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All Classes All Packages
All Classes All Packages
All Classes All Packages
A
- AbaGene - Class in ubic.gemma.core.image.aba
- AbaGene() - Constructor for class ubic.gemma.core.image.aba.AbaGene
- AbaGene(Integer, String, String, String, String, Collection<ImageSeries>) - Constructor for class ubic.gemma.core.image.aba.AbaGene
- ABALinkOutValueObject - Class in ubic.gemma.core.image
-
Value Object for transporting details needed from other websites to provide convenient links to them in gemma
- ABALinkOutValueObject() - Constructor for class ubic.gemma.core.image.ABALinkOutValueObject
- ABALinkOutValueObject(Collection<String>, String, String) - Constructor for class ubic.gemma.core.image.ABALinkOutValueObject
- ABSOLUTE - ubic.gemma.model.common.measurement.MeasurementType
- AbstractAnalyzer - Class in ubic.gemma.core.analysis.expression.diff
-
Analyzer base class.
- AbstractAnalyzer() - Constructor for class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer
- AbstractAsyncFactoryBean<T> - Class in ubic.gemma.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 HibernateCriteria
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 HibernateQuery
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 withAclQueryUtils.formAclRestrictionClause(String)
and add ACL restriction parameters defined inAclQueryUtils.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)
orQuery.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 anAnalysisResultSet
. - 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
-
Inverse of
TGFVO.hasAnnotation
. - AnnotationValueObject - Class in ubic.gemma.model.common.description
- AnnotationValueObject() - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
- AnnotationValueObject(Long) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
- AnnotationValueObject(String, String, String, String, Class<?>) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
- AnnotationValueObject(Characteristic) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
- AnnotationValueObject(Characteristic, Class<?>) - Constructor for class ubic.gemma.model.common.description.AnnotationValueObject
- antibody - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
- anyPublicMethod() - Method in class ubic.gemma.persistence.util.Pointcuts
-
A public method.
- AOI_ALIAS - Static variable in class ubic.gemma.persistence.util.AclQueryUtils
-
Alias used by
AclQueryUtils.formAclRestrictionClause(String, int)
andAclQueryUtils.formNativeAclJoinClause(String)
for the object identityAclObjectIdentity
and the owner identityAclSid
. - 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
- 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()
orCharacteristic.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 withSession.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
-
HQL alias for
Curatable.getCurationDetails()
. - CurationDetails - Class in ubic.gemma.model.common.auditAndSecurity.curation
-
Class encapsulating all the curation information for Curatable objects.
- CurationDetails() - Constructor for class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
- CurationDetailsEvent - Class in ubic.gemma.model.common.auditAndSecurity.eventType
-
Event types that can change
CurationDetails
ofCuratable
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
-
Deprecated.
- 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
- 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
- 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
- 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
DifferentialExpressionAnalysisResult
s keyed byExpressionExperiment
. - 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
DifferentialExpressionAnalysisResult
s keyed byExpressionExperiment
. - 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 accessingObject.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
orGemmaRestApiClient.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
DifferentialExpressionAnalysisResult
s 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
-
Deprecated.
- 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
-
Deprecated.
- 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
-
Deprecated.
- 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 toFactorValue
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
- getFilterablePropertyMeta(String) - Method in class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
- 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
MessageSourceResolvable
s 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 theFilteringDao
. - 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
-
Deprecated.
- 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.use
FactorValue.getMeasurement()
orFactorValue.getCharacteristics()
to retrieve the value. - getValue() - Method in class ubic.gemma.model.expression.experiment.Statement
-
Deprecated.use
Statement.getSubject()
instead - getValue() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
- getValue() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
- getValue() - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject
- getValueObject() - Method in class ubic.gemma.model.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.use
Statement.getSubjectUri()
instead - getValueUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
- getValueUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
- getVariables() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
- getVariables() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
- getVarianceFraction() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
- getVarianceFractions() - Method in class ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
- getVarianceFractions() - Method in class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
- getVariances() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
- getVariances() - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
- getVector() - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
- getVectors() - Method in class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
- getVersion() - Method in class ubic.gemma.core.util.BuildInfo
- getVersion() - Method in class ubic.gemma.model.common.description.LocalFile
- getVisualizationValue() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
- getVisualizationValues() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
- getvMatrix() - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
- getVolume() - Method in class ubic.gemma.model.common.description.BibliographicReference
- getVolume() - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
- getWarnings() - Method in class ubic.gemma.core.analysis.sequence.ProbeMapperConfig
- getWebLink() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
- getWebLink() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
- getWebLinks() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
- getWebLinks() - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
- getWebUri() - Method in class ubic.gemma.model.common.description.ExternalDatabase
- getWebUri() - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
- getWeeklyReport() - Method in interface ubic.gemma.core.analysis.report.WhatsNewService
-
Generate the report from last week.
- getWeeklyReport() - Method in class ubic.gemma.core.analysis.report.WhatsNewServiceImpl
- getWidth() - Method in class ubic.gemma.core.image.aba.Image
- GO - Static variable in class ubic.gemma.model.common.description.ExternalDatabases
- GOEvidenceCode - Enum in ubic.gemma.model.association
-
This enumeration was originally based on GO, but is used for all entities that have evidenciary aspects; Thus it has been expanded to include: Terms from RGD (rat genome database) IED = Inferred from experimental data IAGP = Inferred from association of genotype and phenotype IPM = Inferred from phenotype manipulation QTM = Quantitative Trait Measurement And our own custom code IIA which means Inferred from Imported Annotation to distinguish IEAs that we ourselves have computed See https://geneontology.org/docs/guide-go-evidence-codes/ for documentation of GO evidence codes.
- GOGroupValueObject - Class in ubic.gemma.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 itsStatement
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
-
Initialize a result from
AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort)
retrieved from the HibernateStandardQueryCache
. - 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
-
A lightweight version of
ExpressionExperimentService.loadAndThawWithRefreshCacheMode(Long)
which thaws as perExpressionExperimentService.thawLite(ExpressionExperiment)
. - 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)
withCacheMode.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 aExpressionExperiment
or aExpressionExperimentSubSet
. - loadBioAssaySet(Long) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
- loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
- loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
- loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
-
No need for ACL_VALUE_OBJECT_COLLECTION_READ because the filtering is done in the query.
- loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl
- loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
- loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
- loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
- loadBlacklistedValueObjects(Filters, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
- loadByDescription(String) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
- loadByDescription(String) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl
- loadByDescription(String) - Method in interface ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
- loadByDescription(String) - Method in class ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl
- loadCompositeSequences(ArrayDesign, int, int) - Method in interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao
- loadCompositeSequences(ArrayDesign, int, int) - Method in class ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl
- loadContrastDetailsForResults(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao
- loadContrastDetailsForResults(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl
-
Key method for getting contrasts associated with results.
- loadContrastDetailsForResults(Collection<Long>) - Method in interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
- loadContrastDetailsForResults(Collection<Long>) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl
- loadDatabase(Persister, Collection<?>) - Static method in class ubic.gemma.core.loader.util.ParserAndLoaderTools
-
User the loader to persist the collection.
- loadDetailsValueObjects(Collection<Long>, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
-
Special method for front-end access.
- loadDetailsValueObjects(Collection<Long>, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
- loadDetailsValueObjects(Collection<Long>, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
- loadDetailsValueObjects(Collection<Long>, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
- loadDetailsValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
-
Like
ExpressionExperimentDao.loadDetailsValueObjects(Collection, Taxon, Sort, int, int)
, but returning a list. - loadDetailsValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
- loadDetailsValueObjectsByIds(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
- loadDetailsValueObjectsByIds(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
- loadDetailsValueObjectsByIdsWithCache(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
-
Flavour of
ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection)
, but using the query cache. - loadDetailsValueObjectsByIdsWithCache(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
- loadDetailsValueObjectsByIdsWithCache(Collection<Long>) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
- loadDetailsValueObjectsByIdsWithCache(Collection<Long>) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
- loadDetailsValueObjectsByIdsWithCache(Collection<Long>, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
-
Flavour of
ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection)
, but using the query cache. - loadDetailsValueObjectsByIdsWithCache(Collection<Long>, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl
- loadDetailsValueObjectsWithCache(Collection<Long>, Taxon, Sort, int, int) - Method in interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
- loadDetailsValueObjectsWithCache(Collection<Long>, Taxon, Sort, int, int) - Method in class ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl
- loader() - Method in class ubic.gemma.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
GeneSet
s for the currently logged inUser
- 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
-
Load a
DifferentialExpressionAnalysisResult
toGene
multi-map. - loadResultToGenesMap(ExpressionAnalysisResultSet) - Method in class ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl
- loadStatisticsOnAllEvidence(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
- loadStatisticsOnAllEvidence(String) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
- loadStatisticsOnAllEvidence(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
- loadStatisticsOnAllEvidence(String) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
- loadStatisticsOnExternalDatabases(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
- loadStatisticsOnExternalDatabases(String) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
- loadStatisticsOnExternalDatabases(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
- loadStatisticsOnExternalDatabases(String) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
- loadStatisticsOnManualCuration(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
- loadStatisticsOnManualCuration(String) - Method in class ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl
- loadStatisticsOnManualCuration(String) - Method in interface ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
- loadStatisticsOnManualCuration(String) - Method in class ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl
- loadThawed(Collection<Long>) - Method in interface ubic.gemma.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 toStopWatch.start()
andStopWatch.suspend()
when entering and leaving the region. - Measurement - Class in ubic.gemma.model.common.measurement
- Measurement - Static variable in class ubic.gemma.core.ontology.jena.TGFVO
-
Represents a factor value
Measurement
. - Measurement() - Constructor for class ubic.gemma.model.common.measurement.Measurement
- Measurement.Factory - Class in ubic.gemma.model.common.measurement
- MeasurementKind - Enum in ubic.gemma.model.common.measurement
- measurementOf - Static variable in class ubic.gemma.core.ontology.jena.TGFVO
-
Inverse of
TGFVO.hasMeasurement
. - MeasurementType - Enum in ubic.gemma.model.common.measurement
- MeasurementValueObject - Class in ubic.gemma.model.common.measurement
- MeasurementValueObject() - Constructor for class ubic.gemma.model.common.measurement.MeasurementValueObject
- MeasurementValueObject(Measurement) - Constructor for class ubic.gemma.model.common.measurement.MeasurementValueObject
- MEDIAN - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
- MedianComparator - Static variable in class ubic.gemma.core.analysis.preprocess.OutlierDetails
-
Compare outliers by median correlation Note: this comparator imposes orderings that are inconsistent with equals
- MedicalSubjectHeading - Class in ubic.gemma.model.common.description
- MedicalSubjectHeading() - Constructor for class ubic.gemma.model.common.description.MedicalSubjectHeading
- MedicalSubjectHeading.Factory - Class in ubic.gemma.model.common.description
- merge(ArrayDesign, Collection<ArrayDesign>, String, String, boolean) - Method in interface ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeService
-
Merge array designs based on their sequence content.
- merge(ArrayDesign, Collection<ArrayDesign>, String, String, boolean) - Method in class ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceImpl
- mergeVectors(ExpressionExperiment) - Method in interface ubic.gemma.core.analysis.preprocess.VectorMergingService
- mergeVectors(ExpressionExperiment) - Method in class ubic.gemma.core.analysis.preprocess.VectorMergingServiceImpl
- metabolism - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
- MeterRegistryEhcacheConfigurer - Class in ubic.gemma.core.metrics
-
Add metrics from each available
Ehcache
in the givenCacheManager
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 withExpressionExperiment
. - 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 ofValue
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 givenQuantitationType
. - 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.use
SearchSource.searchBioSequence(SearchSettings)
(SearchSettings)} instead - searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
-
Deprecated.
- searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
- searchBlacklistedEntities(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
- searchBlacklistedEntities(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
- searchBlacklistedEntities(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
- searchCompositeSequence(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
- searchCompositeSequence(SearchSettings) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
- searchCompositeSequence(SearchSettings) - Method in class ubic.gemma.core.search.source.DatabaseSearchSource
- searchCompositeSequence(SearchSettings) - Method in class ubic.gemma.core.search.source.HibernateSearchSource
- searchCompositeSequenceAndGene(SearchSettings) - Method in interface ubic.gemma.core.search.SearchSource
-
Deprecated.
- 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 ofValue
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.use
Statement.setSubject(String)
instead - setValue(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
- setValue(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
- setValue(String) - Method in class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject
- setValueObject(Serializable) - Method in class ubic.gemma.model.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.use
Statement.setSubjectUri(String)
instead - setValueUri(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject
- setValueUri(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject
- setVarianceFraction(Double) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvalue
- setVariances(byte[]) - Method in class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation
- setVariances(double[]) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
- setVector(byte[]) - Method in class ubic.gemma.model.analysis.expression.pca.Eigenvector
- setVersion(String) - Method in class ubic.gemma.model.common.description.LocalFile
- setVisualizationValue(int, int, Double) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
- setVisualizationValues(List<List<Double>>) - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
- setvMatrix(DoubleMatrix<Long, Integer>) - Method in class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject
- setVolume(String) - Method in class ubic.gemma.model.common.description.BibliographicReference
- setVolume(String) - Method in class ubic.gemma.model.common.description.BibliographicReferenceValueObject
- setWarnedAboutGenePix(boolean) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSample
- setWarningThresholdMills(int) - Method in class ubic.gemma.core.search.source.CompositeSearchSource
-
Threshold in milliseconds for a warning to be logged.
- setWebLink(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoContact
- setWebLink(String) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
- setWebLinks(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoPlatform
- setWebLinks(Collection<String>) - Method in class ubic.gemma.core.loader.expression.geo.model.GeoSeries
- setWebUri(String) - Method in class ubic.gemma.model.common.description.ExternalDatabase
- setWebUri(String) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject
- SFARIIntermediateFileParser - Class in ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence
-
Deprecated.
- SFARIIntermediateFileParser() - Constructor for class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser
-
Deprecated.
- SFARILineInfo - Class in ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence
-
Deprecated.
- SFARILineInfo(String) - Constructor for class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo
-
Deprecated.
- ShellDelegatingBlat - Class in ubic.gemma.core.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)
andAclQueryUtils.formNativeAclJoinClause(String)
for the object identityAclObjectIdentity
and the owner identityAclSid
. - 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 aFactorValueBasicValueObject
. - 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
-
Render this with its
PropertyMapping.getObjectAlias()
andPropertyMapping.getPropertyName()
. - toString() - Method in enum ubic.gemma.persistence.util.Sort.Direction
- toString() - Method in class ubic.gemma.persistence.util.Sort
- toString() - Method in class ubic.gemma.persistence.util.Subquery
- toString(int) - Method in class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
- total() - Method in class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
-
Equivalent to getLinksWithMinimumSupport( 0 )
- totalRNA - ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
- totalSize(String) - Static method in class ubic.gemma.core.analysis.sequence.SequenceManipulation
- toText() - Method in class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject
- toXMLString(Object) - Method in class ubic.gemma.model.association.phenotype.PhenotypeMappingType
-
Deprecated.
- transactionalMethod() - Method in class ubic.gemma.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
-
Deprecated.Use
TypedResultTransformer.transformListTyped(List)
instead. - 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
andUserManager
. - 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()
orCacheKeyLock.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
DesignElementDataVector
s 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
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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
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Creates reports that can be shown on the web pages or in social media feeds.
- WhatsNewServiceImpl - Class in ubic.gemma.core.analysis.report
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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
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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
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Copy this search result with the given highlights.
- withResultObject(S) - Method in class ubic.gemma.core.search.SearchResult
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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
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Write a given entity to an appendable with a given content type.
- writeAllEvidenceToFile() - Method in interface ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService
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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
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Deprecated.
- writeDiffExArchiveFile(BioAssaySet, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig) - Method in interface ubic.gemma.core.analysis.service.ExpressionDataFileService
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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
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Deprecated.
- writeFinalLine(BufferedWriter) - Method in class ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Deprecated.
Z
- zeroVarianceFilter(ExpressionDataDoubleMatrix) - Static method in class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
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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
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Standard deviations from the mean
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