Uses of Class
ubic.gemma.model.common.description.ExternalDatabase
Packages that use ExternalDatabase
Package
Description
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Uses of ExternalDatabase in ubic.gemma.core.analysis.sequence
Methods in ubic.gemma.core.analysis.sequence that return ExternalDatabaseModifier and TypeMethodDescriptionstatic ExternalDatabaseShellDelegatingBlat.getSearchedGenome(Taxon taxon) -
Uses of ExternalDatabase in ubic.gemma.core.goldenpath
Methods in ubic.gemma.core.goldenpath that return ExternalDatabase -
Uses of ExternalDatabase in ubic.gemma.core.loader.expression.arrayDesign
Methods in ubic.gemma.core.loader.expression.arrayDesign with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionvoidArrayDesignProbeMapperService.processArrayDesign(ArrayDesign arrayDesign, Taxon taxon, File source, ExternalDatabase sourceDB, boolean ncbiIds) Annotate an array design using a direct source file.voidArrayDesignProbeMapperServiceImpl.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 ExternalDatabaseMethods in ubic.gemma.core.loader.genome with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionvoidBlatResultParser.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 ExternalDatabaseModifier and TypeMethodDescriptionstatic ExternalDatabaseNcbiGeneConverter.getEnsembl()static ExternalDatabaseNcbiGeneConverter.getGenbank() -
Uses of ExternalDatabase in ubic.gemma.model.common.description
Methods in ubic.gemma.model.common.description that return ExternalDatabaseModifier and TypeMethodDescriptionDatabaseEntry.getExternalDatabase()static ExternalDatabaseExternalDatabase.Factory.newInstance()static ExternalDatabaseExternalDatabase.Factory.newInstance(String name, DatabaseType other) Methods in ubic.gemma.model.common.description that return types with arguments of type ExternalDatabaseMethods in ubic.gemma.model.common.description with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionstatic DatabaseEntryDatabaseEntry.Factory.newInstance(String accession, ExternalDatabase externalDatabase) static DatabaseEntryDatabaseEntry.Factory.newInstance(ExternalDatabase externalDatabase) voidDatabaseEntry.setExternalDatabase(ExternalDatabase externalDatabase) Method parameters in ubic.gemma.model.common.description with type arguments of type ExternalDatabaseModifier and TypeMethodDescriptionExternalDatabaseValueObject.fromEntity(Collection<ExternalDatabase> eds) voidExternalDatabase.setExternalDatabases(Set<ExternalDatabase> externalDatabases) Constructors in ubic.gemma.model.common.description with parameters of type ExternalDatabase -
Uses of ExternalDatabase in ubic.gemma.model.genome
Methods in ubic.gemma.model.genome that return ExternalDatabaseMethods in ubic.gemma.model.genome with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionvoidTaxon.setExternalDatabase(ExternalDatabase externalDatabase) Constructors in ubic.gemma.model.genome with parameters of type ExternalDatabaseModifierConstructorDescriptionChromosome(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 ExternalDatabaseModifier and TypeMethodDescriptionSequenceSimilaritySearchResult.getSearchedDatabase()AnnotationAssociation.getSource()Methods in ubic.gemma.model.genome.sequenceAnalysis with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionvoidSequenceSimilaritySearchResult.setSearchedDatabase(ExternalDatabase searchedDatabase) voidAnnotationAssociation.setSource(ExternalDatabase source) -
Uses of ExternalDatabase in ubic.gemma.persistence.persister
Methods in ubic.gemma.persistence.persister that return ExternalDatabaseModifier and TypeMethodDescriptionprotected ExternalDatabaseCommonPersister.persistExternalDatabase(ExternalDatabase database, AbstractPersister.Caches caches) Methods in ubic.gemma.persistence.persister that return types with arguments of type ExternalDatabaseMethods in ubic.gemma.persistence.persister with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionprotected ExternalDatabaseCommonPersister.persistExternalDatabase(ExternalDatabase database, AbstractPersister.Caches caches) -
Uses of ExternalDatabase in ubic.gemma.persistence.service.analysis.expression
Methods in ubic.gemma.persistence.service.analysis.expression with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionExpressionExperimentSetDao.findByAccession(String accession, ExternalDatabase externalDatabase) ExpressionExperimentSetDaoImpl.findByAccession(String accession, ExternalDatabase externalDatabase) -
Uses of ExternalDatabase in ubic.gemma.persistence.service.common.description
Methods in ubic.gemma.persistence.service.common.description that return ExternalDatabaseModifier and TypeMethodDescriptionExternalDatabaseService.create(ExternalDatabase entity) ExternalDatabaseDaoImpl.find(ExternalDatabase externalDatabase) ExternalDatabaseDao.findByName(String name) ExternalDatabaseDaoImpl.findByName(String name) ExternalDatabaseService.findByName(String name) ExternalDatabaseServiceImpl.findByName(String name) ExternalDatabaseDao.findByNameWithAuditTrail(String name) ExternalDatabaseDaoImpl.findByNameWithAuditTrail(String name) ExternalDatabaseService.findByNameWithAuditTrail(String name) ExternalDatabaseServiceImpl.findByNameWithAuditTrail(String name) ExternalDatabaseService.findByNameWithExternalDatabases(String name) ExternalDatabaseServiceImpl.findByNameWithExternalDatabases(String name) ExternalDatabaseService.findOrCreate(ExternalDatabase externalDatabase) ExternalDatabaseService.loadWithExternalDatabases(Long id) ExternalDatabaseServiceImpl.loadWithExternalDatabases(Long id) Methods in ubic.gemma.persistence.service.common.description that return types with arguments of type ExternalDatabaseModifier and TypeMethodDescriptionExternalDatabaseService.create(Collection<ExternalDatabase> entities) ExternalDatabaseDao.findAllByNameIn(Collection<String> names) ExternalDatabaseDaoImpl.findAllByNameIn(Collection<String> names) ExternalDatabaseService.findAllByNameIn(List<String> names) ExternalDatabaseServiceImpl.findAllByNameIn(List<String> names) ExternalDatabaseService.loadAllWithAuditTrail()ExternalDatabaseServiceImpl.loadAllWithAuditTrail()Methods in ubic.gemma.persistence.service.common.description with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionExternalDatabaseService.create(ExternalDatabase entity) ExternalDatabaseDaoImpl.find(ExternalDatabase externalDatabase) ExternalDatabaseService.findOrCreate(ExternalDatabase externalDatabase) voidExternalDatabaseService.remove(ExternalDatabase externalDatabase) voidExternalDatabaseService.update(ExternalDatabase entity) voidExternalDatabaseService.updateReleaseDetails(ExternalDatabase externalDatabase, String releaseVersion, URL releaseUrl, String releaseNote, Date lastUpdated) voidExternalDatabaseServiceImpl.updateReleaseDetails(ExternalDatabase ed, String releaseVersion, URL releaseUrl, String releaseNote, Date lastUpdated) voidExternalDatabaseService.updateReleaseLastUpdated(ExternalDatabase externalDatabase, String note, Date lastUpdated) voidExternalDatabaseServiceImpl.updateReleaseLastUpdated(ExternalDatabase ed, String releaseNote, Date lastUpdated) Method parameters in ubic.gemma.persistence.service.common.description with type arguments of type ExternalDatabaseModifier and TypeMethodDescriptionExternalDatabaseService.create(Collection<ExternalDatabase> entities) voidExternalDatabaseService.remove(Collection<ExternalDatabase> entities) voidExternalDatabaseService.update(Collection<ExternalDatabase> entities) -
Uses of ExternalDatabase in ubic.gemma.persistence.service.genome
Methods in ubic.gemma.persistence.service.genome with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionGeneDao.findByAccession(String accession, ExternalDatabase source) 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 ExternalDatabaseModifier and TypeMethodDescriptionGeneService.findByAccession(String accession, ExternalDatabase source) GeneServiceImpl.findByAccession(String accession, ExternalDatabase source) -
Uses of ExternalDatabase in ubic.gemma.persistence.util
Methods in ubic.gemma.persistence.util with parameters of type ExternalDatabaseModifier and TypeMethodDescriptionstatic voidBusinessKey.checkKey(ExternalDatabase externalDatabase)