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.util
ubic.gemma.model.analysis.expression
ubic.gemma.model.association
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.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.rest.util.args

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.util

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

Modifier and Type	Method	Description
static DatabaseEntry	GenBankUtils.getGenBankAccession(String accession)

Methods in ubic.gemma.core.loader.util with parameters of type DatabaseEntry

Modifier and Type	Method	Description
static String	ExternalDatabaseUtils.getLabel(DatabaseEntry de)	Obtain a label for a given database entry.
static String	ExternalDatabaseUtils.getUri(DatabaseEntry accession)	Obtain a URI for a given database entry.

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

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

Modifier and Type	Method	Description
DatabaseEntry	ExpressionExperimentSet.getAccession()

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

Modifier and Type	Method	Description
void	ExpressionExperimentSet.setAccession(DatabaseEntry 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.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

Subclasses with type arguments of type DatabaseEntry in ubic.gemma.model.common.description

Modifier and Type	Class	Description
class	DatabaseEntryValueObject	ValueObject for database entry

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

Modifier	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	ExpressionExperiment.getAccession()

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

Modifier and Type	Method	Description
void	ExpressionExperiment.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.persistence.persister

Methods in ubic.gemma.persistence.persister that return DatabaseEntry

Modifier and Type	Method	Description
DatabaseEntry	CommonPersister.persistDatabaseEntry(DatabaseEntry entity, Map<String, ExternalDatabase> externalDbCache)	Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.

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

Modifier and Type	Method	Description
void	CommonPersister.fillInDatabaseEntry(DatabaseEntry databaseEntry, Map<String, ExternalDatabase> externalDbCache)	Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.
DatabaseEntry	CommonPersister.persistDatabaseEntry(DatabaseEntry entity, Map<String, ExternalDatabase> externalDbCache)	Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.

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

Subclasses with type arguments of type DatabaseEntry in ubic.gemma.persistence.service.common.description

Modifier and Type	Class	Description
class	DatabaseEntryDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type DatabaseEntry.
class	DatabaseEntryServiceImpl	Spring Service base class for DatabaseEntryService, provides access to all services and entities referenced by this service.

Subinterfaces with type arguments of type DatabaseEntry in ubic.gemma.persistence.service.common.description

Modifier and Type	Interface	Description
interface	DatabaseEntryDao
interface	DatabaseEntryService
interface	DatabaseEntryService

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

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

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)
List<DatabaseEntry>	DatabaseEntryReadService.findByAccession(String accession)
List<DatabaseEntry>	DatabaseEntryReadServiceImpl.findByAccession(String accession)
Collection<DatabaseEntry>	DatabaseEntryReadService.loadAll()
Collection<DatabaseEntry>	DatabaseEntryReadServiceImpl.loadAll()

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	BibliographicReferenceReadService.findByExternalId(DatabaseEntry accession)
BibliographicReference	BibliographicReferenceReadServiceImpl.findByExternalId(DatabaseEntry accession)
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>	ExpressionExperimentReadService.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.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	BioSequenceReadService.findByAccession(DatabaseEntry accession)
BioSequence	BioSequenceReadServiceImpl.findByAccession(DatabaseEntry accession)
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.attachDatabaseEntry(jakarta.persistence.criteria.CriteriaBuilder cb, jakarta.persistence.criteria.From<?,?> parent, String propertyName, DatabaseEntry databaseEntry, List<jakarta.persistence.criteria.Predicate> preds)	Restrict a parent query so a DatabaseEntry-typed property at propertyName matches by business key.
static void	BusinessKey.checkKey(DatabaseEntry accession)
static void	BusinessKey.checkValidKey(DatabaseEntry databaseEntry)
static void	Thaws.thawDatabaseEntry(DatabaseEntry databaseEntry)

Uses of DatabaseEntry in ubic.gemma.rest.util.args

Subclasses with type arguments of type DatabaseEntry in ubic.gemma.rest.util.args

Modifier and Type	Class	Description
class	DatabaseEntryArg<T>	Mutable argument type base class for DatabaseEntry API.
class	DatabaseEntryArgService
class	DatabaseEntryArrayArg