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.model.common.description
ubic.gemma.model.genome
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.association.phenotype
ubic.gemma.persistence.service.association.phenotype.service
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)

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.model.common.description

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

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
void	Taxon.setExternalDatabase(ExternalDatabase externalDatabase)

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

Constructor	Description
Chromosome(String name, ExternalDatabase assemblyDatabase, BioSequence sequence, Taxon taxon)

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
protected ExternalDatabase	CommonPersister.persistExternalDatabase(ExternalDatabase database, AbstractPersister.Caches caches)

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

Modifier and Type	Method	Description
protected ExternalDatabase	CommonPersister.persistExternalDatabase(ExternalDatabase database, AbstractPersister.Caches caches)

Uses of ExternalDatabase in ubic.gemma.persistence.service.association.phenotype

Methods in ubic.gemma.persistence.service.association.phenotype that return types with arguments of type ExternalDatabase

Modifier and Type	Method	Description
Collection<ExternalDatabase>	PhenotypeAssociationDao.findExternalDatabasesWithEvidence()
Collection<ExternalDatabase>	PhenotypeAssociationDaoImpl.findExternalDatabasesWithEvidence()	Gets all External Databases that are used with evidence

Uses of ExternalDatabase in ubic.gemma.persistence.service.association.phenotype.service

Methods in ubic.gemma.persistence.service.association.phenotype.service that return types with arguments of type ExternalDatabase

Modifier and Type	Method	Description
Collection<ExternalDatabase>	PhenotypeAssociationService.findExternalDatabasesWithEvidence()	Gets all External Databases that are used with evidence
Collection<ExternalDatabase>	PhenotypeAssociationServiceImpl.findExternalDatabasesWithEvidence()	Gets all External Databases that are used with evidence

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

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	ExternalDatabaseService.findByName(String name)
ExternalDatabase	ExternalDatabaseServiceImpl.findByName(String name)
ExternalDatabase	ExternalDatabaseDao.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseDaoImpl.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseService.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseServiceImpl.findByNameWithAuditTrail(String name)
ExternalDatabase	ExternalDatabaseService.findByNameWithExternalDatabases(String name)
ExternalDatabase	ExternalDatabaseServiceImpl.findByNameWithExternalDatabases(String name)
ExternalDatabase	ExternalDatabaseService.findOrCreate(ExternalDatabase externalDatabase)
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>	ExternalDatabaseService.findAllByNameIn(List<String> names)
List<ExternalDatabase>	ExternalDatabaseServiceImpl.findAllByNameIn(List<String> names)
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	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	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)