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

Packages that use ExternalDatabase

Package	Description
ubic.gemma.core.analysis.sequence
ubic.gemma.core.goldenpath
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.genome
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.util
ubic.gemma.model.common.description
ubic.gemma.model.genome
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.util

Uses of ExternalDatabase in ubic.gemma.core.analysis.sequence

Methods in ubic.gemma.core.analysis.sequence that return ExternalDatabase

Modifier and Type	Method	Description
static ExternalDatabase	ShellDelegatingBlat.getSearchedGenome(Taxon taxon)	The database a BLAT result was searched against, named for the assembly (rn8, hg38) so that the result records which assembly its coordinates belong to.

Uses of ExternalDatabase in ubic.gemma.core.goldenpath

Methods in ubic.gemma.core.goldenpath that return ExternalDatabase

Modifier and Type	Method	Description
protected ExternalDatabase	GoldenPath.getSearchedDatabase()

Uses of ExternalDatabase in ubic.gemma.core.loader.expression.arrayDesign

Methods in ubic.gemma.core.loader.expression.arrayDesign with parameters of type ExternalDatabase

Modifier and Type	Method	Description
void	ArrayDesignProbeMapperService.processArrayDesign(ArrayDesign arrayDesign, Taxon taxon, File source, ExternalDatabase sourceDB, boolean ncbiIds)	Annotate an array design using a direct source file.
void	ArrayDesignProbeMapperServiceImpl.processArrayDesign(ArrayDesign arrayDesign, Taxon taxon, File source, ExternalDatabase sourceDB, boolean ncbiIds)

Uses of ExternalDatabase in ubic.gemma.core.loader.genome

Methods in ubic.gemma.core.loader.genome that return ExternalDatabase

Modifier and Type	Method	Description
ExternalDatabase	BlatResultParser.getSearchedDatabase()

Methods in ubic.gemma.core.loader.genome with parameters of type ExternalDatabase

Modifier and Type	Method	Description
void	BlatResultParser.setSearchedDatabase(ExternalDatabase searchedDatabase)

Uses of ExternalDatabase in ubic.gemma.core.loader.genome.gene.ncbi

Methods in ubic.gemma.core.loader.genome.gene.ncbi that return ExternalDatabase

Modifier and Type	Method	Description
static ExternalDatabase	NcbiGeneConverter.getEnsembl()
static ExternalDatabase	NcbiGeneConverter.getGenBank()

Uses of ExternalDatabase in ubic.gemma.core.loader.util

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

Modifier and Type	Method	Description
static ExternalDatabase	GenBankUtils.getGenBank()

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

Modifier and Type	Method	Description
static String	ExternalDatabaseUtils.getUri(ExternalDatabase externalDatabase)	Obtain a URI for a given external database.

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

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

Modifier and Type	Class	Description
class	ExternalDatabaseValueObject

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

Modifier and Type	Method	Description
ExternalDatabase	DatabaseEntry.getExternalDatabase()
static ExternalDatabase	ExternalDatabase.Factory.newInstance()
static ExternalDatabase	ExternalDatabase.Factory.newInstance(String name, DatabaseType other)

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

Modifier and Type	Method	Description
Set<ExternalDatabase>	ExternalDatabase.getExternalDatabases()

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

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

Method parameters in ubic.gemma.model.common.description with type arguments of type ExternalDatabase

Modifier and Type	Method	Description
static Collection<ExternalDatabaseValueObject>	ExternalDatabaseValueObject.fromEntity(Collection<ExternalDatabase> eds)
void	ExternalDatabase.setExternalDatabases(Set<ExternalDatabase> externalDatabases)

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

Modifier	Constructor	Description
	ExternalDatabaseValueObject(ExternalDatabase ed)

Uses of ExternalDatabase in ubic.gemma.model.genome

Methods in ubic.gemma.model.genome that return ExternalDatabase

Modifier and Type	Method	Description
ExternalDatabase	Chromosome.getAssemblyDatabase()
ExternalDatabase	Taxon.getExternalDatabase()

Methods in ubic.gemma.model.genome with parameters of type ExternalDatabase

Modifier and Type	Method	Description
static Chromosome	Chromosome.Factory.newInstance(String name, ExternalDatabase assemblyDatabase, BioSequence sequence, Taxon taxon)
void	Chromosome.setAssemblyDatabase(ExternalDatabase assemblyDatabase)
void	Taxon.setExternalDatabase(ExternalDatabase externalDatabase)

Uses of ExternalDatabase in ubic.gemma.model.genome.sequenceAnalysis

Methods in ubic.gemma.model.genome.sequenceAnalysis that return ExternalDatabase

Modifier and Type	Method	Description
ExternalDatabase	SequenceSimilaritySearchResult.getSearchedDatabase()
ExternalDatabase	AnnotationAssociation.getSource()

Methods in ubic.gemma.model.genome.sequenceAnalysis with parameters of type ExternalDatabase

Modifier and Type	Method	Description
void	SequenceSimilaritySearchResult.setSearchedDatabase(ExternalDatabase searchedDatabase)
void	AnnotationAssociation.setSource(ExternalDatabase source)

Uses of ExternalDatabase in ubic.gemma.persistence.persister

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

Modifier and Type	Method	Description
ExternalDatabase	CommonPersister.persistExternalDatabase(ExternalDatabase database, 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 ExternalDatabase

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

Method parameters in ubic.gemma.persistence.persister with type arguments of type ExternalDatabase

Modifier and Type	Method	Description
ArrayDesign	ArrayDesignPersister.doArrayDesign(Object entity, Map<String, ExternalDatabase> xdbCache)	Persister-shrink S2c typed dispatch: returns null if the entity is not an ArrayDesign.
<T extends Identifiable> T	CommonPersister.doCommon(T entity, Map<String, ExternalDatabase> xdbCache)	Persister-shrink S2 typed dispatch: handles the User / Characteristic arms formerly carried by the doPersist override.
<T extends Identifiable> T	GenomePersister.doGenome(T entity, Map<String, ExternalDatabase> xdbCache)	Persister-shrink S2 typed dispatch: handles the Gene / GeneProduct / BioSequence / Taxon / BioSequence2GeneProduct / SequenceSimilaritySearchResult / Chromosome arms formerly carried by the doPersist override.
<T extends Identifiable> T	GenomePersister.doGenomeUpdate(T entity, Map<String, ExternalDatabase> xdbCache)	Persister-shrink S2 typed dispatch for persist-or-update.
protected <T extends Identifiable> T	ArrayDesignPersister.doPersist(T entity, Map<String, ExternalDatabase> xdbCache)	Polymorphic dispatch entry point reached by RelationshipPersister via the still-extant inheritance chain.
protected final <T extends Identifiable> List<T>	CommonPersister.doPersist(Collection<T> entities, Map<String, ExternalDatabase> xdbCache)
protected final <T extends Identifiable> Set<T>	CommonPersister.doPersist(Set<T> entities, Map<String, ExternalDatabase> xdbCache)
protected <T extends Identifiable> T	CommonPersister.doPersist(T entity, Map<String, ExternalDatabase> xdbCache)	Polymorphic dispatch entry point on the persister chain.
protected <T extends Identifiable> T	GenomePersister.doPersist(T entity, Map<String, ExternalDatabase> xdbCache)	Polymorphic dispatch entry point reached by ArrayDesignPersister via the still-extant inheritance chain.
protected <T extends Identifiable> T	RelationshipPersister.doPersist(T entity, Map<String, ExternalDatabase> xdbCache)	Polymorphic dispatch entry point reached by PersisterHelperImpl via its (still-extant) extends RelationshipPersister.
protected <T extends Identifiable> T	ArrayDesignPersister.doPersistOrUpdate(T entity, Map<String, ExternalDatabase> xdbCache)	Polymorphic persist-or-update dispatch entry point reached by the chain.
protected <T extends Identifiable> T	CommonPersister.doPersistOrUpdate(T entity, Map<String, ExternalDatabase> xdbCache)
protected <T extends Identifiable> T	GenomePersister.doPersistOrUpdate(T entity, Map<String, ExternalDatabase> xdbCache)	Polymorphic dispatch entry point for persist-or-update reached by the chain.
protected <T extends Identifiable> T	RelationshipPersister.doPersistOrUpdate(T entity, Map<String, ExternalDatabase> xdbCache)	Polymorphic persist-or-update dispatch entry point.
<T extends Identifiable> T	RelationshipPersister.doRelationship(T entity, Map<String, ExternalDatabase> xdbCache)	Typed dispatch surface for the S2e dispatcher: returns null when the entity is neither Gene2GOAssociation nor ExpressionExperimentSet.
void	CommonPersister.fillInDatabaseEntry(DatabaseEntry databaseEntry, Map<String, ExternalDatabase> externalDbCache)	Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.
ArrayDesign	ArrayDesignPersister.persistArrayDesign(ArrayDesign arrayDesign, Map<String, ExternalDatabase> xdbCache, Map<Object,Taxon> taxonCache, Map<Integer, Chromosome> chromosomeCache)	Look up an existing ArrayDesign by business key (shortName, alternate names, or name — see BusinessKey.matches(CriteriaBuilder, From, ArrayDesign)); otherwise create a new one along with its full graph.
BibliographicReference	CommonPersister.persistBibliographicReference(BibliographicReference reference, Map<String, ExternalDatabase> externalDbCache)	Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.
BioSequence	GenomePersister.persistBioSequence(BioSequence bioSequence, Map<String, ExternalDatabase> xdbCache, Map<Object,Taxon> taxonCache, Map<Integer, Chromosome> chromosomeCache)	Public after S2b: reached by ArrayDesignPersister via @Autowired.
DatabaseEntry	CommonPersister.persistDatabaseEntry(DatabaseEntry entity, Map<String, ExternalDatabase> externalDbCache)	Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.
ExpressionExperimentSet	RelationshipPersister.persistExpressionExperimentSet(ExpressionExperimentSet entity, Map<String, ExternalDatabase> xdbCache)	Persist an ExpressionExperimentSet.
ExternalDatabase	CommonPersister.persistExternalDatabase(ExternalDatabase database, Map<String, ExternalDatabase> externalDbCache)	Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.
Gene	GenomePersister.persistGene(Gene gene, Map<String, ExternalDatabase> xdbCache, Map<Object,Taxon> taxonCache, Map<Integer, Chromosome> chromosomeCache)	Public after S2b: reached by RelationshipPersister via @Autowired.
Gene2GOAssociation	RelationshipPersister.persistGene2GOAssociation(Gene2GOAssociation association, Map<String, ExternalDatabase> xdbCache)	Public after S2d so the S2e dispatcher can reach it.

Uses of ExternalDatabase in ubic.gemma.persistence.service.analysis.expression

Methods in ubic.gemma.persistence.service.analysis.expression with parameters of type ExternalDatabase

Modifier and Type	Method	Description
Collection<ExpressionExperimentSet>	ExpressionExperimentSetDao.findByAccession(String accession, ExternalDatabase externalDatabase)
Collection<ExpressionExperimentSet>	ExpressionExperimentSetDaoImpl.findByAccession(String accession, ExternalDatabase externalDatabase)

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

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

Modifier and Type	Class	Description
class	ExternalDatabaseDaoImpl
class	ExternalDatabaseServiceImpl

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

Modifier and Type	Interface	Description
interface	ExternalDatabaseDao
interface	ExternalDatabaseService

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

Modifier and Type	Method	Description
ExternalDatabase	ExternalDatabaseService.create(ExternalDatabase entity)
ExternalDatabase	ExternalDatabaseDaoImpl.find(ExternalDatabase externalDatabase)
ExternalDatabase	ExternalDatabaseDao.findByName(String name)
ExternalDatabase	ExternalDatabaseDaoImpl.findByName(String name)
ExternalDatabase	ExternalDatabaseReadService.findByName(String name)
ExternalDatabase	ExternalDatabaseReadServiceImpl.findByName(String name)
ExternalDatabase	ExternalDatabaseService.findByName(String name)
ExternalDatabase	ExternalDatabaseServiceImpl.findByName(String name)
ExternalDatabase	ExternalDatabaseDao.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseDaoImpl.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseReadService.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseReadServiceImpl.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseService.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseServiceImpl.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseReadService.findByNameWithExternalDatabases(String name)
ExternalDatabase	ExternalDatabaseReadServiceImpl.findByNameWithExternalDatabases(String name)
ExternalDatabase	ExternalDatabaseService.findByNameWithExternalDatabases(String name)
ExternalDatabase	ExternalDatabaseServiceImpl.findByNameWithExternalDatabases(String name)
ExternalDatabase	ExternalDatabaseService.findOrCreate(ExternalDatabase externalDatabase)
ExternalDatabase	ExternalDatabaseReadService.loadWithExternalDatabases(Long id)
ExternalDatabase	ExternalDatabaseReadServiceImpl.loadWithExternalDatabases(Long id)
ExternalDatabase	ExternalDatabaseService.loadWithExternalDatabases(Long id)
ExternalDatabase	ExternalDatabaseServiceImpl.loadWithExternalDatabases(Long id)

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

Modifier and Type	Method	Description
Collection<ExternalDatabase>	ExternalDatabaseService.create(Collection<ExternalDatabase> entities)
List<ExternalDatabase>	ExternalDatabaseDao.findAllByNameIn(Collection<String> names)
List<ExternalDatabase>	ExternalDatabaseDaoImpl.findAllByNameIn(Collection<String> names)
List<ExternalDatabase>	ExternalDatabaseReadService.findAllByNameIn(List<String> names)
List<ExternalDatabase>	ExternalDatabaseReadServiceImpl.findAllByNameIn(List<String> names)
List<ExternalDatabase>	ExternalDatabaseService.findAllByNameIn(List<String> names)
List<ExternalDatabase>	ExternalDatabaseServiceImpl.findAllByNameIn(List<String> names)
Collection<ExternalDatabase>	ExternalDatabaseReadService.loadAllWithAuditTrail()
Collection<ExternalDatabase>	ExternalDatabaseReadServiceImpl.loadAllWithAuditTrail()
Collection<ExternalDatabase>	ExternalDatabaseService.loadAllWithAuditTrail()
Collection<ExternalDatabase>	ExternalDatabaseServiceImpl.loadAllWithAuditTrail()

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

Modifier and Type	Method	Description
ExternalDatabase	ExternalDatabaseService.create(ExternalDatabase entity)
ExternalDatabase	ExternalDatabaseDaoImpl.find(ExternalDatabase externalDatabase)
ExternalDatabase	ExternalDatabaseService.findOrCreate(ExternalDatabase externalDatabase)
void	ExternalDatabaseReleaseAuditService.recordReleaseDetailsUpdate(ExternalDatabase ed, String note, ReleaseDetailsUpdatePayload payload)	Emit a ReleaseDetailsUpdateEvent for the given external database.
void	ExternalDatabaseReleaseAuditServiceImpl.recordReleaseDetailsUpdate(ExternalDatabase ed, String note, ReleaseDetailsUpdatePayload payload)
void	ExternalDatabaseService.remove(ExternalDatabase externalDatabase)
void	ExternalDatabaseService.update(ExternalDatabase entity)
void	ExternalDatabaseService.updateReleaseDetails(ExternalDatabase externalDatabase, String releaseVersion, URL releaseUrl, String releaseNote, Date lastUpdated)
void	ExternalDatabaseServiceImpl.updateReleaseDetails(ExternalDatabase ed, String releaseVersion, URL releaseUrl, String releaseNote, Date lastUpdated)
void	ExternalDatabaseService.updateReleaseLastUpdated(ExternalDatabase externalDatabase, String note, Date lastUpdated)
void	ExternalDatabaseServiceImpl.updateReleaseLastUpdated(ExternalDatabase ed, String releaseNote, Date lastUpdated)

Method parameters in ubic.gemma.persistence.service.common.description with type arguments of type ExternalDatabase

Modifier and Type	Method	Description
Collection<ExternalDatabase>	ExternalDatabaseService.create(Collection<ExternalDatabase> entities)
void	ExternalDatabaseService.remove(Collection<ExternalDatabase> entities)
void	ExternalDatabaseService.update(Collection<ExternalDatabase> entities)

Uses of ExternalDatabase in ubic.gemma.persistence.service.genome

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

Modifier and Type	Method	Description
Gene	GeneDao.findByAccession(String accession, ExternalDatabase source)
Gene	GeneDaoImpl.findByAccession(String accession, ExternalDatabase source)

Uses of ExternalDatabase in ubic.gemma.persistence.service.genome.gene

Methods in ubic.gemma.persistence.service.genome.gene with parameters of type ExternalDatabase

Modifier and Type	Method	Description
Gene	GeneReadService.findByAccession(String accession, ExternalDatabase source)
Gene	GeneReadServiceImpl.findByAccession(String accession, ExternalDatabase source)
Gene	GeneService.findByAccession(String accession, ExternalDatabase source)
Gene	GeneServiceImpl.findByAccession(String accession, ExternalDatabase source)

Uses of ExternalDatabase in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
static void	BusinessKey.checkKey(ExternalDatabase externalDatabase)