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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.core.context
Base implementation of AsyncFactoryBean.
AbstractAsyncFactoryBean() - Constructor for class ubic.gemma.core.context.AbstractAsyncFactoryBean
 
AbstractAsyncFactoryBean(ExecutorService) - Constructor for class ubic.gemma.core.context.AbstractAsyncFactoryBean
 
AbstractAuditable - Class in ubic.gemma.model.common.auditAndSecurity
An entity which can have an audit trail attached to it.
AbstractAuditable() - Constructor for class ubic.gemma.model.common.auditAndSecurity.AbstractAuditable
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.job
 
AbstractTask() - Constructor for class ubic.gemma.core.job.AbstractTask
 
AbstractTask(C) - Constructor for class ubic.gemma.core.job.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.cache.CacheUtils
Acquire a read-only lock on the given key in the cache.
acquireWriteLock(Cache, Object) - Static method in class ubic.gemma.persistence.cache.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.persister.ArrayDesignsForExperimentCache
 
add(ArrayDesign, Map<CompositeSequence, BioSequence>) - Method in class ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
 
add(ArrayDesign, Set<CompositeSequence>) - Method in class ubic.gemma.persistence.persister.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.
addBeanPostProcessor(ConfigurableBeanFactory, int, BeanPostProcessor) - Static method in class ubic.gemma.core.context.BeanFactoryUtils
Add a BeanPostProcessor at a specific index of a bean factory.
addBinToQuery(String, Long, Long) - Static method in class ubic.gemma.core.analysis.sequence.SequenceBinUtils
Directly ported from jksrc binRange.c and hdb.c From the binRange.c comments: There's a bin for each 128k segment, for each 1M segment, for each 8M segment, for each 64M segment, and for each chromosome (which is assumed to be less than 512M.) A range goes into the smallest bin it will fit in.
addBioAssays(List<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 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.notification.TaskPostProcessing
 
addEmailNotification(CompletableFuture<? extends TaskResult>, EmailNotificationContext, Executor) - Method in class ubic.gemma.core.job.notification.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.persistence.service.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
 
addPropertyDirect(String, Object) - Method in class ubic.gemma.core.config.PropertySourcesConfiguration
Deprecated.
 
addQuantitationType(GeoPlatform, String, Integer) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoValues
 
addRawDataVectors(ExpressionExperiment, QuantitationType, Collection<RawExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
Add raw data vectors with the given quantitation type.
addRawDataVectors(ExpressionExperiment, QuantitationType, Collection<RawExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
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(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.persister.ArrayDesignsForExperimentCache
 
addToColumnData(String, String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
Add a value to a column.
addToDataProcessing(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addToDbXRefs(String, String) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
 
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
 
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
 
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addToDescription(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSubset
 
addToExtractProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
 
addToGrowthProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoChannel
 
addToHybProtocol(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
addToKeyWords(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addToOrganisms(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
 
addToPubmedIds(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
 
addToRepeatsSampleList(GeoSample) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoReplication
 
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.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
 
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.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
 
AlignmentBasedGeneMappingEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
Signifies a mapping based on sequence alignment performed by the system.
AlignmentBasedGeneMappingEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.AlignmentBasedGeneMappingEvent
 
all - 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(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
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.persistence.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.progress.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.persister
Used to hold information for matching to a new experiment, during persisting.
ArrayDesignsForExperimentCache() - Constructor for class ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
 
ArrayDesignSubsumeCheckEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
 
ArrayDesignSubsumeCheckEvent() - Constructor for class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent
 
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.core.context
Async extension of the FactoryBean interface.
AsyncFactoryBeanUtils - Class in ubic.gemma.core.context
Utilities for manipulating async factory beans.
AsyncFactoryBeanUtils() - Constructor for class ubic.gemma.core.context.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.auditAndSecurity
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.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
 
baseCodeConfigurer(PropertySources) - Static method in class ubic.gemma.core.config.SettingsConfig
 
BaseCodeConfigurer - Class in ubic.gemma.core.config
Configure the baseCode library from a given property sources.
BaseCodeConfigurer() - Constructor for class ubic.gemma.core.config.BaseCodeConfigurer
 
BaseCodeOntologySearchException - Exception 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.common
 
BaseValueObject() - Constructor for class ubic.gemma.model.common.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.model.expression.experiment.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.model.expression.experiment.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.model.expression.experiment.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.model.expression.experiment.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
 
BeanFactoryUtils - Class in ubic.gemma.core.context
Utilities for working with bean factories.
BeanFactoryUtils() - Constructor for class ubic.gemma.core.context.BeanFactoryUtils
 
beanInitializationTimeMonitor() - Static method in class ubic.gemma.core.profiling.ProfilingConfig
 
BeanInitializationTimeMonitor - Class in ubic.gemma.core.profiling
Hook into the bean post-processing lifecycle and record bean initialization time.
BeanInitializationTimeMonitor() - Constructor for class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
 
BeanNameGenerator - Class in ubic.gemma.core.context
Our \@Service etc.
BeanNameGenerator() - Constructor for class ubic.gemma.core.context.BeanNameGenerator
 
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.persistence.service.common.description
 
BibliographicReferenceServiceImpl - Class in ubic.gemma.persistence.service.common.description
Implementation of BibliographicReferenceService.
BibliographicReferenceServiceImpl(BibliographicReferenceDao) - Constructor for class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
BibliographicReferenceValueObject - Class in ubic.gemma.model.common.description
represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists in web
BibliographicReferenceValueObject() - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject
Required when using the class as a spring bean.
BibliographicReferenceValueObject(Long) - Constructor for class ubic.gemma.model.common.description.BibliographicReferenceValueObject
 
BibliographicReferenceValueObject(Long, String, String, String, String, String, String, Date, String, String, String, Collection<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.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) - Static method in class ubic.gemma.core.analysis.sequence.SequenceBinUtils
return bin that this start-end segment is in
binFromRange(int, int) - Method in class ubic.gemma.model.genome.PhysicalLocation
 
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.blacklist
 
BlacklistedEntity() - Constructor for class ubic.gemma.model.blacklist.BlacklistedEntity
 
BlacklistedEntityDao - Interface in ubic.gemma.persistence.service.blacklist
 
BlacklistedEntityDaoImpl - Class in ubic.gemma.persistence.service.blacklist
 
BlacklistedEntityDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
 
BlacklistedEntityService - Interface in ubic.gemma.persistence.service.blacklist
 
BlacklistedEntityServiceImpl - Class in ubic.gemma.persistence.service.blacklist
 
BlacklistedEntityServiceImpl(BlacklistedEntityDao) - Constructor for class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
 
BlacklistedExperiment - Class in ubic.gemma.model.blacklist
TODO Document Me
BlacklistedExperiment() - Constructor for class ubic.gemma.model.blacklist.BlacklistedExperiment
 
BlacklistedPlatform - Class in ubic.gemma.model.blacklist
 
BlacklistedPlatform() - Constructor for class ubic.gemma.model.blacklist.BlacklistedPlatform
 
BlacklistedValueObject - Class in ubic.gemma.model.blacklist
 
BlacklistedValueObject() - Constructor for class ubic.gemma.model.blacklist.BlacklistedValueObject
Required when using the class as a spring bean.
blacklistExpressionExperiment(ExpressionExperiment, String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
Blacklist a given dataset.
blacklistExpressionExperiment(ExpressionExperiment, String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
 
blacklistPlatform(ArrayDesign, String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
Blacklist a given platform.
blacklistPlatform(ArrayDesign, String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
 
Blat - Interface in ubic.gemma.core.analysis.sequence
 
BlatAssociation - Class in ubic.gemma.model.genome.sequenceAnalysis
 
BlatAssociation() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
 
BlatAssociation.Factory - Class in ubic.gemma.model.genome.sequenceAnalysis
 
BlatAssociationDao - Interface in ubic.gemma.persistence.service.genome.sequenceAnalysis
 
BlatAssociationDaoImpl - Class in ubic.gemma.persistence.service.genome.sequenceAnalysis
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type BlatAssociation.
BlatAssociationDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl
 
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.analysis.sequence.Blat
 
blatQuery(Collection<BioSequence>, boolean, Taxon) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
blatQuery(Collection<BioSequence>, Taxon) - Method in interface ubic.gemma.core.analysis.sequence.Blat
 
blatQuery(Collection<BioSequence>, Taxon) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
blatQuery(BioSequence) - Method in interface ubic.gemma.core.analysis.sequence.Blat
Run a BLAT search using the gfClient.
blatQuery(BioSequence) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
blatQuery(BioSequence, Taxon, boolean) - Method in interface ubic.gemma.core.analysis.sequence.Blat
Run a BLAT search using the gfClient.
blatQuery(BioSequence, Taxon, boolean) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
BlatResult - Class in ubic.gemma.model.genome.sequenceAnalysis
Represents the result of a BLAT search.
BlatResult() - Constructor for class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
 
BlatResult.Factory - Class in ubic.gemma.model.genome.sequenceAnalysis
 
BlatResult2Psl - Class in ubic.gemma.core.analysis.sequence
Used to convert BlatResult objects into PSL lines that can be displayed in the UCSC Genome Browser.
BlatResult2Psl() - Constructor for class ubic.gemma.core.analysis.sequence.BlatResult2Psl
 
blatResult2PslTrack(BlatResult) - 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(DesignElementDataVector, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
 
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.BibliographicReferenceService
 
browse(int, int) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
browse(int, int) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
Browse through the characteristics, excluding GO annotations.
browse(int, int) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
 
browse(int, int) - Method in interface ubic.gemma.persistence.service.common.description.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.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.BibliographicReferenceService
 
browse(int, int, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
browse(int, int, String, boolean) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
Browse through the characteristics, excluding GO annotations, with sorting.
browse(int, int, String, boolean) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
 
browse(int, int, String, boolean) - Method in interface ubic.gemma.persistence.service.common.description.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.model.expression.experiment.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.cache
Created by tesarst on 04/04/17.
CacheUtils() - Constructor for class ubic.gemma.persistence.cache.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.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
 
ChromosomeUtils - Class in ubic.gemma.persistence.service.genome
A utility class for Chromosome
ChromosomeUtils() - Constructor for class ubic.gemma.persistence.service.genome.ChromosomeUtils
 
CitationValueObject - Class in ubic.gemma.model.common.description
Represents a BibliographicReference as a citation string (which is really super light value object).
CitationValueObject() - Constructor for class ubic.gemma.model.common.description.CitationValueObject
 
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.
clearAuthentication() - Method in interface ubic.gemma.core.util.GemmaRestApiClient
Clear any credentials.
clearAuthentication() - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
 
clearBioAssays() - Method in class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
 
clearCache() - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
 
clearCache() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
clearCache() - 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.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
 
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
 
clearPropertyDirect(String) - Method in class ubic.gemma.core.config.PropertySourcesConfiguration
Deprecated.
 
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.progress.ProgressUpdateAppender
 
close() - Method in class ubic.gemma.core.job.progress.ProgressUpdateAppender.ProgressUpdateContext
 
close() - Method in class ubic.gemma.core.metrics.binder.jpa.Hibernate4QueryMetrics
 
close() - Method in class ubic.gemma.core.profiling.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
 
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
Create processed vectors and update ranks.
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
Create processed vectors and update ranks.
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.cache.CacheUtils
Check if a cache contains a given key.
containsKey(CompositeSequence) - Method in class ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
 
containsKeyInternal(String) - Method in class ubic.gemma.core.config.PropertySourcesConfiguration
Deprecated.
 
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.core.config.SettingsConfig
The default Spring conversion service has limited support for Java 8 types.
convert(Object) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
 
convert(Object, TypeDescriptor, TypeDescriptor) - Method in class ubic.gemma.persistence.util.ServiceBasedEntityConverter
 
convert(Object, TypeDescriptor, TypeDescriptor) - Method in class ubic.gemma.persistence.util.ServiceBasedValueObjectConverter
 
convert(Collection<?>) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter
 
convert(Collection<? 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.model.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.persistence.service.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.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl
 
convertToGOValueObject(GeneSet, String, String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
Method to create a GO group object from an ad hoc entity
convertToGOValueObject(GeneSet, String, String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
 
convertToLightValueObject(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
Constructor to build value object from GeneSet.
convertToLightValueObject(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
 
convertToLightValueObjects(Collection<GeneSet>, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
results will be sorted by size
convertToLightValueObjects(Collection<GeneSet>, boolean) - Method in class ubic.gemma.persistence.service.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.persistence.service.genome.gene.GeneSetValueObjectHelper
Constructor to build value object from GeneSet.
convertToValueObject(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
 
convertToValueObjects(Collection<GeneSet>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
 
convertToValueObjects(Collection<GeneSet>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
 
convertToValueObjects(Collection<GeneSet>, boolean) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
 
convertToValueObjects(Collection<GeneSet>, boolean) - Method in class ubic.gemma.persistence.service.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
 
countResults(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao
Count the number of results in a given result set.
countResults(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
 
countResults(ExpressionAnalysisResultSet) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
 
countResults(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
 
countResults(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao
Count the number of results in a given result set below a given corrected P-value threshold.
countResults(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
 
countResults(ExpressionAnalysisResultSet, double) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
 
countResults(ExpressionAnalysisResultSet, double) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
 
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.auditAndSecurity.curation.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.auditAndSecurity.curation.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.persistence.service.genome.gene.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.persistence.service.common.description.BibliographicReferenceService
 
create(Characteristic) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
 
create(ExternalDatabase) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
 
create(QuantitationType) - Method in 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.persistence.service.genome.gene.GeneService
 
create(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
 
create(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.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.persistence.service.genome.gene.GeneSetService
create an entity in the database based on the value object parameter
createDatabaseEntity(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
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
 
createInstance() - Method in class ubic.gemma.core.security.ManualAuthenticationServiceBasedSecurityContextFactory
 
createInstance() - Method in class ubic.gemma.core.util.TextResourceToSetOfLinesFactoryBean
 
createMeanVariance(ExpressionExperiment, MeanVarianceRelation) - Method in interface ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper
 
createObject() - Method in class ubic.gemma.core.context.AbstractAsyncFactoryBean
Create a new bean as per AbstractAsyncFactoryBean.getObject().
createObject() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceFactory
 
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
 
createProcessedDataVectors(ExpressionExperiment, boolean) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
 
createProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
Create processed data vectors
createProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
createProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
createProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
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.persistence.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.auditAndSecurity.curation
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
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.progress.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.persistence.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(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
 
DataVectorValueObject(DoubleVectorValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
Copy constructor
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.analysis.sequence.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.persistence.service.genome.gene.GeneSetService
Security is handled within method
deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject>) - Method in class ubic.gemma.persistence.service.genome.gene.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.persistence.service.genome.gene.GeneSetService
Security is handled within method, when the set is loaded
deleteDatabaseEntity(DatabaseBackedGeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
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.persistence.service.expression.experiment.FactorValueDeletion
 
deleteFactorValues(Collection<Long>) - Method in class ubic.gemma.persistence.service.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.persistence.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.context.AbstractAsyncFactoryBean
 
destroy() - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
 
destroy() - Method in class ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl
 
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.core.context.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(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.maintenance.TableMaintenanceUtil
 
disableEmail() - Method in class ubic.gemma.persistence.service.maintenance.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(BlacklistedEntity) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
 
doLoadValueObject(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
doLoadValueObject(Characteristic) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
 
doLoadValueObject(DatabaseEntry) - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImpl
 
doLoadValueObject(QuantitationType) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
 
doLoadValueObject(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
Loads a single value objects for the given array design.
doLoadValueObject(BioAssay) - Method in class ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl
 
doLoadValueObject(BioAssayDimension) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl
 
doLoadValueObject(BioMaterial) - Method in class ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl
 
doLoadValueObject(CompositeSequence) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
 
doLoadValueObject(ExperimentalFactor) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl
 
doLoadValueObject(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
doLoadValueObject(FactorValue) - Method in class ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl
 
doLoadValueObject(Geeq) - Method in class ubic.gemma.persistence.service.expression.experiment.GeeqDaoImpl
 
doLoadValueObject(BioSequence) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
 
doLoadValueObject(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
doLoadValueObject(GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
 
doLoadValueObject(BlatResult) - Method in class ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl
 
doLoadValueObject(Taxon) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
 
doLoadValueObjects(Collection<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.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(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(DoubleVectorValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
Copy constructor.
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.maintenance.TableMaintenanceUtil
Query space used by the EXPRESSION_EXPERIMENT2ARRAY_DESIGN table.
EE2C_QUERY_SPACE - Static variable in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
Query space used by the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
EE2CAclQueryUtils - Class in ubic.gemma.persistence.util
This class provides a fast-path to AclQueryUtils that uses the denormalized mask for anonymous users.
EE2CAclQueryUtils() - Constructor for class ubic.gemma.persistence.util.EE2CAclQueryUtils
 
ehcache(String) - Method in class ubic.gemma.persistence.cache.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.cache
 
EhcacheConfig() - Constructor for class ubic.gemma.persistence.cache.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.notification
author: anton date: 10/02/13
EmailNotificationContext(String, String, String) - Constructor for class ubic.gemma.core.job.notification.EmailNotificationContext
 
empty() - Static method in class ubic.gemma.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.
ensureInitialized(OntologyService, OntologyService.InferenceMode, OntologyService.LanguageLevel, Boolean, Boolean) - Static method in class ubic.gemma.core.ontology.OntologyUtils
Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean), but first setting how we load it.
ensureInitializedLite(OntologyService) - Static method in class ubic.gemma.core.ontology.OntologyUtils
Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean), but setting the language level to LITE, Inferencing to NONE, processImports to false, and enable search to false, if the ontology isn't already loaded.
ensureInSession(Collection<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.core.context
Environment profiles used in the Spring context.
EnvironmentProfiles() - Constructor for class ubic.gemma.core.context.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.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
 
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.ProcessedExpressionDataVector
 
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
 
equals(Object) - Method in class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject
 
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.GOGroupValueObject
 
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.gene.PhenotypeGroupValueObject
 
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.
 
escape(String) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils
Escape all reserved Lucene characters in the given query.
escapeLike(String) - Static method in class ubic.gemma.persistence.util.QueryUtils
 
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.cache.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
 
executeUpdateByBatch(Query, String, Collection<S>, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
Execute an update query by a fixed batch size.
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.model.expression.experiment
 
ExperimentalDesignUtils() - Constructor for class ubic.gemma.model.expression.experiment.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.persistence.service.expression.experiment
Types of metadata files that can be attached to an ExpressionExperiment.
ExpressionExperimentPlatformSwitchEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
The event that this 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.expression.experiment
Sets up the array designs before saving an experiment.
ExpressionExperimentPrePersistServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
Sets up the array designs, put the designelements in the data vectors.
ExpressionExperimentPrePersistServiceImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistServiceImpl
 
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.persistence.service.expression.experiment
 
ExpressionExperimentSearchServiceImpl - Class in ubic.gemma.persistence.service.expression.experiment
Handles searching for experiments and experiment sets
ExpressionExperimentSearchServiceImpl(ExpressionExperimentSetService, CoexpressionAnalysisService, DifferentialExpressionAnalysisService, SecurityService, SearchService, TaxonService, ExpressionExperimentService) - Constructor for class ubic.gemma.persistence.service.expression.experiment.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.persistence.service.expression.experiment
 
ExpressionExperimentSetValueObjectHelperImpl - Class in ubic.gemma.persistence.service.expression.experiment
This class will handle population of ExpressionExperimentSetValueObjects.
ExpressionExperimentSetValueObjectHelperImpl() - Constructor for class ubic.gemma.persistence.service.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.model.expression.experiment.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.model.expression.experiment.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.persistence.service.expression.experiment
This interface needed to be extracted for factor value deletions in order to be able to make the methods transactional
FactorValueDeletionImpl - Class in ubic.gemma.persistence.service.expression.experiment
Handles deletions of a factor values.
FactorValueDeletionImpl() - Constructor for class ubic.gemma.persistence.service.expression.experiment.FactorValueDeletionImpl
 
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
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.auditAndSecurity.curation.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 class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
find(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
check to see if the object already exists
find(ExternalDatabase) - Method in class ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl
 
find(Unit) - Method in interface ubic.gemma.persistence.service.common.measurement.UnitDao
 
find(Unit) - Method in class ubic.gemma.persistence.service.common.measurement.UnitDaoImpl
 
find(Protocol) - Method in 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.persistence.service.genome.gene.GeneService
Find all genes at a physical location.
find(PhysicalLocation) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
find(PhysicalLocation) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
Find all genes at a physical location.
find(PhysicalLocation) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
find(Taxon) - Method in class ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl
 
findAlignments(String) - Method in class ubic.gemma.core.goldenpath.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.goldenpath.GoldenPathSequenceAnalysis
Given a physical location, identify overlapping genes or predicted genes.
findBestByUri(String) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicDao
Return the characteristic with the most frequently used non-null value by URI.
findBestByUri(String) - Method in class ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl
 
findBestByUri(String) - Method in interface ubic.gemma.persistence.service.common.description.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.blacklist.BlacklistedEntityDao
 
findByAccession(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
 
findByAccession(String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
 
findByAccession(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
 
findByAccession(String) - Method in interface ubic.gemma.persistence.service.common.description.DatabaseEntryDao
 
findByAccession(String) - Method in class ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImpl
 
findByAccession(String) - Method in interface ubic.gemma.persistence.service.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.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.persistence.service.genome.gene.GeneService
 
findByAccession(String, ExternalDatabase) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByAccession(String, ExternalDatabase) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
findByAccession(String, ExternalDatabase) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
findByAccession(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
 
findByAccession(DatabaseEntry) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
findByAccession(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.expression.experiment.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.persistence.service.genome.gene.GeneService
 
findByAlias(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByAlias(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
Locate genes that match the given alias string
findByAlias(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
Gets all the genes referred to by the alias defined by the search string.
findByAlternateName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
 
findByAlternateName(String) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
 
findByAlternateName(String) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.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.persistence.service.genome.gene.GeneService
Searches for a gene based on its ensembl ID.
findByEnsemblId(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByEnsemblId(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
findByEnsemblId(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
findByExperiment(BioAssaySet) - Method in 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.persistence.service.common.description.BibliographicReferenceService
Get a reference by the unqualified external id.
findByExternalId(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
findByExternalId(String, String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
 
findByExternalId(String, String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
findByExternalId(String, String) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
findByExternalId(String, String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
findByExternalId(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceDao
Find by the external database id, such as for PubMed
findByExternalId(DatabaseEntry) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
findByExternalId(DatabaseEntry) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
 
findByExternalId(DatabaseEntry) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
Retrieve analyses associated with the factor, either through the subset factor or as factors for result sets.
findByFactor(ExperimentalFactor) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.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.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) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
Return all sets that contain the given gene.
findByGene(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
findByGene(Gene, 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.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) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
findByName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
findByName(String, Taxon) - Method in interface ubic.gemma.core.search.GeneSetSearch
 
findByName(String, Taxon) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
 
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductDao
 
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
 
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductService
 
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl
 
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
 
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
findByName(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
findByName(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
findByName(ArrayDesign, String) - Method in interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
 
findByName(ArrayDesign, String) - Method in class ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl
 
findByName(ArrayDesign, String) - Method in interface ubic.gemma.persistence.service.expression.designElement.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.persistence.service.genome.gene.GeneService
 
findByNCBIId(Integer) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByNcbiIds(Collection<Integer>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
Quickly load exact matches.
findByNcbiIds(Collection<Integer>) - Method in class ubic.gemma.persistence.service.genome.gene.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.persistence.service.genome.gene.GeneService
 
findByNCBIIdValueObject(Integer) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByOfficialName(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
findByOfficialName(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByOfficialName(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
findByOfficialName(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
findByOfficialNameInexact(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
findByOfficialNameInexact(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByOfficialNameInexact(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
findByOfficialNameInexact(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
findByOfficialSymbol(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
findByOfficialSymbol(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByOfficialSymbol(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
findByOfficialSymbol(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
findByOfficialSymbol(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
findByOfficialSymbol(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByOfficialSymbol(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
findByOfficialSymbol(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
findByOfficialSymbolInexact(String) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
findByOfficialSymbolInexact(String) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findByOfficialSymbolInexact(String) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
findByOfficialSymbolInexact(String) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
findByOfficialSymbols(Collection<String>, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
Quickly load exact matches.
findByOfficialSymbols(Collection<String>, Long) - Method in class ubic.gemma.persistence.service.genome.gene.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.goldenpath.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.goldenpath.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.persistence.service.genome.gene.GeneSetService
Given a Gemma Gene Id, find all the gene groups it is a member of (filtering is handled when gene sets are loaded)
findGeneSetsByGene(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
findGeneSetsByName(String, Long) - Method in interface ubic.gemma.core.search.GeneSetSearch
Similar to method of same name in GeneSetController.java but here: - no taxon needed - GO groups always searched - GeneSet objects returned instead of GeneSetValueObjects
findGeneSetsByName(String, Long) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
 
findGeneSetsByName(String, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
findGeneSetsByName(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
findGeneSetValueObjectByGoId(String, Long) - Method in interface ubic.gemma.core.search.GeneSetSearch
Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.
findGeneSetValueObjectByGoId(String, Long) - Method in class ubic.gemma.core.search.GeneSetSearchImpl
 
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.persistence.service.genome.gene.GeneService
 
findGOTerms(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
findGroupAuthorities(String) - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
findGroupByName(String) - Method in interface ubic.gemma.core.security.authentication.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.goldenpath.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.auditAndSecurity.curation.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.persistence.service.common.description.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.goldenpath.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.goldenpath.GoldenPathSequenceAnalysis
Check to see if there are mRNAs that overlap with this region.
findSequenceLocations(String) - Method in class ubic.gemma.core.goldenpath.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.persistence.service.common.description.BibliographicReferenceService
Get a reference by the unqualified external id.
findVOByExternalId(String) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
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.model.genome.gene
*
FreeTextGeneResultsValueObject() - Constructor for class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject
default constructor to satisfy java bean contract
FreeTextGeneResultsValueObject(String, String, Long, String, Collection<Long>, String) - Constructor for class ubic.gemma.model.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.blacklist.BlacklistedValueObject
 
fromEntity(CompositeSequence) - Static method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
 
fromEntity(BioSequence) - Static method in class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
 
fromEntity(Taxon) - Static method in class ubic.gemma.model.genome.TaxonValueObject
 
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
 
GemmaRestApiClient - Interface in ubic.gemma.core.util
A minimalist client for accessing Gemma's RESTful API.
GemmaRestApiClient.DataResponse - Interface in ubic.gemma.core.util
 
GemmaRestApiClient.EmptyResponse - Interface in ubic.gemma.core.util
For endpoints that return no data (i.e.
GemmaRestApiClient.ErrorResponse - Interface in ubic.gemma.core.util
 
GemmaRestApiClient.ErrorResponse.Error - Interface in ubic.gemma.core.util
 
GemmaRestApiClient.Redirection - Interface in ubic.gemma.core.util
For endpoint that return a redirection.
GemmaRestApiClient.Response - Interface in ubic.gemma.core.util
A response from the API, which is either a GemmaRestApiClient.DataResponse or GemmaRestApiClient.ErrorResponse.
GemmaRestApiClientException - Exception in ubic.gemma.core.util
 
GemmaRestApiClientException(String, Throwable) - Constructor for exception ubic.gemma.core.util.GemmaRestApiClientException
 
GemmaRestApiClientImpl - Class in ubic.gemma.core.util
 
GemmaRestApiClientImpl(String) - Constructor for class ubic.gemma.core.util.GemmaRestApiClientImpl
 
GemmaRestApiClientImpl(String, ObjectMapper) - Constructor for class ubic.gemma.core.util.GemmaRestApiClientImpl
 
GemmaRestOnly - Annotation 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.common
 
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.maintenance.TableMaintenanceUtil
Recommended batch size to use when retrieving entries from the GENE2CS table either by gene or design element.
GENE2CS_QUERY_SPACE - Static variable in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
Query space used by the GENE2CS table.
Gene2CsStatus - Class in ubic.gemma.persistence.service.maintenance
Used to store information about what happened when the GENE2CS table was updated.
Gene2CsStatus() - Constructor for class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
 
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.persistence.service.genome.gene
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
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.core.context.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.persistence.service.genome.gene
Service for searching genes (and gene sets)
GeneSearchServiceImpl - Class in ubic.gemma.persistence.service.genome.gene
Service for searching genes (and gene sets)
GeneSearchServiceImpl() - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
 
GeneSearchServiceImpl(SearchService, SecurityService, TaxonService, GeneSetSearch, GeneSetService, GeneService, GeneOntologyService, GeneSetValueObjectHelper) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
 
GeneService - Interface in ubic.gemma.persistence.service.genome.gene
 
GeneServiceImpl - Class in ubic.gemma.persistence.service.genome.gene
 
GeneServiceImpl(GeneDao) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
GeneSet - Class in ubic.gemma.model.genome.gene
A grouping of genes that share a common relationship
GeneSet() - Constructor for class ubic.gemma.model.genome.gene.GeneSet
 
GeneSet.Factory - Class in ubic.gemma.model.genome.gene
 
GeneSetDao - Interface in ubic.gemma.persistence.service.genome.gene
The interface for managing groupings of genes.
GeneSetDaoImpl - Class in ubic.gemma.persistence.service.genome.gene
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.gene.GeneSet.
GeneSetDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
GeneSetMember - Class in ubic.gemma.model.genome.gene
 
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.persistence.service.genome.gene
Service for managing gene sets
GeneSetServiceImpl - Class in ubic.gemma.persistence.service.genome.gene
Service for managing gene sets
GeneSetServiceImpl(GeneSetDao) - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
GeneSetValueObject - Class in ubic.gemma.model.genome.gene
Represents a Gene group gene set
GeneSetValueObject() - Constructor for class ubic.gemma.model.genome.gene.GeneSetValueObject
default constructor to satisfy java bean contract
GeneSetValueObject(Long) - Constructor for class ubic.gemma.model.genome.gene.GeneSetValueObject
Create a lightweight wrapper that can be used for security filtering
GeneSetValueObject(GeneSet, Taxon, Long) - Constructor for class ubic.gemma.model.genome.gene.GeneSetValueObject
 
GeneSetValueObjectHelper - Interface in ubic.gemma.persistence.service.genome.gene
* @author tvrossum
GeneSetValueObjectHelperImpl - Class in ubic.gemma.persistence.service.genome.gene
This class will handle population of GeneSetValueObjects.
GeneSetValueObjectHelperImpl() - Constructor for class ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl
 
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_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.blacklist.BlacklistedValueObject
 
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.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.core.util.MailEngine
Return the admin email address used for MailEngine.sendAdminMessage(String, String)
getAdminEmailAddress() - Method in class ubic.gemma.core.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.persistence.service.common.description.BibliographicReferenceDao
 
getAllExperimentLinkedReferences() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
getAllExperimentLinkedReferences() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
Return all the BibRefs that are linked to ExpressionExperiments.
getAllExperimentLinkedReferences() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
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.persistence.service.expression.experiment.ExpressionExperimentSearchService
 
getAllTaxonExperimentGroup(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.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.core.config.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.core.config.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.service.maintenance.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.core.context.SpringContextUtils
Deprecated.
this method does not support producing Gemma Web contexts, please migrate existing code to use SpringContextUtils.getApplicationContext(String[], String...) instead.
getApplicationContext(String[], String...) - Static method in class ubic.gemma.core.context.SpringContextUtils
Obtain an application context for Gemma.
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.persister.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.auditAndSecurity.AbstractAuditable
 
getAuditTrail() - Method in interface ubic.gemma.model.common.auditAndSecurity.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.model.expression.experiment.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.hibernate.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
 
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 interface ubic.gemma.core.analysis.sequence.Blat
 
getBlatScoreThreshold() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
 
getBlatScoreThreshold() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
getBlockCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
 
getBlockCount() - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
 
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.core.config.Settings
Deprecated.
 
getBoolean(String, boolean) - Static method in class ubic.gemma.core.config.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
 
getBytes() - Method in class ubic.gemma.model.analysis.expression.coexpression.IdArray
 
getCache(CacheManager, String) - Static method in class ubic.gemma.persistence.cache.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
 
getCode() - Method in interface ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse.Error
 
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.persistence.service.genome.gene.GeneService
 
getCompositeSequenceCountById(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
getCompositeSequenceDescription() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
 
getCompositeSequenceId() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
 
getCompositeSequenceName() - Method in class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject
 
getCompositeSequences() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
 
getCompositeSequences(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.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.persistence.service.genome.gene.GeneService
Returns a list of compositeSequences associated with the given gene and array design
getCompositeSequences(Gene, ArrayDesign) - Method in class ubic.gemma.persistence.service.genome.gene.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.persistence.service.genome.gene.GeneService
 
getCompositeSequencesById(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
getConditions() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject
 
getConfig() - Method in class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
 
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 interface ubic.gemma.core.util.GemmaRestApiClient.DataResponse
 
getData() - Method in class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
 
getData() - Method in class ubic.gemma.model.expression.bioAssayData.DataVector
 
getData() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
 
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
 
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
 
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 class ubic.gemma.core.image.aba.Image
 
getDisplayName() - Method in enum ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
 
getDistribution() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
 
getDone() - Method in class ubic.gemma.core.job.progress.SubmittedTaskValueObject
 
getDownloadName(ExpressionExperiment) - Method in enum ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
 
getDownloadPath() - Static method in class ubic.gemma.core.config.Settings
Deprecated.
 
getDownregulatedCount() - Method in class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject
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 interface ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse
 
getError() - Method in class ubic.gemma.persistence.service.maintenance.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.DataVector
 
getExpressionExperiment() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
 
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
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.blacklist.BlacklistedEntity
 
getExternalAccession() - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
 
getExternalDatabase() - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
 
getExternalDatabase() - Method in class ubic.gemma.model.common.description.DatabaseEntry
 
getExternalDatabase() - Method in class ubic.gemma.model.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
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.persistence.service.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>, 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>, 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.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
 
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.persister.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.persistence.service.genome.gene.GeneSetService
 
getGeneIdsInGroup(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
getGeneInfo() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
 
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.persistence.service.genome.gene.GeneSearchService
get all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy
getGenesByGOId(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
 
getGenesByName(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
For a biosequence name, get the genes
getGenesByName(String) - Method in class ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl
 
getGenesByName(String) - Method in interface ubic.gemma.persistence.service.genome.biosequence.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
 
getGeneSetId() - Method in class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
 
getGenesInGroup(GeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
Get the gene value objects for the members of the group param
getGenesInGroup(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
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.analysis.sequence.Blat
 
getGfClientExe() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
getGfServerExe() - Method in interface ubic.gemma.core.analysis.sequence.Blat
 
getGfServerExe() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
getGitHash() - Method in class ubic.gemma.core.util.BuildInfo
 
getGOGroupGenes(String, Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSearchService
 
getGOGroupGenes(String, Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
 
getGoId() - Method in class ubic.gemma.model.genome.gene.GOGroupValueObject
 
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.analysis.sequence.Blat
 
getHost() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
getHost() - Method in class ubic.gemma.core.util.NetDatasourceUtil
 
getHostUrl() - Static method in class ubic.gemma.core.config.Settings
Deprecated.
 
getHumanServerPort() - Method in interface ubic.gemma.core.analysis.sequence.Blat
 
getHumanServerPort() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
getHybProtocol() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
 
getId() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
 
getId() - Method in class ubic.gemma.core.analysis.report.AuditableObject
 
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.GemmaSessionBackedValueObject
 
getId() - Method in interface ubic.gemma.model.common.Identifiable
 
getId() - Method in class ubic.gemma.model.common.IdentifiableValueObject
 
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 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 enum ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
 
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
 
getInitializationTime(String, TimeUnit) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
Obtain the time spent initializing a bean.
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
 
getInstantiationTime(String, TimeUnit) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
Obtain the time spent instantiating a bean.
getInstitute() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
 
getInt(String) - Static method in class ubic.gemma.core.config.Settings
Deprecated.
 
getInt(String, int) - Static method in class ubic.gemma.core.config.Settings
Deprecated.
 
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.core.config.Settings
Deprecated.
 
getKeys(Cache) - Static method in class ubic.gemma.persistence.cache.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
 
getKeysInternal() - Method in class ubic.gemma.core.config.PropertySourcesConfiguration
Deprecated.
 
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 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.service.maintenance.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
 
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
 
getLocation() - Method in interface ubic.gemma.core.util.GemmaRestApiClient.Redirection
 
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
 
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
 
getMessage() - Method in interface ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse.Error
 
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.profiling.StopWatchUtils
 
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.analysis.sequence.Blat
 
getMouseServerPort() - Method in class ubic.gemma.core.analysis.sequence.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.blacklist.BlacklistedValueObject
 
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.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.blacklist.BlacklistedEntityDao
 
getNonBlacklistedExpressionExperiments(ArrayDesign) - Method in class ubic.gemma.persistence.service.blacklist.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
 
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.context.AbstractAsyncFactoryBean
 
getObject() - Method in interface ubic.gemma.core.context.AsyncFactoryBean
Obtain a bean asynchronously.
getObject() - Method in class ubic.gemma.model.expression.experiment.Statement
 
getObjectAlias() - Method in interface ubic.gemma.persistence.util.PropertyMapping
Alias in the query/criteria space, if applicable.
getObjectType() - Method in class ubic.gemma.core.context.AbstractAsyncFactoryBean
 
getObjectType() - Method in class ubic.gemma.core.ontology.providers.OntologyServiceFactory
 
getObjectType() - Method in class ubic.gemma.core.security.ManualAuthenticationServiceBasedSecurityContextFactory
 
getObjectType() - Method in class ubic.gemma.core.util.TextResourceToSetOfLinesFactoryBean
 
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
 
getOrderApplied() - Method in class ubic.gemma.model.expression.biomaterial.Treatment
 
getOrderedSamples(ExpressionDataDoubleMatrix, List<ExperimentalFactor>) - Static method in class ubic.gemma.model.expression.experiment.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.model.genome.gene.PhenotypeGroupValueObject
 
getPhenotypeMapping() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
 
getPhenotypeName() - Method in class ubic.gemma.model.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.persistence.service.genome.gene.GeneService
 
getPhysicalLocationsValueObjects(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.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.persistence.service.genome.gene.GeneService
 
getProducts(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
getProgressUpdateCallback() - Method in class ubic.gemma.core.job.progress.ProgressUpdateAppender.ProgressUpdateContext
 
getProgressUpdates() - Method in interface ubic.gemma.core.job.SubmittedTask
Returns queue of log statements from the running task.
getProjectedAccessions(String) - Method in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
Determine the set of external accession values that will be generated during parsing.
getProperty(String) - Static method in class ubic.gemma.core.config.Settings
Deprecated.
 
getPropertyInternal(String) - Method in class ubic.gemma.core.config.PropertySourcesConfiguration
Deprecated.
 
getPropertyName() - Method in 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.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
 
getQueryString() - Method in class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject
 
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.DoubleVectorValueObject
 
getRankByMax() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
 
getRankByMean() - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
 
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.analysis.sequence.Blat
 
getRatServerPort() - Method in class ubic.gemma.core.analysis.sequence.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.blacklist.BlacklistedEntity
 
getReason() - Method in class ubic.gemma.model.blacklist.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
 
getRecordedBeans() - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
 
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.persistence.service.common.description.BibliographicReferenceDao
 
getRelatedExperiments(Collection<BibliographicReference>) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
getRelatedExperiments(Collection<BibliographicReference>) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
 
getRelatedExperiments(Collection<BibliographicReference>) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
getRelatedExperiments(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
Get the ExpressionExperiments, if any, that are linked to the given reference.
getRelatedExperiments(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.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
 
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.analysis.sequence.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.model.genome.gene.GOGroupValueObject
 
getSearchTerm() - Method in class ubic.gemma.model.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
 
getSecondBaselineGroup() - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
 
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.analysis.sequence.Blat
 
getSeqDir() - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
getSeqFiles(ShellDelegatingBlat.BlattableGenome) - Method in interface ubic.gemma.core.analysis.sequence.Blat
 
getSeqFiles(ShellDelegatingBlat.BlattableGenome) - Method in class ubic.gemma.core.analysis.sequence.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
 
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.blacklist.BlacklistedEntity
 
getShortName() - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
 
getShortName() - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
 
getShortName() - Method in class ubic.gemma.model.expression.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.core.context.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.cache.CacheUtils
 
getSize(GeneSetValueObject) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
getSize(GeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
getSizeInBytes() - Method in enum ubic.gemma.model.common.quantitationtype.PrimitiveType
 
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
 
getSourceExperimentShortName() - 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.SlicedDoubleVectorValueObject
Obtain the ID of the vector from which this slice is derived from.
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.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 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.profiling.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.core.config.Settings
Deprecated.
 
getString(String, String) - Static method in class ubic.gemma.core.config.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.progress.SubmittedTaskValueObject
 
getSubmissionTime() - Method in interface ubic.gemma.core.job.SubmittedTask
 
getSubmittedTask(String) - Method in interface ubic.gemma.core.job.TaskRunningService
 
getSubmittedTask(String) - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
 
getSubmittedTasks() - Method in interface ubic.gemma.core.job.TaskRunningService
 
getSubmittedTasks() - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
 
getSubmitter() - Method in class ubic.gemma.core.job.notification.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.AbstractTask
 
getTaskCommand() - Method in interface ubic.gemma.core.job.SubmittedTask
 
getTaskCommand() - Method in interface ubic.gemma.core.job.Task
 
getTaskId() - Method in class ubic.gemma.core.job.notification.EmailNotificationContext
 
getTaskId() - Method in class ubic.gemma.core.job.progress.ProgressData
 
getTaskId() - Method in 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.notification.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
Return the taxon for each of the given experiments (or subsets).
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.persistence.service.genome.gene.GeneSetDao
Return all the taxa of the gene set members.
getTaxa(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
getTaxa(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
Obtain all the taxa for the members of a given gene set.
getTaxa(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
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 experiment or subset.
getTaxon(BioAssaySet) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
getTaxon(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
Returns the taxon of an arbitrary member of the set.
getTaxon(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
getTaxon(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes
getTaxon(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
getTaxonCommonName() - Method in class ubic.gemma.model.genome.gene.GeneValueObject
 
getTaxonCommonName() - Method in class ubic.gemma.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.persistence.service.genome.gene.GeneSetService
get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes
getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
getTechnology() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
 
getTechnologyType() - Method in class ubic.gemma.core.loader.expression.simple.model.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.goldenpath.GoldenPathSequenceAnalysis
Uses default mapping settings
getThreePrimeDistances(BlatResult, ThreePrimeDistanceMethod) - Method in class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis
Given a physical location, find how close it is to the 3' end of a gene it is in, using default mapping settings.
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
 
getTotalTime(String, TimeUnit) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
Obtain the total time spent instantiating and initializing a bean.
getTotalTime(TimeUnit) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
Obtain the total time spent instantiating and initializing beans.
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.blacklist.BlacklistedValueObject
 
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.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
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.persistence.service.genome.gene.GeneSetService
 
getUsersGeneGroups(boolean, Long, boolean) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
getUsersGeneGroupsValueObjects(boolean, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
Returns just the current users gene sets
getUsersGeneGroupsValueObjects(boolean, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
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.
getValue() - Method in class ubic.gemma.model.expression.experiment.Statement
Deprecated.
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.common.BaseValueObject
 
getValueObject(OntologyTerm) - Method in interface ubic.gemma.core.ontology.providers.GeneOntologyService
Converts the given Ontology Term to a Gene Ontology Value Object.
getValueObject(OntologyTerm) - Method in class ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl
 
getValueObjects(Collection<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.
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.model.genome.gene
 
GOGroupValueObject() - Constructor for class ubic.gemma.model.genome.gene.GOGroupValueObject
 
GOGroupValueObject(String, String, Long, String, Collection<Long>, String, String) - Constructor for class ubic.gemma.model.genome.gene.GOGroupValueObject
Method to create a display object from scratch
GoldenPath - Class in ubic.gemma.core.goldenpath
Perform useful queries against GoldenPath (UCSC) databases.
GoldenPath(Taxon) - Constructor for class ubic.gemma.core.goldenpath.GoldenPath
Create a GoldenPath database for a given taxon.
GoldenPathQuery - Class in ubic.gemma.core.goldenpath
 
GoldenPathQuery(Taxon) - Constructor for class ubic.gemma.core.goldenpath.GoldenPathQuery
 
GoldenPathSequenceAnalysis - Class in ubic.gemma.core.goldenpath
Using the Goldenpath databases for comparing sequence alignments to gene locations.
GoldenPathSequenceAnalysis(Taxon) - Constructor for class ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis
 
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.util.SubqueryUtils
Given a prefix and an object alias, guess a reasonable sequence of aliases to use in a query.
guessIsBackground(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
 
guessPrimitiveType(String, String, Object) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
 
guessQuantitationTypeParameters(QuantitationType, String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
 
guessQuantitationTypeParameters(QuantitationType, String, String, Object) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
Attempt to fill in the details of the quantitation type.
guessScaleType(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
 
guessType(String, String) - Static method in class ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
 

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.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
 
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
 
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
 
hashCode() - Method in class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
Returns a hash code based on this entity's identifiers.
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.bioAssayData.SlicedDoubleVectorValueObject
 
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.GOGroupValueObject
 
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.gene.PhenotypeGroupValueObject
 
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.hibernate
 
HibernateUtils() - Constructor for class ubic.gemma.persistence.hibernate.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.analysis.sequence.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.common.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.common
Base implementations for value objects representing persistent objects
IdentifiableValueObject() - Constructor for class ubic.gemma.model.common.IdentifiableValueObject
Default empty constructor for bean-style initialization.
IdentifiableValueObject(Long) - Constructor for class ubic.gemma.model.common.IdentifiableValueObject
Constructor that sets the common property of all identifiable objects, the ID.
IdentifiableValueObject(O) - Constructor for class ubic.gemma.model.common.IdentifiableValueObject
Constructor for a given entity.
IdentifiableValueObject(IdentifiableValueObject<O>) - Constructor for class ubic.gemma.model.common.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.persistence.util.Pointcuts
Matches stuff within Gemma package.
init() - Method in class ubic.gemma.core.loader.expression.arrayExpress.util.ArrayExpressUtil
 
init() - Method in class ubic.gemma.core.loader.expression.geo.util.GeoUtil
 
init() - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NCBIUtil
 
init() - Method in class ubic.gemma.core.util.NetDatasourceUtil
 
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
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.common.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.model.expression.experiment.ExperimentalDesignUtils
 
isBatch(ExperimentalFactorValueObject) - Static method in class ubic.gemma.model.expression.experiment.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.blacklist.BlacklistedEntityDao
 
isBlacklisted(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
 
isBlacklisted(String) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
 
isBlacklisted(String) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
 
isBlacklisted(ArrayDesign) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
 
isBlacklisted(ArrayDesign) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
 
isBlacklisted(ArrayDesign) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
 
isBlacklisted(ArrayDesign) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
 
isBlacklisted(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
 
isBlacklisted(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
 
isBlacklisted(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
 
isBlacklisted(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
 
isBlackListed(String) - Method in interface ubic.gemma.persistence.service.expression.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.service.genome.ChromosomeUtils
This method is only familiar with chromosomes as named in the UCSC GoldenPath database and would have to be modified if the 'rules' are broken by some other source used.
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.model.expression.experiment.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.model.expression.experiment.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.persistence.service.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.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 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.
isEmptyInternal() - Method in class ubic.gemma.core.config.PropertySourcesConfiguration
Deprecated.
 
isEnableAuthorities() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
isEnabled() - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
 
isEnabled() - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl
 
isEnabled() - Method in interface ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
 
isEnabled() - Method in class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl
 
isEnableGroups() - Method in class ubic.gemma.core.security.authentication.UserManagerImpl
 
isErrorFound() - Method in class ubic.gemma.model.common.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.service.genome.taxon.TaxonUtils
 
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.core.context.AbstractAsyncFactoryBean
 
isInitialized() - Method in interface ubic.gemma.core.context.AsyncFactoryBean
Indicate if this bean has been initialized or if its initialization is pending.
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 interface ubic.gemma.model.common.GemmaSessionBackedValueObject
 
isModified() - Method in class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject
 
isModified() - Method in class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject
 
isMouse(Taxon) - Static method in class ubic.gemma.persistence.service.genome.taxon.TaxonUtils
 
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.common.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.service.genome.taxon.TaxonUtils
 
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 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
 
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.common.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.
 
LazyInitByDefaultPostProcessor - Class in ubic.gemma.core.context
Mark beans as lazy-init by default.
LazyInitByDefaultPostProcessor() - Constructor for class ubic.gemma.core.context.LazyInitByDefaultPostProcessor
 
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.persistence.service.common.description.BibliographicReferenceDao
 
listAll() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
listAll() - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
 
listAll() - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
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.
listByIdentifiableBatch(Query, String, Collection<S>, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
 
listByIdentifiableBatch(Query, String, Collection<S>, int, int) - Static method in class ubic.gemma.persistence.util.QueryUtils
 
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.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.auditAndSecurity.curation.CuratableService
 
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.bioAssay.BioAssayService
 
load(Long) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl
 
load(Long) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService
 
load(Long) - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
 
load(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
 
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
 
load(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl
 
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
 
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
 
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
 
load(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.FactorValueService
 
load(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
load(Long, CacheMode) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
Load an experiment by ID with a specific cache mode.
load(Long, CacheMode) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
load(String) - Method in class ubic.gemma.core.loader.genome.taxon.TaxonLoader
 
load(String, String) - Method in interface ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService
Work flow is: The file is first checked to see if readable, and the taxon checked to see it is in Gemma.
load(String, String) - Method in class ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl
 
load(String, String, String, String, boolean) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
 
load(String, String, String, String, Taxon) - Method in class ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
 
load(Collection<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.auditAndSecurity.curation.CuratableService
 
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.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(Collection<Long>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
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.auditAndSecurity.curation.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.auditAndSecurity.curation.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.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.auditAndSecurity.curation.CuratableService
 
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.bioAssay.BioAssayService
 
loadAll() - Method in interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
 
loadAll() - Method in class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
 
loadAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
 
loadAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
 
loadAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
 
loadAll() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
 
loadAll() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
loadAll(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
loadAll(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
loadAll(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
 
loadAll(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
loadAll(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
loadAll(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
loadAllExperimentSetsWithTaxon() - Method in interface ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
 
loadAllExperimentSetsWithTaxon() - Method in class ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
 
loadAllExperimentSetsWithTaxon() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
Security at DAO level.
loadAllExperimentSetsWithTaxon() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
 
loadAllExperimentSetValueObjects(boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
Security filtering is handled by the call to load the set entities ubic.gemma.model.analysis.expression.ExpressionExperimentSetService.loadAllExperimentSetsWithTaxon()
loadAllExperimentSetValueObjects(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
 
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
loadAllReferences() - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
Load references for all experiments.
loadAllReferences() - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
loadAllTaxaWithGenes() - Method in interface ubic.gemma.persistence.service.genome.taxon.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.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.auditAndSecurity.curation.CuratableService
 
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 class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
loadAllValueObjects() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
loadAllValueObjects() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
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
 
loadAndThawLiteWithRefreshCacheMode(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
loadAndThawLiteWithRefreshCacheMode(Long) - 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
 
loadAndThawWithRefreshCacheMode(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
Load an experiment without cache and thaw it as per ExpressionExperimentService.thaw(ExpressionExperiment) with CacheMode.REFRESH.
loadAndThawWithRefreshCacheMode(Long) - 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
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
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
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.persistence.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.persistence.service.genome.gene.GeneService
Returns a detailVO for a geneDd This method may be unnecessary now that we have put all the logic into the GeneService
loadFullyPopulatedValueObject(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
loadGenePhenotypes(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
loadGenePhenotypes(Long) - Method in class ubic.gemma.persistence.service.genome.gene.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.auditAndSecurity.curation.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.persistence.service.genome.gene.GeneService
 
loadMicroRNAs(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
loadMpsNames() - Method in class ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize
 
loadMyGeneSets() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
Returns the GeneSets for the currently logged in User - i.e, ones for which the current user has specific read permissions on (as opposed to data sets which are public).
loadMyGeneSets() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
loadMyGeneSets(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
loadMyGeneSets(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
loadMySetValueObjects(boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
load the user's sets
loadMySetValueObjects(boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
 
loadMySharedGeneSets(Taxon) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
loadMySharedGeneSets(Taxon) - Method in class ubic.gemma.persistence.service.genome.gene.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 class ubic.gemma.persistence.service.AbstractService
 
loadOrFail(Long) - Method in interface ubic.gemma.persistence.service.auditAndSecurity.curation.CuratableService
 
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 class ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl
 
loadOrFail(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
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.auditAndSecurity.curation.CuratableService
 
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 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.auditAndSecurity.curation.CuratableService
 
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 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.auditAndSecurity.curation.CuratableService
 
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 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(Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
loadReference(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
loadReference(Collection<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.
loadReferences(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
Load references for the given experiment IDs.
loadReferences(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
loadRegressedMatrix(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService
Load the regressed coexpression matrix for the given experiment.
loadRegressedMatrix(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl
 
loadResult(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
 
loadResult(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl
loads a neDifferentialExpressionMetaAnalysisResult
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
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.persistence.service.genome.gene.GeneService
Load with objects already thawed.
loadThawed(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.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.persistence.service.genome.gene.GeneService
 
loadThawedLiter(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.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.auditAndSecurity.curation.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.persistence.service.common.description.BibliographicReferenceServiceImpl
 
loadValueObject(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
loadValueObject(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
loadValueObject(GeneSet) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService
 
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledDao
 
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.AbstractVoEnabledService
 
loadValueObjectById(Long) - Method in interface ubic.gemma.persistence.service.auditAndSecurity.curation.CuratableService
 
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.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.GeneServiceImpl
 
loadValueObjectById(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
loadValueObjectById(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
loadValueObjectById(Long, boolean) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
Get a value object for the id param.
loadValueObjectById(Long, boolean) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
 
loadValueObjectByIdLite(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
 
loadValueObjectByIdLite(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
loadValueObjectByIdLite(Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
loadValueObjectByIdLite(Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
loadValueObjects(Collection<C>) - Method in interface ubic.gemma.persistence.service.auditAndSecurity.curation.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 class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
loadValueObjects(Collection<GeneSet>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
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.auditAndSecurity.curation.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.auditAndSecurity.curation.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.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.auditAndSecurity.curation.CuratableService
 
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.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.GeneServiceImpl
 
loadValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
loadValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
Ids of member genes will be filled in
loadValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
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.persistence.service.genome.gene.GeneSetDao
 
loadValueObjectsByIdsLite(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
loadValueObjectsByIdsLite(Collection<Long>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
loadValueObjectsByIdsLite(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
loadValueObjectsByIdsLiter(Collection<Long>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
loadValueObjectsByIdsLiter(Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.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
Load an analysis result set with its all of its associated results.
loadWithResultsAndContrasts(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
 
loadWithResultsAndContrasts(Long) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
 
loadWithResultsAndContrasts(Long) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
 
loadWithResultsAndContrasts(Long, double, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao
Load a slice of an analysis result set with a corrected P-value threshold.
loadWithResultsAndContrasts(Long, double, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
 
loadWithResultsAndContrasts(Long, double, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
 
loadWithResultsAndContrasts(Long, double, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
 
loadWithResultsAndContrasts(Long, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao
Load a slice of an analysis result set.
loadWithResultsAndContrasts(Long, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
 
loadWithResultsAndContrasts(Long, int, int) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService
 
loadWithResultsAndContrasts(Long, int, int) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl
 
localBasePath - Variable in class ubic.gemma.core.loader.util.fetcher.AbstractFetcher
 
LocalDatasetFetcher - Class in ubic.gemma.core.loader.expression.geo.fetcher
Used for testing, but might have other uses, to fetch GEO data from local files instead of the GEO website.
LocalDatasetFetcher(String) - Constructor for class ubic.gemma.core.loader.expression.geo.fetcher.LocalDatasetFetcher
 
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.goldenpath.GoldenPath
 
log - Static variable in class ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
 
log - Static variable in class ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator
 
log - Variable in class ubic.gemma.core.loader.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.core.util
 
MailEngineImpl - Class in ubic.gemma.core.util
 
MailEngineImpl() - Constructor for class ubic.gemma.core.util.MailEngineImpl
 
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
 
ManualAuthenticationServiceBasedSecurityContextFactory - Class in ubic.gemma.core.security
Creates a security context using manual authentication.
ManualAuthenticationServiceBasedSecurityContextFactory() - Constructor for class ubic.gemma.core.security.ManualAuthenticationServiceBasedSecurityContextFactory
 
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_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.profiling.StopWatchUtils
Create a measured region by a StopWatch, which can be used with a try-with-resource statement to StopWatch.start() and StopWatch.suspend() when entering and leaving the region.
Measurement - Class in ubic.gemma.model.common.measurement
 
Measurement - Static variable in class ubic.gemma.core.ontology.jena.TGFVO
Represents a factor value Measurement.
Measurement() - Constructor for class ubic.gemma.model.common.measurement.Measurement
 
Measurement.Factory - Class in ubic.gemma.model.common.measurement
 
MeasurementKind - Enum in ubic.gemma.model.common.measurement
 
measurementOf - Static variable in class ubic.gemma.core.ontology.jena.TGFVO
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.persistence.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
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.analysis.sequence.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.persistence.service.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.model.expression.experiment.ExperimentalDesignUtils
 
nameForR(FactorValue, boolean) - Static method in class ubic.gemma.model.expression.experiment.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
 
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
 
onProgressUpdate(String) - Method in interface ubic.gemma.core.job.progress.ProgressUpdateAppender.ProgressUpdateCallback
 
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
Create a new simple ontology individual.
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
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.
perform(String) - Method in interface ubic.gemma.core.util.GemmaRestApiClient
Access a given REST endpoint.
perform(String) - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
 
perform(String, String, Object, Object...) - Method in interface ubic.gemma.core.util.GemmaRestApiClient
 
perform(String, String, Object, Object...) - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
 
perform(String, MultiValueMap<String, Object>) - Method in interface ubic.gemma.core.util.GemmaRestApiClient
Access a given endpoint REST endpoint with parameters.
perform(String, MultiValueMap<String, Object>) - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
 
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.model.genome.gene
 
PhenotypeGroupValueObject() - Constructor for class ubic.gemma.model.genome.gene.PhenotypeGroupValueObject
 
PhenotypeGroupValueObject(String, String, Long, String, Collection<Long>, String, String, String) - Constructor for class ubic.gemma.model.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
 
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.persistence.util
General-purpose pointcuts to recognize CRUD operations etc.
Pointcuts() - Constructor for class ubic.gemma.persistence.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
 
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ubic.gemma.core.config.BaseCodeConfigurer
 
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ubic.gemma.core.context.LazyInitByDefaultPostProcessor
 
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
 
postProcessValueObjects(List<DifferentialExpressionAnalysisResultSetValueObject>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
 
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.expression.experiment.ExpressionExperimentPrePersistService
Call this before calling the persister.
prepare(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistServiceImpl
 
prepare(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistService
 
prepare(ExpressionExperiment, ArrayDesignsForExperimentCache) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistServiceImpl
 
prepareContext(ApplicationContext) - Static method in class ubic.gemma.core.context.SpringContextUtils
Prepare a given context for prime time.
prepareDatabaseQuery(String, boolean) - Static method in class ubic.gemma.core.search.lucene.LuceneQueryUtils
 
prepareDatabaseQuery(SearchSettings) - 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
Primitive storage types for data vectors.
PrincipalComponentAnalysis - Class in ubic.gemma.model.analysis.expression.pca
 
PrincipalComponentAnalysis() - Constructor for class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
 
PrincipalComponentAnalysis.Factory - Class in ubic.gemma.model.analysis.expression.pca
 
PrincipalComponentAnalysisDao - Interface in ubic.gemma.persistence.service.analysis.expression.pca
 
PrincipalComponentAnalysisDaoImpl - Class in ubic.gemma.persistence.service.analysis.expression.pca
 
PrincipalComponentAnalysisDaoImpl(SessionFactory) - Constructor for class ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImpl
 
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, Blat) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService
 
processArrayDesign(ArrayDesign, Blat) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl
 
processArrayDesign(ArrayDesign, ProbeMapperConfig, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService
 
processArrayDesign(ArrayDesign, ProbeMapperConfig, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
 
processArrayDesign(ArrayDesign, Taxon, File, ExternalDatabase, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService
Annotate an array design using a direct source file.
processArrayDesign(ArrayDesign, Taxon, File, ExternalDatabase, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl
 
processArrayDesign(ArrayDesign, Taxon, Collection<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
 
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, ProcessedDataVectorByGeneCache, ExpressionExperimentDao) - 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.analysis.sequence.Blat
 
processPsl(InputStream, Taxon) - Method in class ubic.gemma.core.analysis.sequence.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.core.context.EnvironmentProfiles
 
ProfilingConfig - Class in ubic.gemma.core.profiling
 
ProfilingConfig() - Constructor for class ubic.gemma.core.profiling.ProfilingConfig
 
ProgressData - Class in ubic.gemma.core.job.progress
 
ProgressData() - Constructor for class ubic.gemma.core.job.progress.ProgressData
 
ProgressData(String, int, String) - Constructor for class ubic.gemma.core.job.progress.ProgressData
 
ProgressData(String, int, String, boolean) - Constructor for class ubic.gemma.core.job.progress.ProgressData
 
ProgressUpdateAppender - Class in ubic.gemma.core.job.progress
This appender is used by remote tasks to send progress notifications to the webapp.
ProgressUpdateAppender() - Constructor for class ubic.gemma.core.job.progress.ProgressUpdateAppender
 
ProgressUpdateAppender.ProgressUpdateCallback - Interface in ubic.gemma.core.job.progress
Callback used to emit progress updates.
ProgressUpdateAppender.ProgressUpdateContext - Class in ubic.gemma.core.job.progress
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.progress.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
 
PropertySourcesConfiguration - Class in ubic.gemma.core.config
Deprecated.
This has been replaced with Spring-based configuration SettingsConfig and usage of Value to inject configurations. You can use @Value("${property}") as replacement.
PropertySourcesConfiguration(PropertySources, DefaultListDelimiterHandler) - Constructor for class ubic.gemma.core.config.PropertySourcesConfiguration
Deprecated.
 
propertySourcesPlaceholderConfigurer(PropertySources) - Static method in class ubic.gemma.core.config.SettingsConfig
Allow for substitution placeholders with values from the settings.
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.analysis.sequence.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.persistence.service.common.description.BibliographicReferenceService
 
refresh(String) - Method in class ubic.gemma.persistence.service.common.description.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.auditAndSecurity.curation.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 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.auditAndSecurity.curation.CuratableService
Removes the entity with given ID from the persistent storage.
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.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.gene.GeneSetService
 
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 class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
remove(Collection<GeneSet>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
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.persistence.service.common.description.BibliographicReferenceService
 
remove(Characteristic) - Method in interface ubic.gemma.persistence.service.common.description.CharacteristicService
 
remove(ExternalDatabase) - Method in interface ubic.gemma.persistence.service.common.description.ExternalDatabaseService
 
remove(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.persistence.service.genome.gene.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 class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
remove(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
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.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.blacklist.BlacklistedEntityDao
 
removeAll() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl
 
removeAll() - Method in interface ubic.gemma.persistence.service.blacklist.BlacklistedEntityService
Remove all blacklisted platforms and experiments.
removeAll() - Method in class ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl
 
removeAll() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
removeAll() - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
removeAll() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetDao
 
removeAll() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
removeAll() - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
removeAll() - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
removeAll() - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
removeAll() - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
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.
 
removeAllRawDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
Remove all raw data vectors.
removeAllRawDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
removeAllRawDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
removeAllRawDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
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.experiment.ExpressionExperimentDao
Remove processed data vectors.
removeProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
removeProcessedDataVectors(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
removeProcessedDataVectors(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
removeRawDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
Remove raw data vectors for a given quantitation type.
removeRawDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
removeRawDataVectors(ExpressionExperiment, QuantitationType) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
removeRawDataVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
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.
 
replaceAllRawDataVectors(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.
replaceAllRawDataVectors(ExpressionExperiment, Collection<RawExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
replaceData(ExpressionExperiment, ArrayDesign, ExpressionDataDoubleMatrix) - Method in interface ubic.gemma.core.loader.expression.DataUpdater
 
replaceData(ExpressionExperiment, ArrayDesign, ExpressionDataDoubleMatrix) - Method in class ubic.gemma.core.loader.expression.DataUpdaterImpl
Replace the data associated with the experiment (or add it if there is none).
replaceData(ExpressionExperiment, ArrayDesign, QuantitationType, DoubleMatrix<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
 
replaceProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
Replace processed data vectors.
replaceProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
replaceProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
replaceProcessedDataVectors(ExpressionExperiment, Collection<ProcessedExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection<RawExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
Replace raw data vectors for a given quantitation type.
replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection<RawExpressionDataVector>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
 
replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection<RawExpressionDataVector>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
replaceRawDataVectors(ExpressionExperiment, QuantitationType, 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
 
reportInitializationTime(BeanInitializationTimeMonitor) - Method in class ubic.gemma.core.profiling.ProfilingConfig
 
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 interface ubic.gemma.core.job.SubmittedTask
Send cancellation request.
requiresLayout() - Method in class ubic.gemma.core.job.progress.ProgressUpdateAppender
 
reset() - Method in class ubic.gemma.core.profiling.BeanInitializationTimeMonitor
Reset recorded times.
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.persistence.util.Pointcuts
A method that can be retried, public and annotated with Retryable.
retryableOrTransactionalServiceMethod() - Method in class ubic.gemma.persistence.util.Pointcuts
A retryable or transactional service method.
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.util.concurrent.GenericStreamConsumer
 
run() - Method in class ubic.gemma.core.util.concurrent.ParsingStreamConsumer
 
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.model.expression.experiment.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.auditAndSecurity.curation.CuratableService
 
save(Collection<C>) - Method in interface ubic.gemma.persistence.service.auditAndSecurity.curation.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.persistence.service.genome.gene.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.persistence.service.genome.gene.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.persistence.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.persistence.service.common.description.BibliographicReferenceService
 
search(String) - Method in class ubic.gemma.persistence.service.common.description.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.persistence.service.common.description.BibliographicReferenceService
 
search(SearchSettingsValueObject) - Method in class ubic.gemma.persistence.service.common.description.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.
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
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.persistence.service.expression.experiment.ExpressionExperimentSearchService
does not include session bound sets
searchExperimentsAndExperimentGroups(String, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl
 
searchExperimentSet(SearchSettings) - 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.persistence.service.expression.experiment.ExpressionExperimentSearchService
 
searchExpressionExperiments(String) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl
 
searchExpressionExperiments(String, Long) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService
 
searchExpressionExperiments(String, Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl
 
searchExpressionExperiments(List<String>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService
 
searchExpressionExperiments(List<String>) - Method in class ubic.gemma.persistence.service.expression.experiment.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.persistence.service.genome.gene.GeneCoreService
Search for genes (by name or symbol)
searchGenes(String, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
searchGenes(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
Search for genes (by name or symbol)
searchGenesAndGeneGroups(String, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSearchService
 
searchGenesAndGeneGroups(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
 
searchGeneSet(SearchSettings) - 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.persistence.service.genome.gene.GeneSearchService
Search for multiple genes at once.
searchMultipleGenes(String, Long) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl
 
searchMultipleGenesGetMap(Collection<String>, Long) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSearchService
Search for multiple genes at once.
searchMultipleGenesGetMap(Collection<String>, Long) - Method in class ubic.gemma.persistence.service.genome.gene.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.core.util.MailEngine
Send an email message to the administrator.
sendAdminMessage(String, String) - Method in class ubic.gemma.core.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.core.util.MailEngine
Send a text email message.
sendMessage(String, String, String) - Method in class ubic.gemma.core.util.MailEngineImpl
 
sendMessage(String, String, String, Map<String, Object>) - Method in interface ubic.gemma.core.util.MailEngine
Send a templated email message.
sendMessage(String, String, String, Map<String, Object>) - Method in class ubic.gemma.core.util.MailEngineImpl
 
sendTaskCompletedNotificationEmail(EmailNotificationContext, TaskResult) - Method in interface ubic.gemma.core.job.notification.TaskMailUtils
 
sendTaskCompletedNotificationEmail(EmailNotificationContext, TaskResult) - Method in class ubic.gemma.core.job.notification.TaskMailUtilsImpl
 
SEQUENCE - ubic.gemma.model.common.description.DatabaseType
 
SequenceBinUtils - Class in ubic.gemma.core.analysis.sequence
Used to assign a bin to a chromosome location, identify bins for a range, or to generate SQL to add to a query on a GoldenPath database.
SequenceBinUtils() - Constructor for class ubic.gemma.core.analysis.sequence.SequenceBinUtils
 
SequenceManipulation - Class in ubic.gemma.core.analysis.sequence
Convenient methods for manipulating BioSequences and PhysicalLocations
SequenceManipulation() - Constructor for class ubic.gemma.core.analysis.sequence.SequenceManipulation
 
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.persistence.util.Pointcuts
A public method defined in a service.
SessionBoundExpressionExperimentSetValueObject - Class in ubic.gemma.model.expression.experiment
 
SessionBoundExpressionExperimentSetValueObject() - Constructor for class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject
Required when using the class as a spring bean.
SessionBoundExpressionExperimentSetValueObject(Long) - Constructor for class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject
default constructor to satisfy java bean contract
SessionBoundGeneSetValueObject - Class in ubic.gemma.model.genome.gene
 
SessionBoundGeneSetValueObject() - Constructor for class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject
default constructor to satisfy java bean contract
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.common.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.blacklist.BlacklistedValueObject
 
setAccession(String) - Method in class ubic.gemma.model.common.description.DatabaseEntry
 
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.service.maintenance.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.auditAndSecurity.AbstractAuditable
 
setAuditTrail(AuditTrail) - Method in interface ubic.gemma.model.common.auditAndSecurity.Auditable
 
setAuditTrail(AuditTrail) - Method in class ubic.gemma.model.common.description.ExternalDatabase
 
setAuthentication(String, String) - Method in interface ubic.gemma.core.util.GemmaRestApiClient
Set credentials used for authenticating API requests.
setAuthentication(String, String) - Method in class ubic.gemma.core.util.GemmaRestApiClientImpl
Set the authentication credentials used by this client.
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 interface ubic.gemma.core.analysis.sequence.Blat
 
setBlatScoreThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
 
setBlatScoreThreshold(double) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
setBlockCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResult
 
setBlockCount(Integer) - Method in class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
 
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
 
setData(double[]) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
 
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.service.maintenance.Gene2CsStatus
 
setErrorFound(boolean) - Method in class ubic.gemma.model.common.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.DataVector
 
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.blacklist.BlacklistedEntity
 
setExternalAccession(DatabaseEntry) - Method in class ubic.gemma.model.expression.biomaterial.BioMaterial
 
setExternalDatabase(ExternalDatabase) - Method in class ubic.gemma.model.common.description.DatabaseEntry
 
setExternalDatabase(ExternalDatabase) - Method in class ubic.gemma.model.genome.Taxon
 
setExternalDatabase(ExternalDatabaseValueObject) - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
 
setExternalDatabase(ExternalDatabaseValueObject) - Method in class ubic.gemma.model.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.model.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 interface ubic.gemma.model.common.GemmaSessionBackedValueObject
 
setId(Long) - Method in class ubic.gemma.model.common.IdentifiableValueObject
Only used by the spring java-beans in jsp files.
setId(Long) - Method in class ubic.gemma.model.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 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(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.service.maintenance.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
 
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 interface ubic.gemma.model.common.GemmaSessionBackedValueObject
 
setModified(boolean) - Method in class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject
 
setModified(boolean) - Method in class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject
 
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.blacklist.BlacklistedValueObject
 
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.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.common.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.model.genome.gene.PhenotypeGroupValueObject
 
setPhenotypeMapping(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
 
setPhenotypeName(String) - Method in class ubic.gemma.model.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.core.config.Settings
Deprecated.
 
setPropertySources(PropertySources) - Method in class ubic.gemma.core.config.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.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
 
setQueryString(String) - Method in class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject
 
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.blacklist.BlacklistedEntity
 
setReason(String) - Method in class ubic.gemma.model.blacklist.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.model.genome.gene.GOGroupValueObject
 
setSearchTerm(String) - Method in class ubic.gemma.model.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
 
setSecondBaselineGroup(FactorValueBasicValueObject) - Method in class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
 
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.blacklist.BlacklistedEntity
 
setShortName(String) - Method in class ubic.gemma.model.blacklist.BlacklistedValueObject
 
setShortName(String) - Method in class ubic.gemma.model.expression.arrayDesign.ArrayDesign
 
setShortName(String) - Method in class ubic.gemma.model.expression.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.job.AbstractTask
 
setTaskCommand(C) - Method in interface ubic.gemma.core.job.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.core.config
Deprecated.
This has been replaced with Spring-based configuration SettingsConfig and usage of Value to inject configurations. You can use @Value("${property}") as replacement.
Settings() - Constructor for class ubic.gemma.core.config.Settings
Deprecated.
 
SettingsConfig - Class in ubic.gemma.core.config
Beans declaration for making the settings available via the Spring Environment and placeholder substitution.
SettingsConfig() - Constructor for class ubic.gemma.core.config.SettingsConfig
 
settingsPropertySources() - Static method in class ubic.gemma.core.config.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.blacklist.BlacklistedValueObject
 
setType(String) - Method in class ubic.gemma.model.common.measurement.MeasurementValueObject
 
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.common.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.
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.common.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.
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.analysis.sequence
Class to manage the gfServer and run BLAT searches.
ShellDelegatingBlat() - Constructor for class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
Create a blat object with settings read from the config file.
ShellDelegatingBlat(String, int, String) - Constructor for class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
ShellDelegatingBlat.BlattableGenome - Enum in ubic.gemma.core.analysis.sequence
 
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(ExpressionExperimentSubSet, BioAssayDimensionValueObject) - Method in class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
Crate a vector that is a slice of this one.
Slice<O> - Class in ubic.gemma.persistence.util
Represents a slice of List.
Slice(List<O>, Sort, Integer, Integer, Long) - Constructor for class ubic.gemma.persistence.util.Slice
 
SlicedDoubleVectorValueObject - Class in ubic.gemma.model.expression.bioAssayData
 
SlicedDoubleVectorValueObject(DoubleVectorValueObject, ExpressionExperimentSubSet, BioAssayDimensionValueObject) - Constructor for class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject
Constructor for creating a 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.model.expression.experiment.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
 
SpringContextUtils - Class in ubic.gemma.core.context
Methods to create Spring contexts for Gemma manually.
SpringContextUtils() - Constructor for class ubic.gemma.core.context.SpringContextUtils
 
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.analysis.sequence.Blat
Start the server, if the port isn't already being used.
startServer(ShellDelegatingBlat.BlattableGenome, int) - Method in class ubic.gemma.core.analysis.sequence.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.analysis.sequence.Blat
 
stopServer(int) - Method in interface ubic.gemma.core.analysis.sequence.Blat
Stop the gfServer, if it was started by this.
stopServer(int) - Method in class ubic.gemma.core.analysis.sequence.ShellDelegatingBlat
 
StopWatchUtils - Class in ubic.gemma.core.profiling
Utilities for working with StopWatch.
StopWatchUtils() - Constructor for class ubic.gemma.core.profiling.StopWatchUtils
 
StopWatchUtils.StopWatchRegion - Class in ubic.gemma.core.profiling
 
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.TaskRunningService
 
submitTask(T) - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
 
submitTaskCommand(C) - Method in interface ubic.gemma.core.job.TaskRunningService
Submit a task and track its progress.
submitTaskCommand(C) - Method in class ubic.gemma.core.job.TaskRunningServiceImpl
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
 
SubmittedTasksMaintenance - Class in ubic.gemma.core.job
 
SubmittedTasksMaintenance() - Constructor for class ubic.gemma.core.job.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.util
 
SubqueryUtils() - Constructor for class ubic.gemma.persistence.util.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.maintenance
 
TableMaintenanceUtilImpl - Class in ubic.gemma.persistence.service.maintenance
Functions for maintaining the database.
TableMaintenanceUtilImpl() - Constructor for class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
 
TAS - ubic.gemma.model.association.GOEvidenceCode
 
Task<C extends TaskCommand> - Interface in ubic.gemma.core.job
 
taskCommand - Variable in class ubic.gemma.core.job.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.
TaskMailUtils - Interface in ubic.gemma.core.job.notification
 
TaskMailUtilsImpl - Class in ubic.gemma.core.job.notification
 
TaskMailUtilsImpl() - Constructor for class ubic.gemma.core.job.notification.TaskMailUtilsImpl
 
TaskPostProcessing - Interface in ubic.gemma.core.job.notification
author: anton date: 10/02/13
TaskPostProcessingImpl - Class in ubic.gemma.core.job.notification
author: anton date: 10/02/13
TaskPostProcessingImpl() - Constructor for class ubic.gemma.core.job.notification.TaskPostProcessingImpl
 
TaskResult - Class in ubic.gemma.core.job
This class describes the result of long-running task.
TaskResult(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
 
TaskRunningServiceImpl - Class in ubic.gemma.core.job
Handles the execution of tasks in threads that can be checked by clients later.
TaskRunningServiceImpl() - Constructor for class ubic.gemma.core.job.TaskRunningServiceImpl
 
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
 
TaxonUtils - Class in ubic.gemma.persistence.service.genome.taxon
A utility class for taxon.
TaxonUtils() - Constructor for class ubic.gemma.persistence.service.genome.taxon.TaxonUtils
 
TaxonValueObject - Class in ubic.gemma.model.genome
 
TaxonValueObject() - Constructor for class ubic.gemma.model.genome.TaxonValueObject
 
TaxonValueObject(Long) - Constructor for class ubic.gemma.model.genome.TaxonValueObject
 
TaxonValueObject(Long, String) - Constructor for class ubic.gemma.model.genome.TaxonValueObject
 
TaxonValueObject(Taxon) - Constructor for class ubic.gemma.model.genome.TaxonValueObject
 
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.core.context.EnvironmentProfiles
 
TestComponent - Annotation Type in ubic.gemma.core.context
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.persistence.service.common.description.BibliographicReferenceDao
 
thaw(Collection<BibliographicReference>) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
thaw(Collection<BibliographicReference>) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
 
thaw(Collection<BibliographicReference>) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
thaw(Collection<ArrayDesign>) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
Thaw a collection of platforms.
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.persistence.service.common.description.BibliographicReferenceDao
 
thaw(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
 
thaw(BibliographicReference) - Method in interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService
 
thaw(BibliographicReference) - Method in class ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl
 
thaw(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
Thaw the given platform as per ArrayDesignDao.thawLite(ArrayDesign) with its probes and genes.
thaw(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
 
thaw(ArrayDesign) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
Thaw a given platform.
thaw(ArrayDesign) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
 
thaw(BioAssay) - Method in interface ubic.gemma.persistence.service.expression.bioAssay.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.persistence.service.genome.gene.GeneService
 
thaw(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
thaw(Gene) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
thaw(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
thaw(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneProductDao
 
thaw(GeneProduct) - Method in class ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl
 
thaw(GeneProduct) - Method in interface ubic.gemma.persistence.service.genome.gene.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.persistence.service.genome.gene.GeneService
 
thawAliases(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
thawAliases(Gene) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
thawAliases(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
Only thaw the Aliases, very light version
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.persistence.service.genome.gene.GeneService
 
thawLite(Collection<Gene>) - Method in class ubic.gemma.persistence.service.genome.gene.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.persistence.service.genome.gene.GeneService
 
thawLite(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
thawLite(Gene) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
thawLite(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
thawLiter(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
 
thawLiter(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
 
thawLiter(Gene) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneService
 
thawLiter(Gene) - Method in class ubic.gemma.persistence.service.genome.gene.GeneServiceImpl
 
thawLiter(Gene) - Method in interface ubic.gemma.persistence.service.genome.GeneDao
 
thawLiter(Gene) - Method in class ubic.gemma.persistence.service.genome.GeneDaoImpl
 
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
 
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
 
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.DifferentialExpressionAnalysisResultSetValueObject
 
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.Gene2OntologyEntryAssociation
 
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.IdentifiableValueObject
 
toString() - Method in class ubic.gemma.model.common.measurement.Measurement
 
toString() - Method in class ubic.gemma.model.common.measurement.Unit
 
toString() - Method in class ubic.gemma.model.common.quantitationtype.QuantitationType
 
toString() - Method in class ubic.gemma.model.common.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.bioAssayData.SlicedDoubleVectorValueObject
 
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.service.association.coexpression.CoexpressionValueObject
 
toString() - Method in class ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink
 
toString() - Method in class ubic.gemma.persistence.service.maintenance.Gene2CsStatus
 
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
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.persistence.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.hibernate.TypedResultTransformer
transformListTyped(List<T>) - Method in interface ubic.gemma.persistence.hibernate.TypedResultTransformer
 
transformTuple(Object[], String[]) - Method in interface ubic.gemma.persistence.hibernate.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.hibernate
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.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.config - package ubic.gemma.core.config
This package contains classes that are used to manage Gemma's Spring context.
ubic.gemma.core.context - package ubic.gemma.core.context
This package contains classes that are used to manage Gemma's Spring context.
ubic.gemma.core.datastructure.matrix - package ubic.gemma.core.datastructure.matrix
 
ubic.gemma.core.goldenpath - package ubic.gemma.core.goldenpath
 
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
Provides functionalities for running background tasks.
ubic.gemma.core.job.notification - package ubic.gemma.core.job.notification
 
ubic.gemma.core.job.progress - package ubic.gemma.core.job.progress
 
ubic.gemma.core.loader.association - package ubic.gemma.core.loader.association
 
ubic.gemma.core.loader.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.profiling - package ubic.gemma.core.profiling
Classes and utilities for profiling the performance of Gemma.
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 - package ubic.gemma.core.security
 
ubic.gemma.core.security.audit - package ubic.gemma.core.security.audit
 
ubic.gemma.core.security.authentication - package ubic.gemma.core.security.authentication
This package contains implementation of gsec UserService and UserManager.
ubic.gemma.core.security.authorization.acl - package ubic.gemma.core.security.authorization.acl
 
ubic.gemma.core.tasks - package ubic.gemma.core.tasks
This package contains task definitions.
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.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.blacklist - package ubic.gemma.model.blacklist
 
ubic.gemma.model.common - package ubic.gemma.model.common
 
ubic.gemma.model.common.auditAndSecurity - package ubic.gemma.model.common.auditAndSecurity
 
ubic.gemma.model.common.auditAndSecurity.curation - package ubic.gemma.model.common.auditAndSecurity.curation
 
ubic.gemma.model.common.auditAndSecurity.eventType - package ubic.gemma.model.common.auditAndSecurity.eventType
 
ubic.gemma.model.common.description - package ubic.gemma.model.common.description
 
ubic.gemma.model.common.measurement - package ubic.gemma.model.common.measurement
 
ubic.gemma.model.common.protocol - package ubic.gemma.model.common.protocol
 
ubic.gemma.model.common.quantitationtype - package ubic.gemma.model.common.quantitationtype
 
ubic.gemma.model.common.search - package ubic.gemma.model.common.search
 
ubic.gemma.model.expression.arrayDesign - package ubic.gemma.model.expression.arrayDesign
 
ubic.gemma.model.expression.bioAssay - package ubic.gemma.model.expression.bioAssay
 
ubic.gemma.model.expression.bioAssayData - package ubic.gemma.model.expression.bioAssayData
 
ubic.gemma.model.expression.biomaterial - package ubic.gemma.model.expression.biomaterial
 
ubic.gemma.model.expression.designElement - package ubic.gemma.model.expression.designElement
 
ubic.gemma.model.expression.experiment - package ubic.gemma.model.expression.experiment
 
ubic.gemma.model.genome - package ubic.gemma.model.genome
 
ubic.gemma.model.genome.biosequence - package ubic.gemma.model.genome.biosequence
 
ubic.gemma.model.genome.gene - package ubic.gemma.model.genome.gene
 
ubic.gemma.model.genome.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 - package ubic.gemma.persistence
This package contains classes related to retrieval and persistence of entities.
ubic.gemma.persistence.cache - package ubic.gemma.persistence.cache
 
ubic.gemma.persistence.hibernate - package ubic.gemma.persistence.hibernate
 
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.auditAndSecurity.curation - package ubic.gemma.persistence.service.auditAndSecurity.curation
 
ubic.gemma.persistence.service.blacklist - package ubic.gemma.persistence.service.blacklist
Service for managing blacklisted entities.
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.service.maintenance - package ubic.gemma.persistence.service.maintenance
Contains classes related to database maintenance.
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.auditAndSecurity.curation.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.auditAndSecurity.curation.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<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 class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
update(Collection<GeneSet>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
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 class ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl
 
update(GeneSet) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
 
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.persistence.service.genome.gene.GeneSetService
AJAX Updates the database entity (permission permitting) with the fields of the param value object
updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject>) - Method in class ubic.gemma.persistence.service.genome.gene.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.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
updateDatabaseEntityMembers(Long, Collection<Long>) - Method in interface ubic.gemma.persistence.service.genome.gene.GeneSetService
Updates the database record for the param gene set value object (permission permitting) with the members specified of the set, not the name or description etc.
updateDatabaseEntityMembers(Long, Collection<Long>) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
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.persistence.service.genome.gene.GeneSetService
AJAX Updates the database entity (permission permitting) with the name and description fields of the param value object
updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject) - Method in class ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl
 
UpdateEEDetailsCommand - Class in ubic.gemma.core.tasks.analysis.expression
 
UpdateEEDetailsCommand() - Constructor for class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
 
updateExpressionExperiment2ArrayDesignEntries(Date) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
Update the EXPRESSION_EXPERIMENT2_ARRAY_DESIGN table.
updateExpressionExperiment2ArrayDesignEntries(Date) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
 
updateExpressionExperiment2CharacteristicEntries(Class<?>, Date, boolean) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
Update a specific level of the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
updateExpressionExperiment2CharacteristicEntries(Class<?>, Date, boolean) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
 
updateExpressionExperiment2CharacteristicEntries(Date, boolean) - Method in interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
Update the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
updateExpressionExperiment2CharacteristicEntries(Date, boolean) - Method in class ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl
 
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.maintenance.TableMaintenanceUtil
If necessary, update the GENE2CS table.
updateGene2CsEntries() - Method in class ubic.gemma.persistence.service.maintenance.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.persistence.util.Pointcuts
Methods that update items in the persistent store
updateRanks(ExpressionExperiment) - Method in interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
Update the ranks of the processed vectors for the given experiment.
updateRanks(ExpressionExperiment) - Method in class ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl
 
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.common
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.sequence.ShellDelegatingBlat.BlattableGenome
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.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.ExpressionExperimentMetaFileType
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.sequence.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.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.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.ExpressionExperimentMetaFileType
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
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