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.core.genome.gene.FreeTextGeneResultsValueObject
setQueryString(String) - Method in class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
setQueryStringency(int) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
setQuick(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setQvalue(int, int, Double) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setqValues(List<List<Double>>) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setQvalueThresholdForStorage(Double) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
setRank(Double) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
setRank(Double) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
setRank(Double) - Method in class ubic.gemma.model.genome.gene.Multifunctionality
setRank(Double) - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
setRankByMax(Double) - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
setRankByMean(Double) - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
setRawExpressionDataVectors(Set<RawExpressionDataVector>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setReason(String) - Method in class ubic.gemma.model.expression.BlacklistedEntity
setReason(String) - Method in class ubic.gemma.model.expression.BlacklistedValueObject
setRecaptchaTester(ReCaptcha) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
setRecords(List<T>) - Method in class ubic.gemma.web.remote.JsonReaderResponse
setRecordSeparator(String) - Method in class ubic.gemma.core.loader.util.parser.RecordParser
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
setRelationship(String) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setRelationship(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setRelativeLinkRanksNegative(byte[]) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
setRelativeLinkRanksPositive(byte[]) - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree
setReleaseDate(Date) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setReleaseUrl(URL) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setReleaseVersion(String) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setRemoteURL(URI) - Method in class ubic.gemma.model.common.description.LocalFile
setRemove(boolean) - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
setRemoveAllNegative(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter: Set the filter to remove all rows that have only negative values.
setRemovePrimaryPublication(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
setReorganized(boolean) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
setRepeats(GeoReplication.ReplicationType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
setReplicateDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign
setReplicates(Map<Integer, GeoReplication>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setReplicatesIssues(byte) - Method in class ubic.gemma.model.expression.experiment.Geeq
setRepMatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
setRepMatches(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setRepresentation(String) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
setRepresentation(PrimitiveType) - Method in class ubic.gemma.model.common.measurement.Measurement
setRepresentation(PrimitiveType) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setReprocessedFromRawData(boolean) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setRequestHeader(String) - Method in class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy: Set the request header used for retrieving the client ID.
setRequireSequences(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.FilterConfig: Set to true if rows lacking associated BioSequences for the element should be removed.
setResolutionMillis(long) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Time resolution for regrouping events in the same batch.
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.core.search.SearchResult: Set the result object.
setResults(Collection<DifferentialExpressionAnalysisResultValueObject>) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
setResults(Collection<GeneDifferentialExpressionMetaAnalysisResultValueObject>) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject
setResults(List<CoexpressionValueObjectExt>) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
setResults(Set<DifferentialExpressionAnalysisResult>) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
setResults(Set<GeneDifferentialExpressionMetaAnalysisResult>) - 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.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(Set<ExpressionAnalysisResultSet>) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
setResultSetsIncluded(Set<ExpressionAnalysisResultSet>) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis
setResultsUsed(Set<DifferentialExpressionAnalysisResult>) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
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
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
setRolePrefix(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
setRootOfTree(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
setRow(int, Double[]) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Sets the row of matrix to the input data.
setRow(Integer) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
setRunningStatus(Boolean) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
setS2n(double) - Method in class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
setSameEvidenceFound(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setSameGeneAndOnePhenotypeAnnotated(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setSameGeneAndPhenotypeChildOrParentAnnotated(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setSameGeneAndPhenotypesAnnotated(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setSameGeneAnnotated(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setSample(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setSample(Collection<GeoSample>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
setSample(BioMaterialValueObject) - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
setSampleCorrespondence(GeoSampleCorrespondence) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSampleDetails(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleGEOAccessions(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSampleNames(List<String>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
setSampleRemovedFlags(Collection<AuditEventValueObject>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
setSamples(Collection<GeoSample>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
setSamples(Collection<GeoSample>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoVariable
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(ScaleType) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setScale(ScaleType) - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
setScanProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setScientificName(String) - Method in class ubic.gemma.model.genome.Taxon
setScientificName(String) - Method in class ubic.gemma.model.genome.TaxonValueObject
setScope(int) - Method in class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy: Set the scope to use for retrieving and storing the client ID.
setScope(String) - Method in class ubic.gemma.web.taglib.ConstantsTag
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.Multifunctionality
setScore(Double) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
setScore(String) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setScoreName(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject
setScoreThreshold(double) - Method in class ubic.gemma.core.loader.genome.BlatResultParser
setScoreType(QuantitationType) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setScoreValue(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject
setScoreValueObject(ScoreValueObject) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setSearchBibrefs(Boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchBioSequences(Boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setSearchCriteria(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setSearchedDatabase(ExternalDatabase) - Method in class ubic.gemma.core.loader.genome.BlatResultParser
setSearchedDatabase(ExternalDatabase) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
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
setSearchOptions(CoexpressionSearchCommand) - Method in class ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand
setSearchPhenotypes(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
setSearchSettings(CoexpressionSearchCommand) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
setSearchSettings(SearchSettings) - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
setSearchString(String) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setSearchTerm(String) - Method in class ubic.gemma.core.genome.gene.GOGroupValueObject
setSearchTerm(String) - Method in class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject
setSecondaryAccession(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
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
setSecondFactorValue(FactorValue) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setSecondGene(Long) - Method in class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink
setSecondObject(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSecondObjectUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSecondPredicate(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSecondPredicateUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSecurityOwner(ExpressionExperiment) - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
setSecurityOwner(ExpressionExperiment) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor
setSecurityOwner(ExpressionExperiment) - Method in class ubic.gemma.model.expression.experiment.FactorValue
setSecurityService(SecurityService) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
setSelectedFactors(Collection<DiffExpressionSelectedFactorCommand>) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
setSelectionThreshold(Double) - Method in class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence: Deprecated.
setSelectionThreshold(Double) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setSequence(String) - Method in class ubic.gemma.model.genome.biosequence.BioSequence
setSequence(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
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.
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
setSeries(Collection<GeoSeries>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setSeriesAppearsIn(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setSeriesFetcher(Fetcher) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
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
setServerFilePath(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setServletConfig(ServletConfig) - Method in class ubic.gemma.rest.security.RestAuthEntryPoint
setServletContext(ServletContext) - Method in class ubic.gemma.web.services.GeneCoexpressionSearchEndpoint
setServletContext(ServletContext) - Method in class ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver
setShared(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject: Deprecated.
setShared(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject
setShared(boolean) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
setShortName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setShortName(String) - Method in class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
setShortName(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setShortName(String) - Method in class ubic.gemma.model.expression.BlacklistedEntity
setShortName(String) - Method in class ubic.gemma.model.expression.BlacklistedValueObject
setShortName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setShortNameIsUnique(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
setShowOnlyEditable(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
setShowStackTrace(Boolean) - Method in class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
setSignupToken(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setSignupTokenDatestamp(Date) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setSingularThreshold(LinkAnalysisConfig.SingularThreshold) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig: Set to modify threshold behaviour: enforce the choice of only one of the two standard thresholds.
setSize(long) - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject
setSize(Integer) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setSize(Long) - Method in class ubic.gemma.model.common.description.LocalFile
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!)
setSort(String) - Method in class ubic.gemma.web.remote.ListBatchCommand
setSortKey() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setSortKey() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject
setSortKey() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject
setSortKey(String) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setSource(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
setSource(ExternalDatabase) - Method in class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
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
setSourceDoneFlag(AtomicBoolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
setSourceExperiment(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
setSourceExperiment(ExpressionExperiment) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet
setSourceName(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setSourceTaxon(Taxon) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
setSourceUrl(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
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
setsScoreAvgPlatformPopularity(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setsScoreAvgPlatformSize(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setsScoreMissingValues(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setsScorePlatformAmount(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setsScorePlatformsTechMulti(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setsScorePublication(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setsScoreRawData(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setsScoreSampleSize(double) - Method in class ubic.gemma.model.expression.experiment.Geeq
setStart(Integer) - Method in class ubic.gemma.web.remote.ListBatchCommand
setStartInBioChar(Long) - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter
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.FilterConfig
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
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.web.util.upload.UploadInfo
setStatusCode(int) - Method in class ubic.gemma.web.util.UnhandledExceptionResolver: Set the status code to use for reporting unhandled exception.
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
setStrength(Double) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation: Deprecated.
setStrength(Double) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject
setStringency(Integer) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setSubject(String) - Method in class ubic.gemma.model.expression.experiment.Statement
setSubjectUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement
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
setSubSeries(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSubSeries(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSubSeriesOf(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSubset(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setSubsetFactor(ExperimentalFactor) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setSubsetFactor(ExperimentalFactor) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setSubsetFactorValue(FactorValue) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setSubsetFactorValue(FactorValue) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
setSubsets(Collection<GeoSubset>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setSubsetSize(double) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setSubsetUsed(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setSubsumedArrayDesigns(Set<ArrayDesign>) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setSubsumees(Collection<ArrayDesign>) - Method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
setSubsumees(Collection<ArrayDesignValueObject>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setSubsumer(ArrayDesign) - Method in class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
setSubsumer(ArrayDesignValueObject) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
setSubsumingArrayDesign(ArrayDesign) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setSuccess(boolean) - Method in class ubic.gemma.web.remote.JsonReaderResponse
setSummaries(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSummaries(Map<Long, CoexpressionSummaryValueObject>) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
setSummary(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSummary(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSuperSeries(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setSuperSeries(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSupplementaryFile(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setSupplementaryFile(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setSupplementaryFile(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setSupport(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setSupportDetails(SupportDetails) - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
setSupportedTaxa(Collection<Integer>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser
setSupportingExperiments(Collection<Long>) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
setSuppressMatching(boolean) - Method in class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
setSymbolIsFromAuthority(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
setTagCount(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setTagLength(int) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setTargetAlignedRegion(PhysicalLocation) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
setTargetChromosome(Chromosome) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
setTargetChromosomeName(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
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
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
setTaskCommand(C) - Method in class ubic.gemma.core.tasks.AbstractTask
setTaskCommand(C) - Method in interface ubic.gemma.core.tasks.Task
setTaskCommand(CharacteristicUpdateCommand) - Method in class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTaskImpl
setTaskCommand(DifferentialExpressionSearchTaskCommand) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskImpl
setTaskExecutor(TaskExecutor) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory: Set the task executor used for initializing ontology service in background.
setTaskId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse
setTaskId(String) - Method in class ubic.gemma.core.job.progress.ProgressData
setTaskId(String) - Method in class ubic.gemma.core.job.TaskCommand
setTaskId(String) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
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(Taxon) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
setTaxon(Taxon) - 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.model.analysis.expression.ExpressionExperimentSet
setTaxon(Taxon) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
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.Gene
setTaxon(Taxon) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
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
setTaxonCommonName(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
setTaxonId(Long) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setTaxonId(Long) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setTaxonId(Long) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
setTaxonId(Long) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setTaxonId(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
setTaxonId(Long) - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
setTaxonName(String) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
setTaxonName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject
setTaxonName(String) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
settaxonService(TaxonService) - Method in class ubic.gemma.web.services.GoTerm2GeneEndpoint
setTaxonService(TaxonService) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
setTaxonService(TaxonService) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint
setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint
setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.Gene2ProbeEndpoint: Sets the "business service" to delegate to.
setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.GeneCoexpressionEndpoint: Sets the "business service" to delegate to.
setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.GeneIDbyTaxonEndpoint
setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.GeneIdEndpoint
setTaxonService(TaxonService) - Method in class ubic.gemma.web.services.GoTerm2GeneEndpoint
setTeaser(String) - Method in class ubic.gemma.web.feed.NewsItem
setTechnology(GeoDataset.PlatformType) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setTechnologyType(TechnologyType) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setTechnologyType(TechnologyType) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
setTerm(String) - Method in class ubic.gemma.model.common.description.BibRefAnnotation
setTermUri(String) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setTextOut(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
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.web.controller.diff.DiffExpressionSearchCommand
setThresholdQvalue(Double) - Method in class ubic.gemma.model.analysis.expression.diff.HitListSize
Settings - Class in ubic.gemma.persistence.util: 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.persistence.util.Settings: Deprecated.
SettingsConfig - Class in ubic.gemma.persistence.util: Beans declaration for making the settings available via the Spring Environment and placeholder substitution.
SettingsConfig() - Constructor for class ubic.gemma.persistence.util.SettingsConfig
setTitle(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoData
setTitle(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
setTitle(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
setTitle(String) - Method in class ubic.gemma.web.feed.NewsItem
setTitleInDataset(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
setToken(String) - Method in class ubic.gemma.web.logging.SlackAppender
setTolerance(Double) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter: Set the value considered to be an insignificant difference between two numbers.
setToRedo(DifferentialExpressionAnalysis) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setTotalRecords(long) - Method in class ubic.gemma.web.remote.JsonReaderResponse
setTotalSize(long) - Method in class ubic.gemma.web.util.upload.UploadInfo
setTreatmentProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
setTreatments(Set<Treatment>) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
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.AbstractCuratableValueObject
setTstat(Double) - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
setType(String) - Method in class ubic.gemma.core.analysis.report.AuditableObject
setType(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample: Sets the sample type (ie.
setType(String) - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication: Deprecated.
setType(String) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
setType(String) - Method in class ubic.gemma.model.expression.BlacklistedValueObject
setType(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject
setType(String) - Method in class ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo
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(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.SimpleExpressionExperimentMetaData
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<Characteristic>) - 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
setUpdateDate(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoDataset
setUpdatedEEIdsPerTaxon(Map<Taxon, Collection<Long>>) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setUpdatedObjects(Collection<Auditable>) - Method in class ubic.gemma.core.analysis.report.WhatsNew
setUpFactorProfiles(LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>) - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject: Initialize the factor profiles.
setUpperCdfCutUsed(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setUpperTail(Boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
setUpperTail(Boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject
setUpperTail(Boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
setUpperTailCut(double) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setUpperTailThreshold(double) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis: Set the threshold, above which correlations are kept.
setUpperTailThreshold(double) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
setUri(String) - Method in class ubic.gemma.model.common.description.DatabaseEntry: Deprecated.
setUrl(String) - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery
setUrl(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
setUrlId(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
setUsable(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoRecord
setUseAbsoluteValue(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis: If set to true, then the absolute value of the correlation is used for histograms and choosing correlations to keep.
setUseAbsoluteValue(boolean) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
setUseAsFraction(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter: Set the filter to interpret the low and high cuts as fractions; that is, if true, lowcut 0.1 means remove 0.1 of the rows with the lowest values.
setUseCharacteristics(Boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
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".
setUseDb(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
setUseEnsembl(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseEsts(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseGo(Boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setUseHighCutAsFraction(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter
setUseIndices(Boolean) - Method in class ubic.gemma.model.common.search.SearchSettingsValueObject
setUseKnownGene(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseLowCutAsFraction(boolean) - Method in class ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter
setUseMiRNA(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseMrnas(boolean) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
setUseMyDatasets(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
setUsePvalueThreshold(boolean) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
setUsePvalueThreshold(boolean) - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis: Default is true; set to false to disable use of the pvalue threshold, in which case only the upper and lower tail thresholds will be used.
setUser(Contact) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
setUser(User) - Method in class ubic.gemma.model.common.auditAndSecurity.JobInfo
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.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
setUserIdRetrievalStrategy(UserIdRetrievalStrategy) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Set the strategy used to retrieve user IDs.
setUserManager(UserManager) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
setUserManager(UserManager) - Method in class ubic.gemma.web.scheduler.SecureMethodInvokingJobDetailFactoryBean
setUserName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User
setUserName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
setUserName(String) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
setUserNotLoggedIn(boolean) - Method in class ubic.gemma.model.BaseValueObject
setUserNotLoggedIn(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
setUserOwned(boolean) - Method in class ubic.gemma.core.search.SearchResultDisplayObject
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.ExpressionExperimentValueObject
setUseWeights(boolean) - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
setUseWeights(boolean) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
setValidateOnly(boolean) - Method in class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
setValue(Double) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
setValue(String) - Method in class ubic.gemma.model.common.description.Characteristic
setValue(String) - Method in class ubic.gemma.model.common.measurement.Measurement
setValue(String) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
setValue(String) - Method in class ubic.gemma.model.expression.experiment.FactorValue: Deprecated.
setValue(String) - Method in class ubic.gemma.model.expression.experiment.Statement: Deprecated.
use Statement.setSubject(String) instead
setValue(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
setValue(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
setValue(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject
setValue(String) - Method in class ubic.gemma.web.util.ConfigurationCookie: Don't use this method if you can help it! Use setProperty instead.
setValue(String) - Method in class ubic.gemma.web.util.LabelValue
setValueObject(Serializable) - Method in class ubic.gemma.model.BaseValueObject
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.Characteristic
setValueUri(String) - Method in class ubic.gemma.model.expression.experiment.Statement: Deprecated.
use Statement.setSubjectUri(String) instead
setValueUri(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
setValueUri(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
setVar(String) - Method in class ubic.gemma.web.taglib.ConstantsTag
setVarianceFraction(Double) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
setVariances(byte[]) - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
setVariances(double[]) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
setVector(byte[]) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
setVersion(String) - Method in class ubic.gemma.model.common.description.LocalFile
setViewSampling(boolean) - Method in class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
setVisualizationValue(int, int, Double) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setVisualizationValues(List<List<Double>>) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
setvMatrix(DoubleMatrix<Long, Integer>) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
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: Threshold in milliseconds for a warning to be logged.
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<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
setWebLinks(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
setWebUri(String) - Method in class ubic.gemma.model.common.description.ExternalDatabase
setWebUri(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
setWhatsNewService(WhatsNewService) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController
SfariDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
SfariDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
SFARIIntermediateFileParser - Class in ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence: Deprecated.
SFARIIntermediateFileParser() - Constructor for class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser: Deprecated.
SFARILineInfo - Class in ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence: Deprecated.
SFARILineInfo(String) - Constructor for class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo: Deprecated.
ShellDelegatingBlat - Class in ubic.gemma.core.apps: Class to manage the gfServer and run BLAT searches.
ShellDelegatingBlat() - Constructor for class ubic.gemma.core.apps.ShellDelegatingBlat: Create a blat object with settings read from the config file.
ShellDelegatingBlat(String, int, String) - Constructor for class ubic.gemma.core.apps.ShellDelegatingBlat
ShellDelegatingBlat.BlattableGenome - Enum in ubic.gemma.core.apps
shock - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
SHORT - ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType
ShortBibliographicReferenceTag - Class in ubic.gemma.web.taglib
ShortBibliographicReferenceTag() - Constructor for class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
shouldRun(Date, ArrayDesign, Class<? extends ArrayDesignAnalysisEvent>) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
show() - Method in class ubic.gemma.web.controller.monitoring.SystemMonitorController
show(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController
show(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.genome.gene.GeneController
showAllArrayDesigns() - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController: Show all array designs, or according to a list of IDs passed in.
showAllArrayDesigns() - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
showAllBioAssays(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
showAllExpressionExperiments(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Show all experiments (optionally conditioned on either a taxon, a list of ids, or a platform)
showAllForExperiments(HttpServletRequest, HttpServletResponse) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
showAllForExperiments(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
showAllLinkSummaries(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showAllPhenotypes(HttpServletRequest) - Method in class ubic.gemma.web.controller.PhenotypeController
showArrayDesign(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
showArrayDesign(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
showArrayDesignByName(String) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
showArrayDesignByName(String) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
showBioAssays(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showBioMaterials(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showByExperimentId(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
showByExperimentShortName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
showById(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
showCompositeSequences(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController: Show (some of) the probes from an array.
showCompositeSequences(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
showExpressionExperiment(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showExpressionExperimentByShortName(String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
showExpressionExperiments(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController: shows a list of BioAssays for an expression experiment subset
showExpressionExperiments(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
showExpressionExperimentSet(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
showForm(HttpServletRequest, HttpServletResponse, BindException) - Method in class ubic.gemma.web.controller.GeneralSearchControllerImpl: Deprecated.
showGeneSet(HttpServletRequest) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: If the current user has access to given gene group will return the gene ids in the gene group;
showHomePage() - Method in class ubic.gemma.web.controller.common.GemmaClassicHomePageController: Deprecated.
showHomePage() - Method in class ubic.gemma.web.controller.common.HomePageController
showMetaAnalysisManager(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
showNeurocartaStatistics() - Method in class ubic.gemma.web.controller.PhenotypeController
showPhenotypeAssociationManager() - Method in class ubic.gemma.web.controller.PhenotypeController
showSubSet(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: shows a list of BioAssays for an expression experiment subset
shutdown() - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
shutdown() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
SID_ALIAS - Static variable in class ubic.gemma.persistence.util.AclQueryUtils: Alias used by AclQueryUtils.formAclRestrictionClause(String, int) and AclQueryUtils.formNativeAclJoinClause(String) for the object identity AclObjectIdentity and the owner identity AclSid.
SidValueObject - Class in ubic.gemma.web.controller.common.auditAndSecurity
SidValueObject() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
SidValueObject(Sid) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
signup(String, String, String, String, String, HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
SignupController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Controller to signup new users.
SignupController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
signupForm() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SignupController
simple - ubic.gemma.core.ontology.GoMetric.Metric
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
SimpleExpressionExperimentCommandValidation - Class in ubic.gemma.web.controller.expression.experiment: Stores information about the validation status of an attempted expression experiment load.
SimpleExpressionExperimentCommandValidation() - Constructor for class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
SimpleExpressionExperimentLoadTaskCommand - Class in ubic.gemma.web.controller.expression.experiment: Extends a SimpleExpressionExperimentMetaData with information about the file
SimpleExpressionExperimentLoadTaskCommand() - Constructor for class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
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() - Constructor for class ubic.gemma.core.loader.genome.SimpleFastaCmd
SimpleHTMLFormatter - Class in ubic.gemma.core.search.lucene: A safer substitute for SimpleHTMLFormatter that escape existing HTML tags and use lowercase <b> tags.
SimpleHTMLFormatter() - Constructor for class ubic.gemma.core.search.lucene.SimpleHTMLFormatter
SimpleHttp - Class in ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
SimpleHttp() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.SimpleHttp
SimpleMarkdownFormatter - Class in ubic.gemma.core.search.lucene
SimpleMarkdownFormatter() - Constructor for class ubic.gemma.core.search.lucene.SimpleMarkdownFormatter
SimplePageContext - Class in ubic.gemma.web.taglib: Deprecated.
SimplePageContext(ServletContext) - Constructor for class ubic.gemma.web.taglib.SimplePageContext: Deprecated.
SimpleThreadFactory - Class in ubic.gemma.core.util: A simple thread factory based on a preferably unique thread name prefix.
SimpleThreadFactory(String) - Constructor for class ubic.gemma.core.util.SimpleThreadFactory
SimpleTreeValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
SimpleTreeValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
SimpleTreeValueObject(TreeCharacteristicValueObject, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
SINGLE_BATCH_SUCCESS - ubic.gemma.model.expression.experiment.BatchEffectType: Indicate that there is a single batch and thus there cannot be a batch effect.
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
singleChannel - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
singleChannelGenomic - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SingleExperimentAnalysis - Class in ubic.gemma.model.analysis
SingleExperimentAnalysis() - Constructor for class ubic.gemma.model.analysis.SingleExperimentAnalysis
SingleExperimentAnalysis(BioAssaySet) - Constructor for class ubic.gemma.model.analysis.SingleExperimentAnalysis
SingleExperimentAnalysisDao<T extends SingleExperimentAnalysis> - Interface in ubic.gemma.persistence.service.analysis
SingleExperimentAnalysisDaoBase<T extends SingleExperimentAnalysis> - Class in ubic.gemma.persistence.service.analysis: Base Spring DAO Class: is able to create, update, remove, load, and find objects of type SingleExperimentAnalysis.
SingleExperimentAnalysisDaoBase(Class<T>, SessionFactory) - Constructor for class ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDaoBase
SingleExperimentAnalysisService<T extends SingleExperimentAnalysis> - Interface in ubic.gemma.persistence.service.analysis: Interface for analysis service manipulating single experiments.
SINGLETON_BATCHES_FAILURE - ubic.gemma.model.expression.experiment.BatchEffectType: Batch contains singleton (i.e.
SingletonBatchesException - Exception 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 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
size() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
size() - Method in interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
size() - Method in class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence
size() - Method in class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics
size() - Method in class ubic.gemma.core.search.SearchResultSet
size() - Method in class ubic.gemma.persistence.util.Slice
SlackAppender - Class in ubic.gemma.web.logging
SlackAppender() - Constructor for class ubic.gemma.web.logging.SlackAppender: Used in log4j.properties via reflection.
SlackAppender(Slack) - Constructor for class ubic.gemma.web.logging.SlackAppender
Slice<O> - Class in ubic.gemma.persistence.util: Represents a slice of List.
Slice(List<O>, Sort, Integer, Integer, Long) - Constructor for class ubic.gemma.persistence.util.Slice
SNORNA - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
SNP - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
SNRNA - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
Sort - Class in ubic.gemma.persistence.util: Represents a directed sort by a property.
Sort.Direction - Enum in ubic.gemma.persistence.util: Direction of the sort.
SortArg<O extends Identifiable> - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be an integer.
SortArg.Sort - Class in ubic.gemma.rest.util.args
SortArg.Sort.Direction - Enum in ubic.gemma.rest.util.args
sortFactors(Collection<ExperimentalFactor>) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils: Sort factors in a consistent way.
SortValueObject - Class in ubic.gemma.rest.util: Represents Sort as part of a PaginatedResponseDataObject.
SortValueObject(Sort) - Constructor for class ubic.gemma.rest.util.SortValueObject
sortVectorDataByDesign(Collection<DoubleVectorValueObject>) - Method in interface ubic.gemma.core.visualization.ExperimentalDesignVisualizationService: Put data vectors in the order you'd want to display the experimental design.
sortVectorDataByDesign(Collection<DoubleVectorValueObject>) - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl
sortVectorDataByDesign(Collection<DoubleVectorValueObject>, 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<DoubleVectorValueObject>, ExperimentalFactor) - Method in class ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl
SourceDomainObjectGenerator - Interface in ubic.gemma.core.loader.util.sdo
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.
spearman(double[], double[], boolean[], boolean[], int, int) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
SpearmanMetrics - Class in ubic.gemma.core.analysis.expression.coexpression.links: Subclass that computes correlations using ranks.
SpearmanMetrics(int) - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
SpearmanMetrics(ExpressionDataDoubleMatrix) - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
SpearmanMetrics(ExpressionDataDoubleMatrix, double) - Constructor for class ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
specialCaseForAssociationFollow(Object, String) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
specialCaseToKeepPrivateOnCreation(Securable) - Method in class ubic.gemma.core.security.authorization.acl.AclAdvice
species - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
specimen - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
SPELL - ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.NormalizationMethod
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
splitAndTrim(String) - Static method in class ubic.gemma.rest.util.args.AbstractArrayArg: Split a string by the ',' comma character and trim the resulting pieces.
SplitExperimentCli - Class in ubic.gemma.core.apps: Split an experiment into parts based on an experimental factor
SplitExperimentCli() - Constructor for class ubic.gemma.core.apps.SplitExperimentCli
SplitExperimentService - Interface in ubic.gemma.core.analysis.preprocess: TODO Document Me
SplitExperimentServiceImpl - Class in ubic.gemma.core.analysis.preprocess: Split an experiment into multiple experiments.
SplitExperimentServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.SplitExperimentServiceImpl
spottedDNAOrcDNA - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
spottedOligonucleotide - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
SpringContextUtil - Class in ubic.gemma.persistence.util: Methods to create Spring contexts for Gemma manually.
SpringContextUtil() - Constructor for class ubic.gemma.persistence.util.SpringContextUtil
sqlTypes() - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
ST - ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
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.model.expression.bioAssayData.DoubleVectorValueObject
StandardQuantitationType - Enum in ubic.gemma.model.common.quantitationtype
StandardQuantitationTypeConverter - Class in ubic.gemma.web.remote
StandardQuantitationTypeConverter() - Constructor for class ubic.gemma.web.remote.StandardQuantitationTypeConverter
start() - Method in interface ubic.gemma.web.util.upload.OutputStreamListener
start() - Method in class ubic.gemma.web.util.upload.UploadListener
startServer(ShellDelegatingBlat.BlattableGenome, int) - Method in interface ubic.gemma.core.apps.Blat: Start the server, if the port isn't already being used.
startServer(ShellDelegatingBlat.BlattableGenome, int) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
StartupListener - Class in ubic.gemma.web.listener: StartupListener class used to initialize the spring context and make it available to the servlet context, so filters that need the spring context can be configured.
StartupListener() - Constructor for class ubic.gemma.web.listener.StartupListener
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
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
STEPSIZE - Static variable in interface ubic.gemma.core.apps.Blat
stopServer(int) - Method in interface ubic.gemma.core.apps.Blat: Stop the gfServer, if it was started by this.
stopServer(int) - Method in class ubic.gemma.core.apps.ShellDelegatingBlat
StopWatchUtils - Class in ubic.gemma.core.util: Utilities for working with StopWatch.
StopWatchUtils() - Constructor for class ubic.gemma.core.util.StopWatchUtils
StopWatchUtils.StopWatchRegion - Class in ubic.gemma.core.util
stowRequestAttributes(HttpServletRequest) - Static method in class ubic.gemma.web.util.RequestUtil: Stores request attributes in session
strain - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
streamByBatch(Query, String, Collection<S>, int) - Static method in class ubic.gemma.persistence.util.QueryUtils: Stream the results of a query by a fixed batch size.
streamByBatch(Query, String, Collection<S>, int, Class<T>) - Static method in class ubic.gemma.persistence.util.QueryUtils
stress - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
STRING - ubic.gemma.model.common.quantitationtype.PrimitiveType
STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
STRING() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
STRINGARRAY - ubic.gemma.model.common.quantitationtype.PrimitiveType
StringArrayArg - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be an array of Strings.
StringPoint - Class in ubic.gemma.web.remote
stripPolyAorT(String, int) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation: Remove a 3' polyA or 5' polyT tail.
subClause() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
subClause() - Method in class ubic.gemma.rest.util.args.FilterArgParser
subClause(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
SubClauseContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
submitTask(T) - Method in interface ubic.gemma.core.job.executor.webapp.TaskRunningService
submitTask(T) - Method in class ubic.gemma.core.job.executor.webapp.TaskRunningServiceImpl
submitTaskCommand(C) - Method in interface ubic.gemma.core.job.executor.webapp.TaskRunningService: Submit a task and track its progress.
submitTaskCommand(C) - Method in class ubic.gemma.core.job.executor.webapp.TaskRunningServiceImpl: We check if there are listeners on task submission queue to decide if remote tasks can be served.
SubmittedTask - Interface in ubic.gemma.core.job: Obtained from the TaskRunningService, can be used to monitor status.
SubmittedTask.Status - Enum in ubic.gemma.core.job
SubmittedTaskAbstract - Class in ubic.gemma.core.job.executor.webapp: Shared code between SubmittedTaskLocal and SubmittedTaskProxy.
SubmittedTaskLocal - Class in ubic.gemma.core.job.executor.webapp: SubmittedTask implementation representing the task running on local TaskRunningService.
SubmittedTaskLocal(TaskCommand, TaskPostProcessing, Executor) - Constructor for class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal
SubmittedTasksMaintenance - Class in ubic.gemma.core.job.executor.webapp
SubmittedTasksMaintenance() - Constructor for class ubic.gemma.core.job.executor.webapp.SubmittedTasksMaintenance
SubmittedTaskValueObject - Class in ubic.gemma.core.job.progress
SubmittedTaskValueObject() - Constructor for class ubic.gemma.core.job.progress.SubmittedTaskValueObject
SubmittedTaskValueObject(SubmittedTask) - Constructor for class ubic.gemma.core.job.progress.SubmittedTaskValueObject
Subquery - Class in ubic.gemma.persistence.util: Represents a subquery right-hand side of a Filter.
Subquery(String, String, List<Subquery.Alias>, Filter) - Constructor for class ubic.gemma.persistence.util.Subquery
Subquery.Alias - Class in ubic.gemma.persistence.util
SubqueryUtils - Class in ubic.gemma.persistence.service
SubqueryUtils() - Constructor for class ubic.gemma.persistence.service.SubqueryUtils
subset(Collection<GeoSample>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues: This creates a new GeoValues that has data only for the selected samples.
subtractMatrices(ExpressionDataDoubleMatrix, ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil: Subtract two matrices.
success - Variable in class ubic.gemma.web.remote.JsonReaderResponse
SUCCESS - Static variable in class ubic.gemma.core.util.AbstractCLI: Exit code used for a successful AbstractCLI.doWork() execution.
summarizeMapResults(Collection<CompositeSequence>) - Method in interface ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService: Non-HQL version of the composite sequence data summary query.
summarizeMapResults(Collection<CompositeSequence>) - 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
summarizeRequest(HttpServletRequest) - Static method in class ubic.gemma.rest.util.ServletUtils: Summarize a HttpServletRequest in a single line format.
supportDetails - Variable in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
SupportDetails - Class in ubic.gemma.model.analysis.expression.coexpression: Represents the datasets in which a link was found in ("supported").
SupportDetails(Long, Long, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SupportDetails: Note that the gene information and isPositive is only used for bookkeeping during creation; it is not part of the persistent entity.
SupportDetails(Gene, Gene, Boolean) - Constructor for class ubic.gemma.model.analysis.expression.coexpression.SupportDetails: Note that the gene information and isPositive is only used for bookkeeping during creation; it is not part of the persistent entity.
SuspiciousValueResult() - Constructor for class ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException.SuspiciousValueResult
SuspiciousValuesForQuantitationException - Exception in ubic.gemma.core.datastructure.matrix: Exception raised when suspicious values are detected in an ExpressionDataMatrix.
SuspiciousValuesForQuantitationException(QuantitationType, String, List<SuspiciousValuesForQuantitationException.SuspiciousValueResult>) - Constructor for exception ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException
SuspiciousValuesForQuantitationException.SuspiciousValueResult - Class in ubic.gemma.core.datastructure.matrix
svd(Long) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDService
svd(Long) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl
svd(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper
svd(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl
SVD - ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.NormalizationMethod
SVDCli - Class in ubic.gemma.core.apps
SVDCli() - Constructor for class ubic.gemma.core.apps.SVDCli
SvdController - Class in ubic.gemma.web.controller.analysis.preprocess: Run SVD on a data set.
SvdController() - Constructor for class ubic.gemma.web.controller.analysis.preprocess.SvdController
SVDException - Exception 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 ubic.gemma.core.analysis.preprocess.svd.SVDException
svdFactorAnalysis(PrincipalComponentAnalysis) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper: Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
svdFactorAnalysis(PrincipalComponentAnalysis) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl
svdFactorAnalysis(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper: Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
svdFactorAnalysis(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl
SVDRelatedPreprocessingException - Exception in ubic.gemma.core.analysis.preprocess: Exception raised if a SVD cannot be computed.
SVDRelatedPreprocessingException(ExpressionExperiment, SVDException) - Constructor for exception ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException
SVDService - Interface in ubic.gemma.core.analysis.preprocess.svd
SVDServiceHelper - 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.
SVDServiceHelperImpl - Class in ubic.gemma.core.analysis.preprocess.svd: Perform SVD on expression data and store the results.
SVDServiceHelperImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl
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
SVDValueObject - Class in ubic.gemma.core.analysis.preprocess.svd: Store information about SVD of expression data and comparisons to factors/batch information.
SVDValueObject() - Constructor for class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
SVDValueObject(Long, List<Long>, double[], DoubleMatrix<Long, Integer>) - Constructor for class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
SVDValueObject(PrincipalComponentAnalysis) - Constructor for class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
swaggerObjectMapper() - Method in class ubic.gemma.rest.util.JacksonConfig: This is the ObjectMapper used by Swagger to generate the /openapi.json endpoint.
SwissProtParser - Class in ubic.gemma.core.loader.genome.gene: This does a very minimal parse of Swissprot records, just to get mRNAs associated with a single protein.
SwissProtParser() - Constructor for class ubic.gemma.core.loader.genome.gene.SwissProtParser
switchExperimentToArrayDesign(ExpressionExperiment, ArrayDesign) - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService: If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatform
switchExperimentToMergedPlatform(ExpressionExperiment) - Method in class ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService: Automatically identify an appropriate merged platform
SYSTEM - ubic.gemma.core.apps.GemmaCLI.CommandGroup
SystemMonitorController - Class in ubic.gemma.web.controller.monitoring: Provide statistics about the system: hibernate, caches etc.
SystemMonitorController() - Constructor for class ubic.gemma.web.controller.monitoring.SystemMonitorController
SystemStatsController - Class in ubic.gemma.web.controller.common.auditAndSecurity: System statistics
SystemStatsController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.SystemStatsController

T

T__0 - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
T__0 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
T__1 - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
T__1 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
T__2 - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
T__2 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
TableMaintenanceUtil - Interface in ubic.gemma.persistence.service
TableMaintenanceUtilImpl - Class in ubic.gemma.persistence.service: Functions for maintaining the database.
TableMaintenanceUtilImpl() - Constructor for class ubic.gemma.persistence.service.TableMaintenanceUtilImpl
TAS - ubic.gemma.model.association.GOEvidenceCode
Task<C extends TaskCommand> - Interface in ubic.gemma.core.tasks
TaskCancelledException - Exception in ubic.gemma.persistence.util: author: anton date: 27/03/13
TaskCancelledException(String) - Constructor for exception ubic.gemma.persistence.util.TaskCancelledException
taskCommand - Variable in class ubic.gemma.core.tasks.AbstractTask
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
TaskCommand(Long) - Constructor for class ubic.gemma.core.job.TaskCommand: Convenience constructor for case where all the job needs to know is the id.
TaskCommandToTaskMatcher - Interface in ubic.gemma.core.job.executor.common
TaskCommandToTaskMatcherImpl - Class in ubic.gemma.core.job.executor.common
TaskCommandToTaskMatcherImpl() - Constructor for class ubic.gemma.core.job.executor.common.TaskCommandToTaskMatcherImpl
TaskCompletionController - Class in ubic.gemma.web.controller: Exposes progress status service check result to the front end.
TaskCompletionController() - Constructor for class ubic.gemma.web.controller.TaskCompletionController
TaskPostProcessing - Interface in ubic.gemma.core.job.executor.common: author: anton date: 10/02/13
TaskPostProcessingImpl - Class in ubic.gemma.core.job.executor.common: author: anton date: 10/02/13
TaskPostProcessingImpl() - Constructor for class ubic.gemma.core.job.executor.common.TaskPostProcessingImpl
TaskResult - Class in ubic.gemma.core.job: This class describes the result of long-running task.
TaskResult(String) - Constructor for class ubic.gemma.core.job.TaskResult
TaskResult(TaskCommand, Object) - Constructor for class ubic.gemma.core.job.TaskResult
TaskRunningService - Interface in ubic.gemma.core.job.executor.webapp
TaskRunningServiceImpl - Class in ubic.gemma.core.job.executor.webapp: Handles the execution of tasks in threads that can be checked by clients later.
TaskRunningServiceImpl() - Constructor for class ubic.gemma.core.job.executor.webapp.TaskRunningServiceImpl
TAXA_IN_USE - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
TaxaWebService - Class in ubic.gemma.rest: RESTful interface for taxa.
TaxaWebService() - Constructor for class ubic.gemma.rest.TaxaWebService: Required by spring
TaxaWebService(TaxonService, ExpressionExperimentService, PhenotypeAssociationManagerService, TaxonArgService, DatasetArgService, GeneArgService) - Constructor for class ubic.gemma.rest.TaxaWebService: Constructor for service autowiring
Taxon - Class in ubic.gemma.model.genome
Taxon() - Constructor for class ubic.gemma.model.genome.Taxon: No-arg constructor added to satisfy javabean contract
TAXON_HUMAN - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
TAXON_MOUSE - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
TAXON_RAT - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants: Deprecated.
Taxon.Factory - Class in ubic.gemma.model.genome
TaxonArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for Taxon API
TaxonArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.TaxonArg
TaxonArgService - Class in ubic.gemma.rest.util.args
TaxonArgService(TaxonService, ChromosomeService, GeneService) - Constructor for class ubic.gemma.rest.util.args.TaxonArgService
TaxonArrayArg - Class in ubic.gemma.rest.util.args
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
TaxonIdArg - Class in ubic.gemma.rest.util.args: Long argument type for taxon API, referencing the Taxon ID.
TaxonLoader - Class in ubic.gemma.core.loader.genome.taxon: Load taxa into the system.
TaxonLoader() - Constructor for class ubic.gemma.core.loader.genome.taxon.TaxonLoader
TaxonLoaderCli - Class in ubic.gemma.core.apps
TaxonLoaderCli() - Constructor for class ubic.gemma.core.apps.TaxonLoaderCli
TaxonNameArg - Class in ubic.gemma.rest.util.args: String argument type for taxon API, referencing the Taxon scientific name or common name.
TaxonNcbiIdArg - Class in ubic.gemma.rest.util.args: Long argument type for taxon API, referencing the Taxon ID.
TaxonParser - Class in ubic.gemma.core.loader.genome.taxon: Parse the "names.dmp" file from NCBI, ftp://ftp.ncbi.nih.gov/pub/taxonomy/.
TaxonParser() - Constructor for class ubic.gemma.core.loader.genome.taxon.TaxonParser
TaxonPropertyEditor - Class in ubic.gemma.web.propertyeditor: Used to convert Taxon from and into strings for display in forms.
TaxonPropertyEditor(TaxonService) - Constructor for class ubic.gemma.web.propertyeditor.TaxonPropertyEditor
taxonService - Variable in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
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
TaxonUtility - Class in ubic.gemma.persistence.util: A utility class for taxon.
TaxonUtility() - Constructor for class ubic.gemma.persistence.util.TaxonUtility
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
TaxonWithUsageStatisticsValueObject(Taxon, Long) - Constructor for class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject
technicalReplicateExtract - ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType
technicalReplicateLabeledExtract - ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType
TechnologyType - Enum in ubic.gemma.model.expression.arrayDesign
temperature - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
TEMPERATURE - ubic.gemma.model.common.measurement.MeasurementKind
test(BioAssaySet) - Static method in class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtils
TEST - Static variable in class ubic.gemma.persistence.util.EnvironmentProfiles
TestComponent - Annotation Type in ubic.gemma.persistence.util: This will exclude the component or configuration from component scanning.
TEXT - ubic.gemma.core.loader.entrez.EutilFetch.Mode
TEXT_PARAM - Static variable in class ubic.gemma.web.view.TextView: Name of parameter used to retrieve the text from the model.
TEXT_TAB_SEPARATED_VALUES_UTF8 - Static variable in class ubic.gemma.rest.util.MediaTypeUtils
TEXT_TAB_SEPARATED_VALUES_UTF8_TYPE - Static variable in class ubic.gemma.rest.util.MediaTypeUtils
TextView - Class in ubic.gemma.web.view: Simply prints text to the client.
TextView() - Constructor for class ubic.gemma.web.view.TextView
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<T>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
thaw(Collection<T>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService
thaw(Collection<T>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao: Thaw a collection of vectors.
thaw(Collection<DifferentialExpressionAnalysis>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
thaw(Collection<DifferentialExpressionAnalysis>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl
thaw(Collection<BibliographicReference>) - Method in interface ubic.gemma.core.annotation.reference.BibliographicReferenceService
thaw(Collection<BibliographicReference>) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
thaw(Collection<BibliographicReference>) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
thaw(Collection<BibliographicReference>) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
thaw(Collection<ArrayDesign>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
thaw(Collection<ArrayDesign>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
thaw(Collection<BioAssay>) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
thaw(Collection<BioAssay>) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl
thaw(Collection<DesignElementDataVector>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorService: Thaw both raw and processed vectors.
thaw(Collection<DesignElementDataVector>) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl: Deprecated.
thaw(Collection<BioMaterial>) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
thaw(Collection<BioMaterial>) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
thaw(Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
thaw(Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
thaw(Collection<CompositeSequence>) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
thaw(Collection<CompositeSequence>) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl
thaw(Collection<BioSequence>) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
thaw(Collection<BioSequence>) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
thaw(Collection<BioSequence>) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
thaw(Collection<BioSequence>) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
thaw(Collection<AnnotationAssociation>) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao
thaw(Collection<AnnotationAssociation>) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl
thaw(Collection<BlatAssociation>) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao
thaw(Collection<BlatAssociation>) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl
thaw(Collection<BlatResult>) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao
thaw(Collection<BlatResult>) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl
thaw(Collection<BlatResult>) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService
thaw(Collection<BlatResult>) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl
thaw(T) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao
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.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.core.annotation.reference.BibliographicReferenceService
thaw(BibliographicReference) - Method in class ubic.gemma.core.annotation.reference.BibliographicReferenceServiceImpl
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(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.ArrayDesignService
thaw(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
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.BioAssayDimensionDao
thaw(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl
thaw(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
thaw(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl
thaw(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao: Thaw the given BioMaterial.
thaw(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
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.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.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(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
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.BioSequenceService
thaw(BioSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
thaw(Gene) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
thaw(Gene) - Method in class ubic.gemma.core.genome.gene.service.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.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.BlatResultService
thaw(BlatResult) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl
thawAliases(Gene) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
thawAliases(Gene) - Method in class ubic.gemma.core.genome.gene.service.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
thawBioAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
thawBioAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
thawBioAssays(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
thawBioAssays(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
thawForFrontEnd(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
thawForFrontEnd(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
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<ArrayDesign>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
thawLite(Collection<ArrayDesign>) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
thawLite(Collection<Gene>) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
thawLite(Collection<Gene>) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
thawLite(Collection<Gene>) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
thawLite(Collection<Gene>) - 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.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.BioAssayDimensionDao
thawLite(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl
thawLite(BioAssayDimension) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
thawLite(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl
thawLite(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService: Partially thaw the expression experiment given - do not thaw the raw data.
thawLite(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
thawLite(Gene) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
thawLite(Gene) - Method in class ubic.gemma.core.genome.gene.service.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.ExpressionExperimentService
thawLiter(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
thawLiter(Gene) - Method in interface ubic.gemma.core.genome.gene.service.GeneService
thawLiter(Gene) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl
thawLiter(Gene) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
thawLiter(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
thawWithoutVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
thawWithoutVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
thirdPartyReanalysis - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
ThreadPoolTaskExecutorMetrics - Class in ubic.gemma.core.metrics.binder
ThreadPoolTaskExecutorMetrics(ThreadPoolTaskExecutor) - Constructor for class ubic.gemma.core.metrics.binder.ThreadPoolTaskExecutorMetrics
ThreePrimeDistanceMethod - Enum in ubic.gemma.model.genome.sequenceAnalysis
time - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
TIME - ubic.gemma.model.common.measurement.MeasurementKind
TimeUtil - Class in ubic.gemma.core.util
TimeUtil() - Constructor for class ubic.gemma.core.util.TimeUtil
TMP_DATA_DIR - Static variable in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
toAnalysis() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
toAnalysis() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
toDesignElementDataVector(ExpressionExperiment, CompositeSequence, QuantitationType) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
toEntity() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
toggleUsability(String) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoBrowserService
toggleUsability(String) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
toggleUsability(String) - Method in class ubic.gemma.web.controller.expression.experiment.GeoRecordBrowserController
tokenNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer: Deprecated.
Use FilterArgLexer.VOCABULARY instead.
tokenNames - Static variable in class ubic.gemma.rest.util.args.FilterArgParser: Deprecated.
Use FilterArgParser.VOCABULARY instead.
toList() - Method in interface ubic.gemma.core.search.SearchService.SearchResultMap
toModifiable() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject
tooFewDistinctValues(ExpressionDataDoubleMatrix, double) - Static method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter: Remove rows that have a low diversity of values (equality judged based on tolerancee set in RowLevelFilter).
tooFewDistinctValues(ExpressionDataDoubleMatrix, double, double) - Static method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
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
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
toProcessedDataVectors() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
toRawDataVectors() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Same as toProcessedDataVectors but uses RawExpressionDataVector
toResponse(JsonMappingException) - Method in class ubic.gemma.rest.providers.JsonMappingExceptionMapper
toResponse(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper
toString() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
toString() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
toString() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt
toString() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis
toString() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
toString() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
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.filter.FilterConfig
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.datastructure.matrix.ExpressionDataDoubleMatrix
toString() - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement
toString() - Method in class ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException.SuspiciousValueResult
toString() - Method in class ubic.gemma.core.image.aba.AbaGene
toString() - Method in class ubic.gemma.core.loader.expression.geo.GeoConverterImpl
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.GeoRecord
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.genome.gene.ncbi.model.NcbiGeneHistory
toString() - Method in class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
toString() - Method in class ubic.gemma.core.search.SearchResult
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.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
toString() - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
toString() - Method in class ubic.gemma.model.analysis.expression.coexpression.SupportDetails
toString() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult
toString() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
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.ExpressionAnalysisResultSet
toString() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression
toString() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
toString() - Method in class ubic.gemma.model.association.Gene2GeneAssociation
toString() - Method in class ubic.gemma.model.association.Gene2GeneIdAssociation
toString() - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
toString() - Method in class ubic.gemma.model.common.AbstractDescribable
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
toString() - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType
toString() - Method in class ubic.gemma.model.common.description.AnnotationValueObject
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.LocalFile
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.search.SearchSettings
toString() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
toString() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssay.BioAssayValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
toString() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
toString() - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
toString() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
toString() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperiment
toString() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
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.Statement
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.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.phenotype.valueObject.DumpsValueObject
toString() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
toString() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
toString() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
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.sequenceAnalysis.SequenceSimilaritySearchResult
toString() - Method in class ubic.gemma.model.genome.Taxon
toString() - Method in class ubic.gemma.persistence.model.Gene2CsStatus
toString() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject
toString() - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
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 ubic.gemma.persistence.util.Sort.Direction
toString() - Method in class ubic.gemma.persistence.util.Sort
toString() - Method in class ubic.gemma.persistence.util.Subquery
toString() - Method in class ubic.gemma.rest.util.args.AbstractArg
toString() - Method in class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
toString() - Method in class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand
toString() - Method in class ubic.gemma.web.controller.visualization.FactorProfile
toString() - Method in class ubic.gemma.web.controller.visualization.GeneExpressionProfile
toString() - Method in class ubic.gemma.web.controller.visualization.VisualizationValueObject
toString() - Method in class ubic.gemma.web.remote.EntityDelegator
toString() - Method in class ubic.gemma.web.util.LabelValue
toString(int) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
total() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject: Equivalent to getLinksWithMinimumSupport( 0 )
totalRecords - Variable in class ubic.gemma.web.remote.JsonReaderResponse
totalRNA - ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
totalSize(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
toText() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
toXMLString(Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.
transactionalMethod() - Method in class ubic.gemma.core.util.Pointcuts: A transactional method, public and annotated with Transactional.
transferTo(File) - Method in class ubic.gemma.web.util.upload.CommonsMultipartFile: Deprecated.
transformedCount - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
transformList(List) - Method in interface ubic.gemma.persistence.util.TypedResultTransformer: Deprecated.
Use TypedResultTransformer.transformListTyped(List) instead.
transformListTyped(List<T>) - Method in interface ubic.gemma.persistence.util.TypedResultTransformer
transformTuple(Object[], String[]) - Method in interface ubic.gemma.persistence.util.TypedResultTransformer
TRANSPOSON - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
treatment - 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: No-arg constructor added to satisfy javabean contract
Treatment.Factory - Class in ubic.gemma.model.expression.biomaterial
TreeCharacteristicValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
TreeCharacteristicValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject: Required when using the class as a spring bean.
TreeCharacteristicValueObject(String, String) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
TreeCharacteristicValueObject(String, String, TreeSet<TreeCharacteristicValueObject>) - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
trim() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject: Deprecated.
because this is too ad hoc and messy
TRNA - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
TroubledStatusFlagEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType: Sets the trouble flag of curation details of any Curatable object.
TroubledStatusFlagEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent
TsvFileService<T> - Interface in ubic.gemma.core.analysis.service: Interface for services that produce TSV serialization.
TTEST - ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType
TWO_WAY_ANOVA_NO_INTERACTION - ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType
TWO_WAY_ANOVA_WITH_INTERACTION - ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType
TwoChannelMissingValueController - Class in ubic.gemma.web.controller.analysis.preprocess: Run misssing value computation via web request.
TwoChannelMissingValueController() - Constructor for class ubic.gemma.web.controller.analysis.preprocess.TwoChannelMissingValueController
TwoChannelMissingValueHelperService - Interface in ubic.gemma.core.analysis.preprocess
TwoChannelMissingValues - Interface in ubic.gemma.core.analysis.preprocess
TwoChannelMissingValuesImpl - Class in ubic.gemma.core.analysis.preprocess: Computes a missing value matrix for ratiometric data sets.
TwoChannelMissingValuesImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl
TwoChannelMissingValueTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression
TwoChannelMissingValueTaskCommand(ExpressionExperiment) - Constructor for class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
TwoChannelMissingValueTaskCommand(ExpressionExperiment, double, Collection<Double>) - Constructor for class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
TwoChannelMissingValueTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression: Space task for computing two channel missing values.
TwoChannelMissingValueTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskImpl
TWOCOLOR - ubic.gemma.model.expression.arrayDesign.TechnologyType: Indicates this platform uses two channels and expression measurements are ratios.
type - Variable in class ubic.gemma.core.analysis.report.AuditableObject
TypedResultTransformer<T> - Interface in ubic.gemma.persistence.util: Overrides Hibernate ResultTransformer interface to include type safety.
typeStringToGeneType(String) - Static method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo: Convert string to GeneType.

U

U - ubic.gemma.model.analysis.expression.diff.Direction: Up
U - ubic.gemma.model.common.auditAndSecurity.AuditAction: Update
ubic.gemma.core.analysis.expression - package ubic.gemma.core.analysis.expression
ubic.gemma.core.analysis.expression.coexpression - package ubic.gemma.core.analysis.expression.coexpression
ubic.gemma.core.analysis.expression.coexpression.links - package ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff - package ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess - package ubic.gemma.core.analysis.preprocess
ubic.gemma.core.analysis.preprocess.batcheffects - package ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.filter - package ubic.gemma.core.analysis.preprocess.filter
ubic.gemma.core.analysis.preprocess.normalize - package ubic.gemma.core.analysis.preprocess.normalize
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.util - package ubic.gemma.core.analysis.util
ubic.gemma.core.annotation.reference - package ubic.gemma.core.annotation.reference
ubic.gemma.core.apps - package ubic.gemma.core.apps
ubic.gemma.core.association.phenotype - package ubic.gemma.core.association.phenotype
ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence - package ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence
ubic.gemma.core.datastructure.matrix - package ubic.gemma.core.datastructure.matrix
ubic.gemma.core.expression.experiment - package ubic.gemma.core.expression.experiment
ubic.gemma.core.expression.experiment.service - package ubic.gemma.core.expression.experiment.service
ubic.gemma.core.externalDb - package ubic.gemma.core.externalDb
ubic.gemma.core.genome.gene - package ubic.gemma.core.genome.gene
ubic.gemma.core.genome.gene.service - package ubic.gemma.core.genome.gene.service
ubic.gemma.core.image - package ubic.gemma.core.image
ubic.gemma.core.image.aba - package ubic.gemma.core.image.aba
ubic.gemma.core.job - package ubic.gemma.core.job
ubic.gemma.core.job.executor.common - package ubic.gemma.core.job.executor.common
ubic.gemma.core.job.executor.webapp - package ubic.gemma.core.job.executor.webapp
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.association.phenotype - package ubic.gemma.core.loader.association.phenotype
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
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.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.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.util - package ubic.gemma.core.loader.expression.geo.util
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
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.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.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 - package ubic.gemma.core.logging
ubic.gemma.core.logging.log4j - package ubic.gemma.core.logging.log4j
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.cache - package ubic.gemma.core.metrics.binder.cache
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.jena - package ubic.gemma.core.ontology.jena: This package contains all the Jena-related code for ontologies that Gemma needs.
ubic.gemma.core.ontology.providers - package ubic.gemma.core.ontology.providers
ubic.gemma.core.search - package ubic.gemma.core.search
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.audit - package ubic.gemma.core.security.audit
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.tasks - package ubic.gemma.core.tasks
ubic.gemma.core.tasks.analysis.coexp - package ubic.gemma.core.tasks.analysis.coexp
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.visualization - package ubic.gemma.core.visualization
ubic.gemma.model - package ubic.gemma.model
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.annotations - package ubic.gemma.model.annotations
ubic.gemma.model.association - package ubic.gemma.model.association
ubic.gemma.model.association.coexpression - package ubic.gemma.model.association.coexpression
ubic.gemma.model.association.phenotype - package ubic.gemma.model.association.phenotype
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 - package ubic.gemma.model.expression
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.gene.phenotype - package ubic.gemma.model.genome.gene.phenotype
ubic.gemma.model.genome.gene.phenotype.valueObject - package ubic.gemma.model.genome.gene.phenotype.valueObject
ubic.gemma.model.genome.sequenceAnalysis - package ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.hibernate - package ubic.gemma.persistence.hibernate
ubic.gemma.persistence.model - package ubic.gemma.persistence.model
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.coexpression - package ubic.gemma.persistence.service.analysis.expression.coexpression
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.association.coexpression - package ubic.gemma.persistence.service.association.coexpression
ubic.gemma.persistence.service.association.phenotype - package ubic.gemma.persistence.service.association.phenotype
ubic.gemma.persistence.service.association.phenotype.service - package ubic.gemma.persistence.service.association.phenotype.service
ubic.gemma.persistence.service.common - package ubic.gemma.persistence.service.common
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.util - package ubic.gemma.persistence.util
ubic.gemma.rest - package ubic.gemma.rest
ubic.gemma.rest.analytics - package ubic.gemma.rest.analytics
ubic.gemma.rest.analytics.ga4 - package ubic.gemma.rest.analytics.ga4
ubic.gemma.rest.annotations - package ubic.gemma.rest.annotations
ubic.gemma.rest.providers - package ubic.gemma.rest.providers
ubic.gemma.rest.security - package ubic.gemma.rest.security
ubic.gemma.rest.serializers - package ubic.gemma.rest.serializers
ubic.gemma.rest.servlet - package ubic.gemma.rest.servlet
ubic.gemma.rest.swagger.resolver - package ubic.gemma.rest.swagger.resolver
ubic.gemma.rest.util - package ubic.gemma.rest.util
ubic.gemma.rest.util.args - package ubic.gemma.rest.util.args
ubic.gemma.web.controller - package ubic.gemma.web.controller
ubic.gemma.web.controller.analysis.expression.coexpression.links - package ubic.gemma.web.controller.analysis.expression.coexpression.links
ubic.gemma.web.controller.analysis.preprocess - package ubic.gemma.web.controller.analysis.preprocess
ubic.gemma.web.controller.analysis.sequence - package ubic.gemma.web.controller.analysis.sequence
ubic.gemma.web.controller.coexpressionSearch - package ubic.gemma.web.controller.coexpressionSearch
ubic.gemma.web.controller.common - package ubic.gemma.web.controller.common
ubic.gemma.web.controller.common.auditAndSecurity - package ubic.gemma.web.controller.common.auditAndSecurity
ubic.gemma.web.controller.common.auditAndSecurity.recaptcha - package ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
ubic.gemma.web.controller.common.description.bibref - package ubic.gemma.web.controller.common.description.bibref
ubic.gemma.web.controller.common.rss - package ubic.gemma.web.controller.common.rss
ubic.gemma.web.controller.diff - package ubic.gemma.web.controller.diff
ubic.gemma.web.controller.expression.arrayDesign - package ubic.gemma.web.controller.expression.arrayDesign
ubic.gemma.web.controller.expression.bioAssay - package ubic.gemma.web.controller.expression.bioAssay
ubic.gemma.web.controller.expression.biomaterial - package ubic.gemma.web.controller.expression.biomaterial
ubic.gemma.web.controller.expression.designElement - package ubic.gemma.web.controller.expression.designElement
ubic.gemma.web.controller.expression.experiment - package ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.genome - package ubic.gemma.web.controller.genome
ubic.gemma.web.controller.genome.gene - package ubic.gemma.web.controller.genome.gene
ubic.gemma.web.controller.monitoring - package ubic.gemma.web.controller.monitoring
ubic.gemma.web.controller.visualization - package ubic.gemma.web.controller.visualization
ubic.gemma.web.feed - package ubic.gemma.web.feed
ubic.gemma.web.job.progress - package ubic.gemma.web.job.progress
ubic.gemma.web.listener - package ubic.gemma.web.listener
ubic.gemma.web.logging - package ubic.gemma.web.logging
ubic.gemma.web.metrics - package ubic.gemma.web.metrics
ubic.gemma.web.metrics.binder.servlet - package ubic.gemma.web.metrics.binder.servlet
ubic.gemma.web.persistence - package ubic.gemma.web.persistence
ubic.gemma.web.propertyeditor - package ubic.gemma.web.propertyeditor
ubic.gemma.web.remote - package ubic.gemma.web.remote
ubic.gemma.web.scheduler - package ubic.gemma.web.scheduler
ubic.gemma.web.services - package ubic.gemma.web.services
ubic.gemma.web.taglib - package ubic.gemma.web.taglib
ubic.gemma.web.taglib.arrayDesign - package ubic.gemma.web.taglib.arrayDesign
ubic.gemma.web.taglib.common.auditAndSecurity - package ubic.gemma.web.taglib.common.auditAndSecurity
ubic.gemma.web.taglib.expression.experiment - package ubic.gemma.web.taglib.expression.experiment
ubic.gemma.web.tasks.analysis.sequence - package ubic.gemma.web.tasks.analysis.sequence
ubic.gemma.web.util - package ubic.gemma.web.util
ubic.gemma.web.util.upload - package ubic.gemma.web.util.upload
ubic.gemma.web.view - package ubic.gemma.web.view
uMatrixAsExpressionData() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
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.
UnhandledExceptionMapper - Class in ubic.gemma.rest.providers: Render unhandled exceptions.
UnhandledExceptionMapper() - Constructor for class ubic.gemma.rest.providers.UnhandledExceptionMapper
UnhandledExceptionResolver - Class in ubic.gemma.web.util: Resolver used when no other resolver can intervene.
UnhandledExceptionResolver() - Constructor for class ubic.gemma.web.util.UnhandledExceptionResolver
UNINFORMATIVE_HEADERS_FAILURE - 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
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
UNKNOWN - ubic.gemma.core.job.SubmittedTask.Status
UNKNOWN - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
UNKNOWN - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus
UNKNOWN - ubic.gemma.model.common.quantitationtype.GeneralType
unmarkAsMissing(Collection<BioAssay>) - Method in interface ubic.gemma.core.analysis.service.OutlierFlaggingService: Reverts the action of markAsMissing.
unmarkAsMissing(Collection<BioAssay>) - Method in class ubic.gemma.core.analysis.service.OutlierFlaggingServiceImpl
unmarkOutlier(Collection<Long>) - Method in class ubic.gemma.web.controller.expression.bioAssay.BioAssayController
unmatchAllBioAssays(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: Completely reset the pairing of bioassays to biomaterials, so they are no longer paired.
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
unPackFile(Collection<LocalFile>) - Method in interface ubic.gemma.core.loader.util.fetcher.HttpArchiveFetcherInterface
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<? super String>) - 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 - ubic.gemma.model.common.quantitationtype.ScaleType: An unscaled measurement is one that has no inherent scale; e.g., a categorial value.
UnsuitableForAnalysisException - Exception in ubic.gemma.core.analysis.expression.coexpression.links: *
UnsuitableForAnalysisException(ExpressionExperiment, String) - Constructor for exception ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException
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
UnsupportedQuantitationScaleConversionException - Exception in ubic.gemma.core.analysis.preprocess: Exception raised when data from a given scale cannot be converted to another scale.
UnsupportedQuantitationScaleConversionException(ScaleType, ScaleType) - Constructor for exception ubic.gemma.core.analysis.preprocess.UnsupportedQuantitationScaleConversionException
UnsupportedRawdataFileFormatException - Exception 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 ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException
UP - Static variable in enum ubic.gemma.model.analysis.expression.diff.Direction: Aliases for readability.
update(C) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
update(User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
update(UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl
update(String) - Method in interface ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
update(String) - Method in class ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl
update(String, String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
update(Collection<C>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.CuratableService
update(Collection<O>) - Method in class ubic.gemma.persistence.service.AbstractService
update(Collection<O>) - Method in interface ubic.gemma.persistence.service.BaseService: Updates all entities in the given collection in the persistent storage.
update(Collection<T>) - Method in class ubic.gemma.persistence.service.AbstractDao
update(Collection<T>) - Method in interface ubic.gemma.persistence.service.BaseDao
update(Collection<CoexpressionAnalysis>) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
update(Collection<ExpressionExperimentSet>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
update(Collection<User>) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
update(Collection<ExternalDatabase>) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
update(Collection<QuantitationType>) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
update(Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
update(Collection<ExperimentalDesign>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
update(Collection<ExperimentalFactor>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
update(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
update(Collection<FactorValue>) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService
update(Collection<DatabaseBackedGeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
update(Collection<GeneProduct>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
update(Collection<GeneSet>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
update(Collection<GeneSet>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
update(Collection<Taxon>) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
update(O) - Method in class ubic.gemma.persistence.service.AbstractService
update(O) - Method in interface ubic.gemma.persistence.service.BaseService: Updates the given entity in the persistent storage.
update(T) - Method in class ubic.gemma.persistence.service.AbstractDao
update(T) - Method in interface ubic.gemma.persistence.service.BaseDao
update(CoexpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
update(DifferentialExpressionAnalysis) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
update(ExpressionExperimentSet) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
update(ExpressionExperimentSet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
update(PhenotypeAssociation) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
update(Contact) - Method in interface ubic.gemma.persistence.service.common.auditAndSecurity.ContactService
update(User) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl
update(UserGroup) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl
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(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService
update(BioMaterial) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
update(CompositeSequence) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
update(ExperimentalDesign) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
update(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
update(FactorValue) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService
update(BioSequence) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
update(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
update(GeneSet) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService
update(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
update(EvidenceValueObject<? extends PhenotypeAssociation>) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Modify an existing evidence
update(EvidenceValueObject<? extends PhenotypeAssociation>) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
update(BlatResult) - Method in interface ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService
update(Taxon) - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService
UPDATE - Static variable in enum ubic.gemma.model.common.auditAndSecurity.AuditAction: Aliases, for readability.
updateBasics(UpdateEEDetailsCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
updateBioMaterials(Collection<BioMaterialValueObject>) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService: Update the biomaterials that are described by the given valueObjects.
updateBioMaterials(Collection<BioMaterialValueObject>) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl
updateBioMaterials(BioMaterialValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
updateCharacteristics(Collection<AnnotationValueObject>) - Method in class ubic.gemma.web.controller.common.CharacteristicBrowserController: Update characteristics associated with entities.
updateCounts() - Method in class ubic.gemma.web.controller.common.GemmaClassicHomePageController: Deprecated.
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent: 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
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionEvent
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent
updateCurationDetails(CurationDetails, AuditEvent) - Method in class ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent
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.AbstractCuratableDao
updateCurationDetailsFromAuditEvent(Curatable, AuditEvent) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDaoImpl
updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService: AJAX Updates the database entity (permission permitting) with the fields of the param value object
updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject>) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
updateDatabaseEntity(ExpressionExperimentSetValueObject) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: Update corresponding entity based on value object
updateDatabaseEntity(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
updateDatabaseEntityMembers(Long, Collection<Long>) - Method in interface ubic.gemma.core.genome.gene.service.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<Long>) - Method in class ubic.gemma.core.genome.gene.service.GeneSetServiceImpl
updateDatabaseEntityMembers(Long, Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: 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.
updateDatabaseEntityMembers(Long, Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl: update the members of the experiment set with the given ids
updateDatabaseEntityNameDesc(ExpressionExperimentSetValueObject, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService: Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.
updateDatabaseEntityNameDesc(ExpressionExperimentSetValueObject, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject) - Method in interface ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneSetServiceImpl
UpdateEE2CCli - Class in ubic.gemma.core.apps
UpdateEE2CCli() - Constructor for class ubic.gemma.core.apps.UpdateEE2CCli
UpdateEEDetailsCommand - Class in ubic.gemma.core.tasks.analysis.expression
UpdateEEDetailsCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
updateExperimentalFactors(ExperimentalFactorValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
updateExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager
updateExperimentSet(SessionBoundExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
updateExpressionExperiment2ArrayDesignEntries() - Method in interface ubic.gemma.persistence.service.TableMaintenanceUtil: Update the EXPRESSION_EXPERIMENT2_ARRAY_DESIGN table.
updateExpressionExperiment2ArrayDesignEntries() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilImpl
updateExpressionExperiment2CharacteristicEntries(boolean) - Method in interface ubic.gemma.persistence.service.TableMaintenanceUtil: Update the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
updateExpressionExperiment2CharacteristicEntries(boolean) - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilImpl
updateExpressionExperiment2CharacteristicEntries(Class<?>, boolean) - Method in interface ubic.gemma.persistence.service.TableMaintenanceUtil: Update a specific level of the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
updateExpressionExperiment2CharacteristicEntries(Class<?>, boolean) - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilImpl
updateFactorValueCharacteristics(FactorValueValueObject[]) - Method in class ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
updateFromGEO(String) - Method in interface ubic.gemma.core.loader.expression.geo.service.GeoService: Refetch and reprocess the GEO series, updating select information.
updateFromGEO(String) - Method in class ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
updateGene2CsEntries() - Method in interface ubic.gemma.persistence.service.TableMaintenanceUtil: If necessary, update the GENE2CS table.
updateGene2CsEntries() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilImpl
updateGeneSet(SessionBoundGeneSetValueObject) - Method in interface ubic.gemma.web.persistence.SessionListManager
updateGeneSet(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.persistence.SessionListManagerImpl
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
updateMembers(Long, Collection<Long>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Updates the given group (permission permitting) with the given list of memberIds.
updateMembers(Long, Collection<Long>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
updateModifiedSupportDetails(BioAssaySet, Collection<SupportDetails>, Collection<SupportDetails>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
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
updateNameDesc(ExpressionExperimentSetValueObject) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.
updateNameDesc(DatabaseBackedGeneSetValueObject) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
updateNodeDegree(Gene, GeneCoexpressionNodeDegree) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao: This is a maintenance method.
updateNodeDegree(Gene, GeneCoexpressionNodeDegree) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
updateNodeDegrees(Taxon) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionService
updateNodeDegrees(Taxon) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl
updateNumDatasetsSupporting() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression: Refresh the value of numDataSetsSupporting after updating supportDetails (use during modification of the data...)
updatePermission(SecurityInfoValueObject) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
updatePermission(SecurityInfoValueObject) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
updatePermissions(SecurityInfoValueObject[]) - Method in interface ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
updatePermissions(SecurityInfoValueObject[]) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl
updatePubMed(Long, String) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController: AJAX.
UpdatePubMedCli - Class in ubic.gemma.core.apps: Identify experiments in Gemma that have no publication Fetch their GEO records and check for pubmed IDs Add the publications where we find them.
UpdatePubMedCli() - Constructor for class ubic.gemma.core.apps.UpdatePubMedCli
UpdatePubMedCommand - Class in ubic.gemma.core.tasks.analysis.expression
UpdatePubMedCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
UpdatePubMedCommand(Long) - Constructor for class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
updater() - Method in class ubic.gemma.core.util.Pointcuts: Methods that update items in the persistent store
updateRanks(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
updateRanks(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
updateRelativeNodeDegrees(Map<Long, List<Double>>, Map<Long, List<Double>>) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
updateRelativeNodeDegrees(Map<Long, List<Double>>, Map<Long, List<Double>>) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl
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
updateReport(EntityDelegator<ArrayDesign>) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
updateReport(EntityDelegator<ArrayDesign>) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
updateReportById(Long) - Method in interface ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
updateReportById(Long) - Method in class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignControllerImpl
updateSessionGroup(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX updates a session group
updateSessionGroups(Collection<SessionBoundGeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: Deprecated.
updateSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Updates the session group.
updateSet(GemmaSessionBackedValueObject) - Method in class ubic.gemma.web.persistence.AbstractSetListContainer
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
updateTaxaWithGenesUsable(Collection<Taxon>) - 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
updateUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController: AJAX Updates the session group and user database groups.
updateUserAndSessionGroups(Collection<GeneSetValueObject>) - Method in class ubic.gemma.web.controller.genome.gene.GeneSetController: AJAX Updates the session group and user database groups.
updateUserGroups(UserDetails, Collection<String>) - Method in interface ubic.gemma.core.security.authentication.UserManager: Update the groups a user belong to.
updateUserGroups(UserDetails, Collection<String>) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
upload(InputStream) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController: Ajax.
UploadInfo - Class in ubic.gemma.web.util.upload
UploadInfo() - Constructor for class ubic.gemma.web.util.upload.UploadInfo
UploadInfo(int, long, long, String) - Constructor for class ubic.gemma.web.util.upload.UploadInfo
UploadListener - Class in ubic.gemma.web.util.upload: This is created when a multipart request is received (via the CommonsMultipartMonitoredResolver).
UploadListener(HttpServletRequest) - Constructor for class ubic.gemma.web.util.upload.UploadListener
UploadListener(HttpServletRequest, long) - Constructor for class ubic.gemma.web.util.upload.UploadListener
URL - Static variable in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
useDataFromGeo() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
usedToBe(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
User - Class in ubic.gemma.model.common.auditAndSecurity: A user of the software system, who is authenticated.
User() - Constructor for class ubic.gemma.model.common.auditAndSecurity.User
User.Factory - Class in ubic.gemma.model.common.auditAndSecurity
UserCounterListener - Class in ubic.gemma.web.listener: Count active sessions
UserCounterListener() - Constructor for class ubic.gemma.web.listener.UserCounterListener
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
userExists(String) - Method in interface ubic.gemma.core.security.authentication.UserManager
userExists(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
UserFormMultiActionController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Controller to edit profile of users.
UserFormMultiActionController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController
UserGroup - Class in ubic.gemma.model.common.auditAndSecurity: An organized group of researchers with an identifiable leader and group members.
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
UserGroupValueObject - Class in ubic.gemma.web.controller.common.auditAndSecurity
UserGroupValueObject() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
UserIdRetrievalStrategy - Interface in ubic.gemma.rest.analytics.ga4: Strategy for retrieving a user ID.
UserListController - Interface in ubic.gemma.web.controller.common.auditAndSecurity: Note: do not use parameterized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take.
UserListControllerImpl - Class in ubic.gemma.web.controller.common.auditAndSecurity: For display and editing of users.
UserListControllerImpl() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserListControllerImpl
UserManager - Interface in ubic.gemma.core.security.authentication: Overrides gsec's UserManager to provide Gemma-specific types.
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
UserQuery - Class in ubic.gemma.model.common.auditAndSecurity
UserQuery() - Constructor for class ubic.gemma.model.common.auditAndSecurity.UserQuery
UserQuery.Factory - Class in ubic.gemma.model.common.auditAndSecurity
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
UserTracker - Class in ubic.gemma.web.listener: Basic bean to hold number of sessions.
UserTracker() - Constructor for class ubic.gemma.web.listener.UserTracker
UserUpdateCommand - Class in ubic.gemma.web.controller.common.auditAndSecurity: Just like a regular user; but has 'new password' and 'confirm password' fields.
UserUpdateCommand() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
UserValueObject - Class in ubic.gemma.web.controller.common.auditAndSecurity
UserValueObject() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
UserValueObject(User) - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
UserValueObject(User, String) - Constructor for class ubic.gemma.rest.RootWebService.UserValueObject
userWithEmailExists(String) - Method in interface ubic.gemma.core.security.authentication.UserManager
userWithEmailExists(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl

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.
validate(SimpleExpressionExperimentLoadTaskCommand) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
validateEvidence(EvidenceValueObject<PhenotypeAssociation>) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Validate an Evidence before we create it
validateEvidence(EvidenceValueObject<PhenotypeAssociation>) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
ValidateEvidenceValueObject - Class in ubic.gemma.model.genome.gene.phenotype.valueObject
ValidateEvidenceValueObject() - Constructor for class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject
validatePhenotypeAssociationForm(EvidenceValueObject<PhenotypeAssociation>) - Method in class ubic.gemma.web.controller.PhenotypeController
validateRequest(HttpServletRequest) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
validateSignupToken(String, String) - Method in interface ubic.gemma.core.security.authentication.UserManager
validateSignupToken(String, String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
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.
value() - Method in annotation type ubic.gemma.rest.annotations.CacheControls
valueId - Variable in class ubic.gemma.model.common.description.CharacteristicValueObject: A unique ontology identifier (i.e.
ValueObject - Annotation Type in ubic.gemma.model: Annotate class representing value objects.
valueObject2Entity(EvidenceValueObject<? extends PhenotypeAssociation>) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelper: Deprecated.

Changes all type of evidenceValueObject to their corresponding entities
valueObject2Entity(EvidenceValueObject<? extends PhenotypeAssociation>) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelperImpl: Deprecated.
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(String) - Static method in enum ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.NormalizationMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.SingularThreshold: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.apps.GemmaCLI.CommandGroup: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.apps.ShellDelegatingBlat.BlattableGenome: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.job.SubmittedTask.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.entrez.EutilFetch.Mode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoSample.LibraryStrategy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.ontology.GoMetric.Metric: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.analysis.expression.diff.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.association.GOEvidenceCode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.common.auditAndSecurity.AuditAction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.common.description.DatabaseType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.common.measurement.MeasurementKind: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.common.measurement.MeasurementType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.common.quantitationtype.GeneralType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.common.quantitationtype.PrimitiveType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.common.quantitationtype.ScaleType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.common.search.SearchSettings.SearchMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.expression.arrayDesign.TechnologyType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.expression.experiment.BatchEffectType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.expression.experiment.FactorType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.genome.biosequence.PolymerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.genome.biosequence.SequenceType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.persistence.util.Filter.Operator: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ubic.gemma.persistence.util.Sort.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.CompositeSequenceArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatabaseEntryArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatabaseEntryArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatasetArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatasetArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.ExcludeArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.ExpLevelConsolidationArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.FactorValueArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.FactorValueArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.FilterArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.GeneArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.GeneArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.LimitArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.OffsetArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.PlatformArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.PlatformArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.QuantitationTypeArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.QueryArg
valueOf(String) - Static method in enum ubic.gemma.rest.util.args.SortArg.Sort.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.SortArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.StringArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.TaxonArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.TaxonArrayArg: Used by RS to parse value of request parameters.
values() - Static method in enum ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.NormalizationMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.SingularThreshold: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.apps.GemmaCLI.CommandGroup: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.apps.ShellDelegatingBlat.BlattableGenome: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.expression.experiment.ExpressionExperimentMetaFileType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.job.SubmittedTask.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.entrez.EutilFetch.Mode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoSample.LibraryStrategy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.ontology.GoMetric.Metric: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.analysis.expression.diff.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.association.GOEvidenceCode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.common.auditAndSecurity.AuditAction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.common.description.DatabaseType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.common.measurement.MeasurementKind: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.common.measurement.MeasurementType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.common.quantitationtype.GeneralType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.common.quantitationtype.PrimitiveType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.common.quantitationtype.ScaleType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.common.search.SearchSettings.SearchMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.expression.arrayDesign.TechnologyType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.expression.experiment.BatchEffectType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.expression.experiment.FactorType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.genome.biosequence.PolymerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.genome.biosequence.SequenceType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.persistence.util.Filter.Operator: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.persistence.util.Sort.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ubic.gemma.rest.util.args.SortArg.Sort.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
valueUri2Characteristic(String) - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper: Deprecated.

Helper method.
valueUri2Characteristic(String) - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl: Deprecated.
var - Variable in class ubic.gemma.web.taglib.ConstantsTag: The single variable to expose.
VAR - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
VectorElementValueObject() - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
VectorElementValueObject(String, Map<String, Double>) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
VectorElementValueObject(DoubleVectorValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject
VectorMergingCli - Class in ubic.gemma.core.apps: For experiments that used multiple array designs, merge the expression profiles
VectorMergingCli() - Constructor for class ubic.gemma.core.apps.VectorMergingCli
VectorMergingService - Interface in ubic.gemma.core.analysis.preprocess
VectorMergingServiceImpl - Class in ubic.gemma.core.analysis.preprocess: Tackles the problem of concatenating DesignElementDataVectors for a single experiment.
VectorMergingServiceImpl() - Constructor for class ubic.gemma.core.analysis.preprocess.VectorMergingServiceImpl
vectorsToMatrix(Collection<? extends DesignElementDataVector>) - Method in class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
vectorsToMatrix(Collection<? extends DesignElementDataVector>) - Method in class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
vectorsToMatrix(Collection<? extends DesignElementDataVector>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
vectorsToMatrix(Collection<? extends DesignElementDataVector>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix: Convert DesignElementDataVectors into Double matrix.
vectorsToMatrix(Collection<? extends DesignElementDataVector>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
vectorsToMatrix(Collection<? extends DesignElementDataVector>) - Method in class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
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
VIEW_DIR - Static variable in interface ubic.gemma.core.analysis.report.DatabaseViewGenerator
VIEW_FILE_SUFFIX - Static variable in interface ubic.gemma.core.analysis.report.DatabaseViewGenerator
visitCharacteristics(Long, Collection<StatementValueObject>, FactorValueOntologyUtils.StatementVisitor<String, E>) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Visit the characteristics of a FactorValue and generate their annotation IDs.
visitErrorNode(ErrorNode) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
visitStatements(Long, Collection<StatementValueObject>, FactorValueOntologyUtils.StatementVisitor<FactorValueOntologyUtils.AnnotationIds, E>) - Static method in class ubic.gemma.core.ontology.FactorValueOntologyUtils: Visit the statements of a FactorValue and generate their annotation IDs.
visitTerminal(TerminalNode) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
VisualizationValueObject - Class in ubic.gemma.web.controller.visualization: Stores expression profile data from one expression experiment for plotting.
VisualizationValueObject() - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
VisualizationValueObject(Collection<DoubleVectorValueObject>, Collection<GeneValueObject>, Double, Collection<DifferentialExpressionValueObject>) - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
VisualizationValueObject(Collection<DoubleVectorValueObject>, List<GeneValueObject>, Collection<Long>) - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
VisualizationValueObject(Collection<DoubleVectorValueObject>, List<GeneValueObject>, Collection<Long>, Double) - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
VisualizationValueObject(DoubleVectorValueObject) - Constructor for class ubic.gemma.web.controller.visualization.VisualizationValueObject
visualizeCorrMat(Long, Double, String, Boolean, Boolean, Boolean, Boolean, OutputStream) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizeMeanVariance(Long, Double, Boolean, OutputStream) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizeProbeCorrDist(Long, OutputStream) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
visualizePvalueDist(Long, Long, Long, String, Integer, OutputStream) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
VOCABULARY - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
VOCABULARY - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
VOLUME - ubic.gemma.model.common.measurement.MeasurementKind

W

waitForDownload(FutureTask<Boolean>) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
waitForDownload(FutureTask<Boolean>, long, File) - Method in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
WebApplicationExceptionMapper - Class in ubic.gemma.rest.providers: Map WebApplicationException so that it always expose a ResponseErrorObject entity.
WebApplicationExceptionMapper() - Constructor for class ubic.gemma.rest.providers.WebApplicationExceptionMapper
WebConstants - Class in ubic.gemma.web.controller: Constant values used throughout the web portion of Gemma.
WebConstants() - Constructor for class ubic.gemma.web.controller.WebConstants
weekly(HttpServletRequest, HttpServletResponse) - Method in class ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController
WellComposedErrorBody - Class in ubic.gemma.rest.util: Object acting as a payload for the ResponseErrorObject.
WellComposedErrorBody(Response.Status, String) - Constructor for class ubic.gemma.rest.util.WellComposedErrorBody: Creates a new well composed error body that can be used as a payload for a GemmaApiException, or ResponseErrorObject.
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
WhatsNewController - Class in ubic.gemma.web.controller.common.auditAndSecurity: Controller to provide information on "what's new" in the system
WhatsNewController() - Constructor for class ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController
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 object that are new in the system.
WhatsNewServiceImpl() - Constructor for class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
WHOLE_CHROMOSOME - ubic.gemma.model.genome.biosequence.SequenceType
WHOLE_GENOME - ubic.gemma.model.genome.biosequence.SequenceType
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)
withHighlights(Map<String, String>) - Method in class ubic.gemma.core.search.SearchResult: Copy this search result with the given highlights.
withResultObject(S) - Method in class ubic.gemma.core.search.SearchResult: Create a search result from an existing one, replacing the result object with the target one.
write(byte[]) - Method in class ubic.gemma.web.util.upload.MonitoredOutputStream
write(byte[], int, int) - Method in class ubic.gemma.web.util.upload.MonitoredOutputStream
write(int) - Method in class ubic.gemma.web.util.upload.MonitoredOutputStream
write(Writer, ExpressionDataMatrix<?>, Map<CompositeSequence, Collection<Gene>>, boolean, boolean) - Method in class ubic.gemma.core.datastructure.matrix.MatrixWriter
write(Writer, ExpressionDataMatrix<?>, Map<CompositeSequence, Collection<Gene>>, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.core.datastructure.matrix.MatrixWriter
write(Writer, ExpressionExperiment, boolean) - Method in class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriter
write(Writer, ExpressionExperiment, Collection<BioAssay>, boolean, boolean) - Method in class ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriter
write(T, File, String) - Method in class ubic.gemma.core.analysis.service.AbstractFileService
write(T, File, String) - Method in interface ubic.gemma.core.analysis.service.FileService
write(T, Writer, String) - Method in class ubic.gemma.core.analysis.service.AbstractFileService
write(T, Writer, String) - Method in interface ubic.gemma.core.analysis.service.FileService: Write a given entity to an appendable with a given content type.
writeAllEvidenceToFile() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService: Deprecated.

Creates a dump of all evidence in the database that can be downloaded on the client, this is run once per month by Quartz
writeAllEvidenceToFile() - Method in class ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl: Deprecated.
writeCharacteristics(Long, Collection<StatementValueObject>, JsonGenerator) - Method in class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer
writeDiffExArchiveFile(BioAssaySet, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Writes to the configured gemma.appdata.home The file created is a zip archive containing at least two files.
writeDiffExArchiveFile(BioAssaySet, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeEigenGenes(Long) - Method in class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
writeErrorToResponse(int, String, HttpServletResponse) - Static method in class ubic.gemma.web.util.JsonUtil
writeErrorToResponse(Exception, HttpServletResponse) - Static method in class ubic.gemma.web.util.JsonUtil
writeErrorToResponse(AuthenticationException, HttpServletResponse) - Static method in class ubic.gemma.web.util.JsonUtil
writeFinalHeader(BufferedWriter) - Static method in class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo: Deprecated.
writeFinalLine(BufferedWriter) - Method in class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo: Deprecated.
writeFolder - Variable in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
writeJson(T, File) - Method in class ubic.gemma.core.analysis.service.AbstractFileService
writeJson(T, File) - Method in interface ubic.gemma.core.analysis.service.JsonFileService
writeJson(T, Writer) - Method in class ubic.gemma.core.analysis.service.AbstractFileService
writeJson(T, Writer) - Method in interface ubic.gemma.core.analysis.service.JsonFileService: Write a given entity to JSON.
writeJSON(Writer, ExpressionDataMatrix<?>) - Method in class ubic.gemma.core.datastructure.matrix.MatrixWriter
writeOrLocateCoexpressionDataFile(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write or located the coexpression data file for a given experiment
writeOrLocateCoexpressionDataFile(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDesignFile(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create an experimental design file for a given experiment.
writeOrLocateDesignFile(ExpressionExperiment, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeOrLocateDiffExpressionDataFiles(ExpressionExperiment, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Locate or create the differential expression data file(s) for a given experiment.
writeOrLocateDiffExpressionDataFiles(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
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
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
writeProcessedExpressionData(ExpressionExperiment, Writer) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Write processed expression data to a given writer for a given quantitation type.
writeProcessedExpressionData(ExpressionExperiment, Writer) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeProcessedExpressionDataFile(ExpressionExperiment, boolean, String, boolean) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService: Create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).
writeProcessedExpressionDataFile(ExpressionExperiment, boolean, String, boolean) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeRawExpressionData(ExpressionExperiment, QuantitationType, Writer) - 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, Writer) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeReport(Element, Document, String) - Method in class ubic.gemma.web.services.AbstractGemmaEndpoint: This method should/can only be used when the wrapper is manually built in the specific endpoints (ie.
writeSequencesToFile(Collection<BioSequence>, File) - Static method in class ubic.gemma.core.analysis.sequence.SequenceWriter: Write a collection of sequences in FASTA format
writeStatements(Long, Collection<StatementValueObject>, JsonGenerator) - Method in class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer
writeToDebugLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger: Write to log with severity = "debug"
writeToErrorLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger: Write to log with severity = "error"
writeToFatalLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger: Write to log with severity = "fatal"
writeToInfoLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger: Write to log with severity = "info"
writeToLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger: Defaults to writing to log with severity = "info"
writeToRdf(String, Writer) - Method in interface ubic.gemma.core.ontology.FactorValueOntologyService
writeToRdf(String, Writer) - Method in class ubic.gemma.core.ontology.FactorValueOntologyServiceImpl: Write a small RDF model for a given factor value or annotation.
writeToResponse(JSONObject, HttpServletResponse) - Static method in class ubic.gemma.web.util.JsonUtil
writeToWarnLog(String, String, String, String, String) - Method in class ubic.gemma.web.util.JavascriptLogger: Write to log with severity = "warn"
writeTsv(T, File) - Method in class ubic.gemma.core.analysis.service.AbstractFileService
writeTsv(T, File) - Method in interface ubic.gemma.core.analysis.service.TsvFileService
writeTsv(T, Writer) - Method in interface ubic.gemma.core.analysis.service.TsvFileService: Write the given entity to tabular format.
writeTsv(ExpressionDataMatrix<?>, Writer) - Method in class ubic.gemma.core.datastructure.matrix.MatrixWriter
writeTsv(ExpressionAnalysisResultSet, Writer) - Method in class ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileServiceImpl
writeTsv(ExpressionExperiment, Writer) - Method in class ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl
writeTsvToAppendable(ExpressionAnalysisResultSet, Map<Long, List<Gene>>, Writer) - Method in interface ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileService: Write the analysis result set to an Appendable using a tabular format.
writeTsvToAppendable(ExpressionAnalysisResultSet, Map<Long, List<Gene>>, Writer) - Method in class ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileServiceImpl
writeWithStringifiedGeneAnnotations(Writer, ExpressionDataMatrix<?>, Map<CompositeSequence, String[]>, boolean) - Method in class ubic.gemma.core.datastructure.matrix.MatrixWriter: Alternate method that uses annotations in string form (e.g., read from another file).
writeWithStringifiedGeneAnnotations(Writer, ExpressionDataMatrix<?>, Map<CompositeSequence, String[]>, boolean, boolean, boolean, boolean) - Method in class ubic.gemma.core.datastructure.matrix.MatrixWriter
WS - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
WS - Static variable in class ubic.gemma.rest.util.args.FilterArgParser

X

X - ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
XML - ubic.gemma.core.loader.entrez.EutilFetch.Mode
XML_PARAM - Static variable in class ubic.gemma.web.view.XmlView: Name of the parameter that is used to retrieve the xml from the model.
XMLUtils - Class in ubic.gemma.core.util: Handy methods for dealing with XML.
XMLUtils() - Constructor for class ubic.gemma.core.util.XMLUtils
XmlView - Class in ubic.gemma.web.view: Model should contain a single value matching XML_PARAM
XmlView() - Constructor for class ubic.gemma.web.view.XmlView
XREF - Static variable in class ubic.gemma.model.association.phenotype.PhenotypeMappingType: Deprecated.

Z

zeroVarianceFilter(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter: Remove rows that have a variance of zero (within a small constant)
Zscore - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
ZSCORE - ubic.gemma.model.common.quantitationtype.StandardQuantitationType: Standard deviations from the mean

_

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

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