Uses of Class
ubic.gemma.model.common.description.DatabaseEntry

Packages that use DatabaseEntry

Package	Description
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.simple.model
ubic.gemma.core.loader.util.parser
ubic.gemma.model.association
ubic.gemma.model.association.phenotype
ubic.gemma.model.blacklist
ubic.gemma.model.common.description
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.gene.phenotype.valueObject
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome.biosequence
ubic.gemma.persistence.util
ubic.gemma.web.taglib

Uses of DatabaseEntry in ubic.gemma.core.loader.expression.geo

Methods in ubic.gemma.core.loader.expression.geo that return types with arguments of type DatabaseEntry

Modifier and Type	Method	Description
Collection<DatabaseEntry>	GeoDomainObjectGenerator.getProjectedAccessions(String geoAccession)	Determine the set of external accession values that will be generated during parsing.

Uses of DatabaseEntry in ubic.gemma.core.loader.expression.simple.model

Methods in ubic.gemma.core.loader.expression.simple.model that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	SimpleExpressionExperimentMetaData.getExternalReference()

Methods in ubic.gemma.core.loader.expression.simple.model with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	SimpleExpressionExperimentMetaData.setExternalReference(DatabaseEntry externalReference)

Uses of DatabaseEntry in ubic.gemma.core.loader.util.parser

Methods in ubic.gemma.core.loader.util.parser that return DatabaseEntry

Modifier and Type	Method	Description
static DatabaseEntry	ExternalDatabaseUtils.getGenbankAccession(String accession)

Uses of DatabaseEntry in ubic.gemma.model.association

Methods in ubic.gemma.model.association that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	ReferenceAssociation.getReferencedDatabaseEntry()

Methods in ubic.gemma.model.association with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	ReferenceAssociation.setReferencedDatabaseEntry(DatabaseEntry referencedDatabaseEntry)

Uses of DatabaseEntry in ubic.gemma.model.association.phenotype

Methods in ubic.gemma.model.association.phenotype that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	PhenotypeAssociation.getEvidenceSource()	Deprecated.

Methods in ubic.gemma.model.association.phenotype with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	PhenotypeAssociation.setEvidenceSource(DatabaseEntry evidenceSource)	Deprecated.

Uses of DatabaseEntry in ubic.gemma.model.blacklist

Methods in ubic.gemma.model.blacklist that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	BlacklistedEntity.getExternalAccession()

Methods in ubic.gemma.model.blacklist with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	BlacklistedEntity.setExternalAccession(DatabaseEntry externalAccession)

Uses of DatabaseEntry in ubic.gemma.model.common.description

Methods in ubic.gemma.model.common.description that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	BibliographicReference.getPubAccession()
static DatabaseEntry	DatabaseEntry.Factory.newInstance()
static DatabaseEntry	DatabaseEntry.Factory.newInstance(String accession, ExternalDatabase externalDatabase)
static DatabaseEntry	DatabaseEntry.Factory.newInstance(ExternalDatabase externalDatabase)

Methods in ubic.gemma.model.common.description that return types with arguments of type DatabaseEntry

Modifier and Type	Method	Description
static Comparator<DatabaseEntry>	DatabaseEntry.getComparator()	Compares DatabaseEntry by version.

Methods in ubic.gemma.model.common.description with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	BibliographicReference.setPubAccession(DatabaseEntry pubAccession)

Constructors in ubic.gemma.model.common.description with parameters of type DatabaseEntry

Constructor	Description
DatabaseEntryValueObject(DatabaseEntry de)

Uses of DatabaseEntry in ubic.gemma.model.expression.arrayDesign

Methods in ubic.gemma.model.expression.arrayDesign that return types with arguments of type DatabaseEntry

Modifier and Type	Method	Description
Set<DatabaseEntry>	ArrayDesign.getExternalReferences()

Method parameters in ubic.gemma.model.expression.arrayDesign with type arguments of type DatabaseEntry

Modifier and Type	Method	Description
void	ArrayDesign.setExternalReferences(Set<DatabaseEntry> externalReferences)

Uses of DatabaseEntry in ubic.gemma.model.expression.bioAssay

Methods in ubic.gemma.model.expression.bioAssay that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	BioAssay.getAccession()

Methods in ubic.gemma.model.expression.bioAssay with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	BioAssay.setAccession(DatabaseEntry accession)

Uses of DatabaseEntry in ubic.gemma.model.expression.biomaterial

Methods in ubic.gemma.model.expression.biomaterial that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	BioMaterial.getExternalAccession()

Methods in ubic.gemma.model.expression.biomaterial with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	BioMaterial.setExternalAccession(DatabaseEntry externalAccession)

Uses of DatabaseEntry in ubic.gemma.model.expression.experiment

Methods in ubic.gemma.model.expression.experiment that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	BioAssaySet.getAccession()
DatabaseEntry	ExpressionExperiment.getAccession()

Methods in ubic.gemma.model.expression.experiment with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	BioAssaySet.setAccession(DatabaseEntry accession)

Uses of DatabaseEntry in ubic.gemma.model.genome

Methods in ubic.gemma.model.genome that return types with arguments of type DatabaseEntry

Modifier and Type	Method	Description
Set<DatabaseEntry>	Gene.getAccessions()

Method parameters in ubic.gemma.model.genome with type arguments of type DatabaseEntry

Modifier and Type	Method	Description
void	Gene.setAccessions(Set<DatabaseEntry> accessions)

Uses of DatabaseEntry in ubic.gemma.model.genome.biosequence

Methods in ubic.gemma.model.genome.biosequence that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	BioSequence.getSequenceDatabaseEntry()

Methods in ubic.gemma.model.genome.biosequence with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	BioSequence.setSequenceDatabaseEntry(DatabaseEntry sequenceDatabaseEntry)

Uses of DatabaseEntry in ubic.gemma.model.genome.gene

Methods in ubic.gemma.model.genome.gene that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	GeneSet.getSourceAccession()

Methods in ubic.gemma.model.genome.gene that return types with arguments of type DatabaseEntry

Modifier and Type	Method	Description
Set<DatabaseEntry>	GeneProduct.getAccessions()

Methods in ubic.gemma.model.genome.gene with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	GeneSet.setSourceAccession(DatabaseEntry sourceAccession)

Method parameters in ubic.gemma.model.genome.gene with type arguments of type DatabaseEntry

Modifier and Type	Method	Description
void	GeneProduct.setAccessions(Set<DatabaseEntry> accessions)

Uses of DatabaseEntry in ubic.gemma.model.genome.gene.phenotype.valueObject

Constructors in ubic.gemma.model.genome.gene.phenotype.valueObject with parameters of type DatabaseEntry

Constructor	Description
EvidenceSourceValueObject(DatabaseEntry de)

Uses of DatabaseEntry in ubic.gemma.persistence.persister

Methods in ubic.gemma.persistence.persister with parameters of type DatabaseEntry

Modifier and Type	Method	Description
protected void	CommonPersister.fillInDatabaseEntry(DatabaseEntry databaseEntry, AbstractPersister.Caches caches)

Uses of DatabaseEntry in ubic.gemma.persistence.service.common.description

Methods in ubic.gemma.persistence.service.common.description that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	DatabaseEntryService.findLatestByAccession(String accession)	Find the latest (as per its version or ID) database entry by accession.
DatabaseEntry	DatabaseEntryServiceImpl.findLatestByAccession(String accession)

Methods in ubic.gemma.persistence.service.common.description that return types with arguments of type DatabaseEntry

Modifier and Type	Method	Description
List<DatabaseEntry>	DatabaseEntryDao.findByAccession(String accession)
List<DatabaseEntry>	DatabaseEntryDaoImpl.findByAccession(String accession)

Methods in ubic.gemma.persistence.service.common.description with parameters of type DatabaseEntry

Modifier and Type	Method	Description
protected DatabaseEntryValueObject	DatabaseEntryDaoImpl.doLoadValueObject(DatabaseEntry entity)
BibliographicReference	BibliographicReferenceDao.findByExternalId(DatabaseEntry externalId)	Find by the external database id, such as for PubMed
BibliographicReference	BibliographicReferenceDaoImpl.findByExternalId(DatabaseEntry externalId)
BibliographicReference	BibliographicReferenceService.findByExternalId(DatabaseEntry accession)
BibliographicReference	BibliographicReferenceServiceImpl.findByExternalId(DatabaseEntry accession)

Uses of DatabaseEntry in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type DatabaseEntry

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByAccession(DatabaseEntry accession)

Uses of DatabaseEntry in ubic.gemma.persistence.service.genome.biosequence

Methods in ubic.gemma.persistence.service.genome.biosequence with parameters of type DatabaseEntry

Modifier and Type	Method	Description
BioSequence	BioSequenceDao.findByAccession(DatabaseEntry accession)
BioSequence	BioSequenceDaoImpl.findByAccession(DatabaseEntry databaseEntry)
BioSequence	BioSequenceService.findByAccession(DatabaseEntry accession)
BioSequence	BioSequenceServiceImpl.findByAccession(DatabaseEntry accession)

Uses of DatabaseEntry in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type DatabaseEntry

Modifier and Type	Method	Description
static void	BusinessKey.addRestrictions(DetachedCriteria queryObject, DatabaseEntry databaseEntry)
static void	BusinessKey.attachCriteria(Criteria queryObject, DatabaseEntry databaseEntry, String propertyName)	Restricts query to the given DatabaseEntry association
static void	BusinessKey.attachCriteria(DetachedCriteria queryObject, DatabaseEntry databaseEntry, String attributeName)
static void	BusinessKey.checkKey(DatabaseEntry accession)
static void	BusinessKey.checkValidKey(DatabaseEntry databaseEntry)

Uses of DatabaseEntry in ubic.gemma.web.taglib

Methods in ubic.gemma.web.taglib with parameters of type DatabaseEntry

Modifier and Type	Method	Description
void	DatabaseEntryTag.setDatabaseEntry(DatabaseEntry databaseEntry)