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

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

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

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

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

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

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

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

Acquire a read-only lock on the given key in the cache.

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(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.

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

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

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.

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.

addEventsToMap(Map<Long, Collection<AuditEvent>>, Long, AuditEvent) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao

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

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

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

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.

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

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

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

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).

addUserToGroup(UserGroup, User) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl

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

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

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

AffyProbeNameFilter - Class in ubic.gemma.core.analysis.preprocess.filter

AffyProbeNameFilter(AffyProbeNameFilter.Pattern[]) - Constructor for class ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter

AffyProbeNameFilter.Pattern - Enum 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

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.job.executor.webapp.TaskRunningServiceImpl

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.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

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

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

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

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

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

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

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_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

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.

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

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.

appearsInMultipleSeries() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample

append(LoggingEvent) - Method in class ubic.gemma.core.job.executor.common.ProgressUpdateAppender

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.

ArchiveFetcher - Interface in ubic.gemma.core.loader.util.fetcher

Interface defining a class that downloads archives and unpacks them.

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

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

An event involving the analysis of an ArrayDesign

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

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

Methods to generate annotations for array designs, based on information already in the database.

ArrayDesignAnnotationService.OutputType - Enum in ubic.gemma.core.analysis.service

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

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

ArrayDesignDao - Interface in ubic.gemma.persistence.service.expression.arrayDesign

Created by tesarst on 13/03/17.

ArrayDesignDaoImpl - Class in ubic.gemma.persistence.service.expression.arrayDesign

ArrayDesignDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl

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

The mapping of probes to genes for an ArrayDesign

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

ArrayDesignMapResultService - Interface in ubic.gemma.core.analysis.sequence

ArrayDesignMapResultServiceImpl - Class in ubic.gemma.core.analysis.sequence

Supports obtaining detailed information about the sequence analysis of probes on microarrays.

ArrayDesignMapResultServiceImpl(BlatResultService, BlatAssociationService, ArrayDesignService, CompositeSequenceService) - Constructor for class ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl

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

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

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

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

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

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

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

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

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

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

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

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

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 - 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 - 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

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

baseCodeConfigurer(PropertySources) - Static method in class ubic.gemma.persistence.util.SettingsConfig

BaseCodeConfigurer - Class in ubic.gemma.persistence.util

Configure the baseCode library from a given property sources.

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

BaseCodeOntologySearchException - Exception in ubic.gemma.core.search

Exception that wraps a baseCode OntologySearchException.

BaseCodeOntologySearchException(OntologySearchException) - Constructor for exception ubic.gemma.core.search.BaseCodeOntologySearchException

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

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.

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(BatchInformationEvent, boolean, boolean) - Constructor for class ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails

BatchEffectDetails.BatchEffectStatistics - Class in ubic.gemma.core.analysis.preprocess.batcheffects

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

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

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

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

bindImplementationSpecificMetrics(MeterRegistry) - Method in class ubic.gemma.core.metrics.binder.cache.EhCache24Metrics

bindTo(MeterRegistry) - Method in class ubic.gemma.core.job.executor.webapp.TaskRunningServiceImpl

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.ThreadPoolExecutorMetrics

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

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

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

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.

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

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, 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

BrowsingDao<T> - Interface in ubic.gemma.persistence.service

Support for paging through the data.

build() - Method in class ubic.gemma.persistence.util.Filters.FiltersClauseBuilder

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.

BuildInfo - Class in ubic.gemma.core.util

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

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

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

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

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

CacheKeyLock - Interface in ubic.gemma.persistence.cache

Represents a lock over a cache key.

CacheKeyLock.LockAcquisition - Interface in ubic.gemma.persistence.cache

Represents an acquired lock on a cache key.

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

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

CANCELLING - ubic.gemma.core.job.SubmittedTask.Status

canConvertFromId(Class<? extends IdentifiableValueObject<?>>) - Method in class ubic.gemma.core.search.SearchServiceImpl

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

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.

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

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

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

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

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

cleanUp(File) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher

cleanUpQueryName(String) - Static method in class ubic.gemma.core.loader.genome.BlatResultParser

clear() - Method in 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.

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

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

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

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.cache.CacheKeyLock.LockAcquisition

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

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

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

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.

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

compare(DifferentialExpressionAnalysisResult, DifferentialExpressionAnalysisResult) - Method in class ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator

compare(Describable, Describable) - Method in class ubic.gemma.persistence.util.DescribableComparator

compare(FactorValue, FactorValue) - Method in class ubic.gemma.persistence.util.FactorValueComparator

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

Compare a pair of ontology terms.

compareTo(Object) - Method in class ubic.gemma.model.genome.ChromosomeLocation

compareTo(Object) - Method in class ubic.gemma.model.genome.PhysicalLocation

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

COMPLETED - ubic.gemma.core.job.SubmittedTask.Status

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

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

CompositeSequenceMapSummary - Class in ubic.gemma.core.analysis.sequence

This is a convenience object to hold the results of CompositeSequence mapping results.

CompositeSequenceMapSummary(CompositeSequence) - Constructor for class ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary

CompositeSequenceMapValueObject - Class in ubic.gemma.core.analysis.sequence

CompositeSequenceMapValueObject() - Constructor for class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject

CompositeSequenceParser - Class in ubic.gemma.core.loader.expression.arrayDesign

Parse the "old" array description format.

CompositeSequenceParser() - Constructor for class ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser

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

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

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.MeterRegistryEhcacheConfigurer

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

connect(int) - Method in class ubic.gemma.core.util.NetDatasourceUtil

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

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

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

convertMembers2GeneValueObjects(Collection<GeneSetMember>) - Static method in class ubic.gemma.model.genome.gene.GeneValueObject

A static method for easily converting GeneSetMembers into GeneValueObjects

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

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

cosine - ubic.gemma.core.ontology.GoMetric.Metric

count - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType

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.

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<GeneSet>) - Method in interface ubic.gemma.core.genome.gene.service.GeneSetService

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.

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

createEELink(BioAssaySet, Long, Long, Long) - Method in class ubic.gemma.persistence.service.association.coexpression.LinkCreator

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, List<GrantedAuthority>) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl

createInstance() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory

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

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

creator() - Method in class ubic.gemma.core.util.Pointcuts

Methods that create new objects in the persistent store

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

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

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

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

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

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

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.

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

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.

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_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 - 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

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

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

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

deleteFactorValues(Collection<Long>) - Method in interface ubic.gemma.core.expression.experiment.FactorValueDeletion

deleteFactorValues(Collection<Long>) - Method in class ubic.gemma.core.expression.experiment.FactorValueDeletionImpl

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

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_BETWEEN_BIOMATERIAL_AND_BIOASSAYS - Static variable in class ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils

DESC - ubic.gemma.persistence.util.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

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.persistence.util.AbstractAsyncFactoryBean

destroyInstance(T) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory

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

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

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

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

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.

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

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

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

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

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.

disableEmail() - Method in interface ubic.gemma.persistence.service.TableMaintenanceUtil

disableEmail() - Method in class ubic.gemma.persistence.service.TableMaintenanceUtilImpl

For use in tests.

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

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

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.

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

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

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

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

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.

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).

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

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

EhcacheKeyLock - Class in ubic.gemma.persistence.cache

EhcacheKeyLock(Ehcache, Object, boolean) - Constructor for class ubic.gemma.persistence.cache.EhcacheKeyLock

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.

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

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.

EntityNotFoundException - Exception in ubic.gemma.core.association.phenotype

Deprecated.

EntityNotFoundException(String) - Constructor for exception ubic.gemma.core.association.phenotype.EntityNotFoundException

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

eq - ubic.gemma.persistence.util.Filter.Operator

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, 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.

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

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

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

EXP - ubic.gemma.model.association.GOEvidenceCode

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

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

ExperimentalDesignDao - Interface in ubic.gemma.persistence.service.expression.experiment

ExperimentalDesignDaoImpl - Class in ubic.gemma.persistence.service.expression.experiment

ExperimentalDesignDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl

ExperimentalDesignImporter - Interface in ubic.gemma.core.loader.expression.simple

Parse a description of ExperimentalFactors from a file, and associate it with a given ExpressionExperiment.

ExperimentalDesignImporterImpl - Class in ubic.gemma.core.loader.expression.simple

See interface for docs.

ExperimentalDesignImporterImpl() - Constructor for class ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl

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

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

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

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

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

ExperimentPlatformSwitchHelperService - Interface in ubic.gemma.core.loader.expression

Use to finish final transactional step in updating platform

experimentType - Variable in class ubic.gemma.core.loader.expression.geo.model.GeoDataset

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

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

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

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

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

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

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

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

ExpressionExperimentLoadTask - Interface in ubic.gemma.core.tasks.analysis.expression

ExpressionExperimentLoadTaskCommand - Class in ubic.gemma.core.tasks.analysis.expression

ExpressionExperimentLoadTaskCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand

ExpressionExperimentLoadTaskCommand(boolean, boolean, String, boolean, boolean, String) - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand

ExpressionExperimentLoadTaskImpl - Class in ubic.gemma.core.tasks.analysis.expression

ExpressionExperimentLoadTaskImpl() - Constructor for class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskImpl

ExpressionExperimentMetaFileType - Enum in ubic.gemma.core.expression.experiment

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

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

The event that this 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

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

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

ExpressionExperimentSetDao - Interface in ubic.gemma.persistence.service.analysis.expression

ExpressionExperimentSetDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression

ExpressionExperimentSetDaoImpl(SessionFactory, ExpressionExperimentDao) - Constructor for class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl

ExpressionExperimentSetService - Interface in ubic.gemma.persistence.service.expression.experiment

ExpressionExperimentSetServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment

Spring Service base class for ubic.gemma.model.analysis.expression.ExpressionExperimentSetService, provides access to all services and entities referenced by this service.

ExpressionExperimentSetServiceImpl(ExpressionExperimentSetDao) - 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

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

ExpressionPersister - Class in ubic.gemma.persistence.persister

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

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

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

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

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

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.

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

extractTermsDnf(SearchSettings, boolean) - 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

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

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

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

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

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.

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

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

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

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

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.

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(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(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.

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

FilterCriteriaUtils - Class in ubic.gemma.persistence.util

Utilities for integrating Filter with Hibernate Criteria API.

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

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, 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.

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.

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(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.

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.

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

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

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.

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

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.

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.

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, int, boolean) - Method in interface ubic.gemma.core.ontology.OntologyService

Deprecated.

findExperimentsCharacteristicTags(String, int, boolean, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService

Deprecated.

findExperimentsCharacteristicTags(String, int, 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

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.

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

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

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

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

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, int) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl

findTerms(String, int) - Method in interface ubic.gemma.core.ontology.OntologyService

findTerms(String, int, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService

Given a search string will look through the loaded ontologies for terms that match the search term.

findTerms(String, int, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl

findTermsInexact(String, int, Taxon) - Method in interface ubic.gemma.core.ontology.OntologyService

findTermsInexact(String, int, Taxon, long, TimeUnit) - Method in interface ubic.gemma.core.ontology.OntologyService

Given a search string will first look through the characteristic database for any entries that have a match.

findTermsInexact(String, int, Taxon, long, TimeUnit) - Method in class ubic.gemma.core.ontology.OntologyServiceImpl

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

FOLDCHANGE - ubic.gemma.model.common.quantitationtype.ScaleType

Deprecated, do not use.

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.

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.

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

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

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.

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.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

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

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

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

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

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

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

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

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

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

geneExpressionRTPCRbased - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType

geneExpressionSAGEbased - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType

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

GeneOntologyService - Interface in ubic.gemma.core.ontology.providers

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

Gene Ontology

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

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.

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.

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

generateSummary(Long) - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService

Generate a value object that contain summary information about links, biomaterials, and datavectors

generateSummary(Long) - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl

generateSummaryObjects() - Method in interface ubic.gemma.core.analysis.report.ExpressionExperimentReportService

Generates reports on ALL experiments, including 'private' ones.

generateSummaryObjects() - Method in class ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl

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

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 - 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

GeneSetDao - Interface in ubic.gemma.persistence.service.genome.gene

The interface for managing groupings of genes.

GeneSetDaoImpl - Class in ubic.gemma.persistence.service.genome.gene

Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.gene.GeneSet.

GeneSetDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl

GeneSetMember - Class in ubic.gemma.model.genome.gene

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

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

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

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

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.

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(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

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

Deprecated.

getActiveExperiments() - Method in class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject

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

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

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

getAllTaxonExperimentGroup(Long) - Method in interface ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchService

getAllTaxonExperimentGroup(Long) - Method in class ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchServiceImpl

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

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

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

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.

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

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.

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

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

getArrayDesignName() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject

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

getArrayDesigns() - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData

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

getArrayDesignShortName() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject

getArrayDesignsUsageFrequency(int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao

Obtain dataset usage frequency by platform currently used.

getArrayDesignsUsageFrequency(int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl

getArrayDesignsUsageFrequency(Collection<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

getAssemblyDatabase() - Method in class ubic.gemma.model.genome.Chromosome

getAssociationType() - Method in class ubic.gemma.model.association.phenotype.PhenotypeAssociation

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

getAuthorities() - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup

getAuthority() - Method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority

getAuthorList() - Method in class ubic.gemma.model.common.description.BibliographicReference

getAuthorList() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject

getAutoRunFrequencyHours() - Method in class ubic.gemma.model.common.auditAndSecurity.UserQuery

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.

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

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

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

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

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.

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

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

getBoolean(String) - Static method in class ubic.gemma.persistence.util.Settings

Deprecated.

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

getCache(CacheManager, String) - Static method in class ubic.gemma.persistence.util.CacheUtils

Obtain a cache by its name, raising an exception if unavailable.

getCacheName() - Method in class ubic.gemma.core.ontology.providers.GemmaOntologyService

getCacheName() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl

getCacheName() - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService

getCacheName() - Method in class ubic.gemma.core.ontology.providers.PatoOntologyService

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

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.SearchTimeoutException

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

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

getClassName() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject

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

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

getCoexpressionMatrix() - Method in class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix

getCol() - Method in class ubic.gemma.core.loader.expression.arrayDesign.Reporter

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

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.

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

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

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(InputStream) - Method in class ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParser

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

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

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

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

getCurrentUserIsOwner() - Method in class ubic.gemma.model.genome.gene.GeneSetValueObject

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

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

getDatabaseSupplier() - Method in class ubic.gemma.model.common.description.ExternalDatabase

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

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

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

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

getDatasetsAvailable() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject

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

getDatasetShortName() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition

getDataSetsSupporting() - Method in class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression

getDatasetsTested() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject

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

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

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

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

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

getDetail() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEvent

getDetail() - Method in class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject

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(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

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

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

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

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, 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

getEeIds() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand

getEeQuery() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand

getEeSetId() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand

getEeSetName() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand

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

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

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

getEmail() - Method in class ubic.gemma.model.common.auditAndSecurity.Contact

getEmailAlert() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject

getEnabled() - Method in class ubic.gemma.model.common.auditAndSecurity.User

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

getEntityId() - Method in class ubic.gemma.core.job.TaskCommand

getEntityTransformer() - Method in class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao

Obtain an entity transformer for the results of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).

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

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

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

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

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

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

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

getExperimentsInSet(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao

getExperimentsInSet(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl

getExperimentsInSet(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService

Get the (security-filtered) list of experiments in a set.

getExperimentsInSet(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl

getExperimentsLackingPublications() - 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

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(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.

getExpressionExperimentIds() - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject

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

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

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

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

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

getFactorValue() - Method in class ubic.gemma.model.analysis.expression.diff.ContrastResult

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

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

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

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.

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

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

getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService

getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao

getFilterablePropertyAllowedValues(String) - Method in interface ubic.gemma.persistence.service.FilteringDao

Obtain a short list of allowed values for the given property, or null if unrestricted.

getFilterablePropertyAllowedValues(String) - Method in interface ubic.gemma.persistence.service.FilteringService

getFilterablePropertyConfigAttributes(String) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService

getFilterablePropertyConfigAttributes(String) - Method in 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.

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

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

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.

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

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

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.

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.

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

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

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

getGeneExonOverlaps(String, String, String, String, Gene) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation

Given a gene, find out how much of it overlaps with exons provided as starts and sizes.

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

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

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

getGeneId() - Method in class ubic.gemma.core.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

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

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

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

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(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<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

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

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

getGeneSetId() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand

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

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(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

getGroupMembers() - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup

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

getGroups() - Method in class ubic.gemma.model.common.auditAndSecurity.User

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

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

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

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.

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, 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

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

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() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition

Obtain the key that is locked.

getKey(String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser

getKey(Collection<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(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

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.

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

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

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

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, 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

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

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, 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

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

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

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

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

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

getModified() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject

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

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

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

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

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

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

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

getNormalizationDescription() - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign

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

getNumberOfConfigurations() - Static method in class ubic.gemma.persistence.util.Settings

Deprecated.

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

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

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

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

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

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

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

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.core.util.TextResourceToSetOfLinesFactoryBean

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.core.util.TextResourceToSetOfLinesFactoryBean

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

getOldStyleCharacteristics() - Method in class ubic.gemma.model.expression.experiment.FactorValue

Deprecated.

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

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

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

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, 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

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

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

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

getPasswordHint() - Method in class ubic.gemma.model.common.auditAndSecurity.User

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

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

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

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

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

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

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

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(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

getProbeLoadings() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis

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

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, Properties) - Static method in class ubic.gemma.persistence.util.Settings

Deprecated.

getProperty(String) - Static method in class ubic.gemma.persistence.util.Settings

Deprecated.

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

getPvalueDistribution() - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet

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

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

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

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

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(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

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

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

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

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

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

getResource(String) - Static method in class ubic.gemma.persistence.util.Settings

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

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.

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

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

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

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

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

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

getScore() - Method in class ubic.gemma.core.analysis.sequence.GeneMappingSummary

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

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

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

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

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

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

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

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, short) - Static method in class ubic.gemma.persistence.util.Settings

Deprecated.

getShort(String, Short) - Static method in class ubic.gemma.persistence.util.Settings

Deprecated.

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.

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(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(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

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

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

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

getStopWatch() - Method in class ubic.gemma.core.util.StopWatchUtils.StopWatchRegion

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, 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

getSubmittedTasks() - Method in interface ubic.gemma.core.job.executor.webapp.TaskRunningService

getSubmittedTasks() - Method in class ubic.gemma.core.job.executor.webapp.TaskRunningServiceImpl

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

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

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

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

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(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

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

getTaxaWithDatasets() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService

getTaxaWithDatasets() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl

getTaxaWithEvidence() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService

getTaxaWithEvidence() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl

getTaxaWithGenes() - Method in interface ubic.gemma.persistence.service.genome.taxon.TaxonService

getTaxaWithGenes() - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl

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

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

getTaxon() - Method in class ubic.gemma.core.analysis.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(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

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

getTaxonCommonName() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject

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.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

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

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

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

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.

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

getTitleInDataset() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample

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

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

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

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

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(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

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

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

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

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

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

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

getWidth() - Method in class ubic.gemma.core.image.aba.Image

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

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.

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

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

H

H2Dialect - Class in ubic.gemma.persistence.hibernate

H2Dialect() - Constructor for class ubic.gemma.persistence.hibernate.H2Dialect

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(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

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

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

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.

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)

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

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

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

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

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

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

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

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.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

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.".

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

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

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

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

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

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

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

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

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

isCurrentUserHasWritePermission() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject

isCurrentUserIsOwner() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject

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

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.

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

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

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

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.

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

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.

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

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

Deprecated.

Indicate if this FactorValue is a measurement.

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

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(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

isOntologyEnabled() - Method in class ubic.gemma.core.ontology.providers.GemmaOntologyService

isOntologyEnabled() - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl

isOntologyEnabled() - Method in class ubic.gemma.core.ontology.providers.MondoOntologyService

isOntologyEnabled() - Method in class ubic.gemma.core.ontology.providers.PatoOntologyService

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'.

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.

isPublik() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject

isPubmedIdInvalid() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject

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

isReadOnly() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock

Indicate if this lock is read-only.

isReadOnly() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition

Indicate if this lock acquisition is read-only.

isReadOnly() - Method in class ubic.gemma.persistence.cache.EhcacheKeyLock

isReadOnly() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLock

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

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

isSingleton() - Method in class ubic.gemma.core.util.TextResourceToSetOfLinesFactoryBean

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

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

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

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

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

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

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.

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

LATEST_EVIDENCE_EXPORT - Static variable in class ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants

Deprecated.

LEFT - ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod

lessOrEq - ubic.gemma.persistence.util.Filter.Operator

lessThan - ubic.gemma.persistence.util.Filter.Operator

like - ubic.gemma.persistence.util.Filter.Operator

likelyExternalReference(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants

likelyId(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants

likelyProbeDescription(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants

likelyProbeOrganism(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants

likelySequence(String) - Static method in class ubic.gemma.core.loader.expression.geo.util.GeoConstants

lin - 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

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.

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

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(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(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

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(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

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

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

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(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

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

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

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

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

loadDatabase(Persister, Collection<?>) - Static method in class ubic.gemma.core.loader.util.ParserAndLoaderTools

User the loader to persist the collection.

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

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.

loadForExperiment(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService

loadForExperiment(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl

loadFromDirectory(File) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedService

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

Load from a SOFT file.

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

loadFullMatrix(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService

Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.

loadFullMatrix(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl

loadFullyPopulatedValueObject(Long) - Method in interface ubic.gemma.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

loadGenePhenotypes(Long) - Method in interface ubic.gemma.core.genome.gene.service.GeneService

loadGenePhenotypes(Long) - Method in class ubic.gemma.core.genome.gene.service.GeneServiceImpl

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

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

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

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

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

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

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

locatePrimaryReference(ExpressionExperiment) - Method in class ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder

lock() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock

Acquire a lock on the cache key.

lock() - Method in class ubic.gemma.persistence.cache.EhcacheKeyLock

lock() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLock

lockInterruptibly() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock

Acquire a lock interruptibly on a cache key.

lockInterruptibly() - Method in class ubic.gemma.persistence.cache.EhcacheKeyLock

lockInterruptibly() - Method in class ubic.gemma.persistence.cache.StaticCacheKeyLock

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.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

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

LOGBASEUNKNOWN - ubic.gemma.model.common.quantitationtype.ScaleType

logERatio - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType

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

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

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.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser

Deprecated.

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.

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.

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

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

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

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

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

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_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_RUNTIME_MINUTES - Static variable in class ubic.gemma.core.job.TaskCommand

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

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

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

metabolism - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType

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

methylationArraybased - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType

methylationByGenomeTiling - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType

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

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.

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.

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 Disease 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.

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

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

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

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

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

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

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

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

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

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

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

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

OLIGO - ubic.gemma.model.genome.biosequence.SequenceType

Represents a (synthetic) oligonucleotide.

oligonucleotideBeads - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType

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

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

onStart() - Method in interface ubic.gemma.core.job.executor.common.ExecutingTask.TaskLifecycleHandler

Whenever the task execution begins.

onSuccess() - Method in interface ubic.gemma.core.job.executor.common.ExecutingTask.TaskLifecycleHandler

On successful completion.

ONTOLOGY - ubic.gemma.model.common.description.DatabaseType

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

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

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

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

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.

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

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

Phenotype And Trait Ontology

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

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

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

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

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.

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

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

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

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

postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ubic.gemma.persistence.util.BaseCodeConfigurer

postProcessBeforeInitialization(Object, String) - Method in class ubic.gemma.core.util.BeanInitializationTimeMonitor

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.

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

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

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

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

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

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.

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

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

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(PropertySources) - 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

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

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

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

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

queryAndCache(Gene) - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionDao

queryAndCache(Gene) - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl

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.

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.

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

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

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

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

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

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

RelationshipPersister - Class in ubic.gemma.persistence.persister

Persist objects like Gene2GOAssociation.

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

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(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<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<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

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.

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

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

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

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

removeGroupAuthority(UserGroup, String) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl

removeGroupAuthority(String, GrantedAuthority) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl

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).

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)

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

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)

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

removeUserFromGroup(User, UserGroup) - Method in class ubic.gemma.core.security.authentication.UserServiceImpl

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

renameFile(File, File) - Static method in class ubic.gemma.persistence.util.EntityUtils

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

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).

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

requestCancellation() - Method in class ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal

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

Send cancellation request.

requiresLayout() - Method in class ubic.gemma.core.job.executor.common.ProgressUpdateAppender

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

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

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

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

RTPCR - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType

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(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(Integer) - Method in interface ubic.gemma.core.analysis.report.DatabaseViewGenerator

runAll(Integer) - Method in class ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl

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

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

saver() - Method in class ubic.gemma.core.util.Pointcuts

This is a specially behaved method that create transient entities or save persistent one.

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

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

ScanDateExtractor - Interface in ubic.gemma.core.analysis.preprocess.batcheffects

Generic interface for classes that extract scan dates from raw data files.

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(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

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.

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

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.

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

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, 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)

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

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

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

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

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.

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

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

SearchSource - Interface in ubic.gemma.core.search

Search source that provides SearchResult from a search engine.

SearchTimeoutException - Exception in ubic.gemma.core.search

Indicate that the search failed due to a TimeoutException.

SearchTimeoutException(String, TimeoutException) - Constructor for exception ubic.gemma.core.search.SearchTimeoutException

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

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

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.

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

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.

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

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(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.

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

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

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

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(Set<AlternateName>) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign

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

setAnalysis(DifferentialExpressionAnalysis) - Method in class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet

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

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

setAnalysisId(Long) - Method in class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject

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

setArrayDesign(ArrayDesign) - Method in class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand

setArrayDesign(ArrayDesign) - Method in class ubic.gemma.model.expression.designElement.CompositeSequence

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

setArrayDesignName(String) - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject

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

setArrayDesigns(Collection<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

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.

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

setAuthorities(Set<GroupAuthority>) - Method in class ubic.gemma.model.common.auditAndSecurity.UserGroup

setAuthority(String) - Method in class ubic.gemma.model.common.auditAndSecurity.GroupAuthority

setAuthorList(String) - Method in class ubic.gemma.model.common.description.BibliographicReference

setAuthorList(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject

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

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

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(List<BioAssay>) - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimension

setBioAssays(Set<BioAssay>) - Method in class ubic.gemma.model.expression.experiment.BioAssaySet

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

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

setBytes(byte[]) - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray

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

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(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

setClassName(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject

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

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

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

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

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

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

setData(byte[]) - Method in class ubic.gemma.model.expression.bioAssayData.DataVector

setDatabaseSupplier(Contact) - Method in class ubic.gemma.model.common.description.ExternalDatabase

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

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

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

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

setDiffExpressionEvidence(DiffExpressionEvidenceValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject

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

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

setEditable(boolean) - Method in class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject

Deprecated.

setEditor(String) - Method in class ubic.gemma.model.common.description.BibliographicReference

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

setEeIds(Collection<Long>) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand

setEeQuery(String) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand

setEeSetId(Long) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand

setEeSetName(String) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand

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

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.model.common.auditAndSecurity.User

setEnabled(Boolean) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache

setEnabled(Boolean) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl

setEnableGroups(boolean) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl

setEnableSearch(boolean) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory

Enable full-text search for the ontology.

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

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

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

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

setEnsemblId(String) - Method in class ubic.gemma.model.genome.Gene

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

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

setEntityId(Long) - Method in class ubic.gemma.core.job.TaskCommand

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

setErrorFound(boolean) - Method in class ubic.gemma.model.BaseValueObject

setErrorState(String) - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject

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

setExcludedWordsFromStemming(Set<String>) - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory

Set the list of words that should be excluded from stemming.

setExcludePattern(String) - Method in class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher

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

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

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

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

setExpressionExperimentSets(Collection<ExpressionExperimentSetValueObject>) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject

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

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

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

setFactors(Collection<ExperimentalFactor>) - Method in class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand

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

setFactorValues(Set<FactorValue>) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial

setFactorValues(Set<FactorValue>) - Method in class ubic.gemma.model.expression.experiment.ExperimentalFactor

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

setFilter(boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser

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.

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

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

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

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<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

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

setGroups(Set<UserGroup>) - Method in class ubic.gemma.model.common.auditAndSecurity.User

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

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

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

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

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

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

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

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

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

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(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

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

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

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

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.

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

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

setLocalURL(URI) - Method in class ubic.gemma.model.common.description.LocalFile

setLockCheckIntervalMillis(long) - Method in class ubic.gemma.persistence.cache.EhcacheKeyLock

Set the interval to check for lock acquisition in milliseconds when EhcacheKeyLock.lockInterruptibly() is used.

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

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

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

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

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

setMembers(Set<GeneSetMember>) - Method in class ubic.gemma.model.genome.gene.GeneSet

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

setMergees(Set<ArrayDesign>) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign

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

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

setMetadata(String) - Method in class ubic.gemma.model.expression.bioAssay.BioAssay

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

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

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

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

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

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

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

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

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

setNormalizationDescription(String) - Method in class ubic.gemma.model.expression.experiment.ExperimentalDesign

setNormalizationMethod(LinkAnalysisConfig.NormalizationMethod) - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig

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

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

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

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

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

setNumPhenotypes(Long) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject

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

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

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

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

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

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

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

setPasswordHint(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User

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

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

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

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

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

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

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

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

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

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

setProperty(String, Object) - Static method in class ubic.gemma.persistence.util.Settings

Deprecated.

Set an environment/application variable programatically.

setPropertySources(PropertySources) - Method in class ubic.gemma.persistence.util.BaseCodeConfigurer

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

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

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(QuantitationTypeValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject

setQuantitationTypeDescription(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData

setQuantitationTypeName(String) - Method in class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

setShowOnlyEditable(boolean) - Method in class ubic.gemma.model.genome.gene.phenotype.EvidenceFilter

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!)

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

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

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

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

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(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(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

setTaxonName(String) - Method in class ubic.gemma.core.search.SearchResultDisplayObject

setTaxonName(String) - Method in class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject

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

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

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

settingsPropertySources() - Static method in class ubic.gemma.persistence.util.SettingsConfig

Property sources populated from various settings files.

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

setTitleInDataset(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample

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

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(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

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

setUserName(String) - Method in class ubic.gemma.model.common.auditAndSecurity.User

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

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

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

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

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

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

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.

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

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

SimpleMarkdownFormatter - Class in ubic.gemma.core.search.lucene

SimpleMarkdownFormatter() - Constructor for class ubic.gemma.core.search.lucene.SimpleMarkdownFormatter

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

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.

sortFactors(Collection<ExperimentalFactor>) - Static method in class ubic.gemma.core.analysis.util.ExperimentalDesignUtils

Sort factors in a consistent way.

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

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

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

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

StaticCacheKeyLock - Class in ubic.gemma.persistence.cache

Implementation of the CacheKeyLock interface that uses a static week map to store locks by key.

StaticCacheKeyLock(Cache, Object, boolean) - Constructor for class ubic.gemma.persistence.cache.StaticCacheKeyLock

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

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

STRINGARRAY - ubic.gemma.model.common.quantitationtype.PrimitiveType

stripPolyAorT(String, int) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation

Remove a 3' polyA or 5' polyT tail.

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.

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

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

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

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

T

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

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.

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

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

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

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

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

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

TextResourceToSetOfLinesFactoryBean - Class in ubic.gemma.core.util

Converts a text resource into a set of lines.

TextResourceToSetOfLinesFactoryBean(Resource) - Constructor for class ubic.gemma.core.util.TextResourceToSetOfLinesFactoryBean

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

ThreadPoolExecutorMetrics - Class in ubic.gemma.core.metrics.binder

ThreadPoolExecutorMetrics(ThreadPoolExecutor, String) - Constructor for class ubic.gemma.core.metrics.binder.ThreadPoolExecutorMetrics

ThreadPoolTaskExecutorMetrics - Class in ubic.gemma.core.metrics.binder

ThreadPoolTaskExecutorMetrics(ThreadPoolTaskExecutor) - Constructor for class ubic.gemma.core.metrics.binder.ThreadPoolTaskExecutorMetrics

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

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

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(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 )

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.

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

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.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.cache - package ubic.gemma.persistence.cache

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

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.

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

unlock() - Method in interface ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition

Release the lock on the cache key previously acquired with CacheKeyLock.lock() or CacheKeyLock.lockInterruptibly().

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

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, 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<FactorValue>) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService

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.

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

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

UpdateEEDetailsCommand - Class in ubic.gemma.core.tasks.analysis.expression

UpdateEEDetailsCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand

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

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

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

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

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...)

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

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

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

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

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

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

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

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.

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

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.

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.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.

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.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.

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 - 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

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.

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.

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

WhatsNew - Class in ubic.gemma.core.analysis.report

A value object to hold onto the 'new' objects.

WhatsNew() - Constructor for class ubic.gemma.core.analysis.report.WhatsNew

WhatsNew(Date) - Constructor for class ubic.gemma.core.analysis.report.WhatsNew

WhatsNewService - Interface in ubic.gemma.core.analysis.report

Creates reports that can be shown on the web pages or in social media feeds.

WhatsNewServiceImpl - Class in ubic.gemma.core.analysis.report

Service to collect data on 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(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.

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

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.

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

writeSequencesToFile(Collection<BioSequence>, File) - Static method in class ubic.gemma.core.analysis.sequence.SequenceWriter

Write a collection of sequences in FASTA format

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.

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

X

X - ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern

XML - ubic.gemma.core.loader.entrez.EutilFetch.Mode

XMLUtils - Class in ubic.gemma.core.util

Handy methods for dealing with XML.

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

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

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