Ensembl Data Access Interface v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Data Access Interface
v1.09
A C D E G H P R S T U

A

addGeneByIDOnParent(Integer, DNASequence) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
 
addGeneByStableIDOnParent(String, DNASequence) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
 
AssemblyDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 

C

ChromosomeDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 
CoordinateSystemDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 

D

DAOCollectionCoreFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOCollectionFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOCollectionFuncgenFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOCollectionVariationFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOComparaFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOCoreFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOFuncgenFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOSingleSpeciesCoreFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOSingleSpeciesFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOSpeciesFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DAOVariationFactory - Interface in uk.ac.roslin.ensembl.dao.factory
 
DatabaseDAO - Interface in uk.ac.roslin.ensembl.dao
 
DNASequenceDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 

E

ExonDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 

G

GeneDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 
getAllCoreDatabasesForVersion(int) - Method in interface uk.ac.roslin.ensembl.dao.DatabaseDAO
 
getAssemblyDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getChromosomeByName(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ChromosomeDAO
 
getChromosomeDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getChromosomes() - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ChromosomeDAO
 
getCollectionSpeciesProperties(CollectionCoreDatabase) - Method in interface uk.ac.roslin.ensembl.dao.DatabaseDAO
 
getComparaDivision() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory
 
getComparaFactory(EnsemblComparaDivision) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getComponentMappingsByStartStop(DNASequence, Integer, Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.AssemblyDAO
 
getConfiguration() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
getCoordinateSystemDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getCoordinateSystems() - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.CoordinateSystemDAO
 
getDatabase() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCollectionCoreFactory
 
getDatabase() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
getDatabase() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesCoreFactory
 
getDatabaseName() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
getDatabases() - Method in interface uk.ac.roslin.ensembl.dao.DatabaseDAO
 
getDBType() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
getDBVersion() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
getEnsemblSchemaVersion() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
getExonByID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ExonDAO
 
getExonByStableID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ExonDAO
 
getExonDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getExonsForTranscript(Transcript) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ExonDAO
 
getFullSequence(EnsemblDNASequenceReader) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
 
getGeneByID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
 
getGeneByStableID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
 
getGeneDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getGeneMappingsOnRegion(DNASequence, Coordinate) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
 
getGenus_Species() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesFactory
 
getHomologiesForGene(Gene) - Method in interface uk.ac.roslin.ensembl.dao.compara.HomologyDAO
 
getHomologyDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory
 
getMybatisSchemaFilePath() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
getNewSqlSession() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
getProteinFeatureDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getProteinFeaturesByTranslationID(int) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ProteinFeatureDAO
 
getRegionsOfConservedSynteny(Chromosome, Coordinate, Species) - Method in interface uk.ac.roslin.ensembl.dao.compara.HomologyDAO
 
getRegistry() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
getSequenceByID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
 
getSequenceByStartStop(EnsemblDNASequenceReader, Integer, Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
 
getSequenceDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getSpecies() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCollectionFactory
 
getSpecies() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSpeciesFactory
 
getSpeciesProperties(SingleSpeciesCoreDatabase) - Method in interface uk.ac.roslin.ensembl.dao.DatabaseDAO
 
getTranscriptByID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranscriptDAO
 
getTranscriptByStableID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranscriptDAO
 
getTranscriptDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getTranscriptsForGene(Gene) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranscriptDAO
 
getTranslationByTranscriptID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranslationDAO
 
getTranslationDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory
 
getValidatedSequence(DNASequence) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
 
getValidatedSequences(List<? extends DNASequence>) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
 

H

HomologyDAO - Interface in uk.ac.roslin.ensembl.dao.compara
 

P

ProteinFeatureDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 

R

ReInitializationDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 
reInitialize(CoreObject) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ReInitializationDAO
 

S

setDatabaseName(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
setDBType(DatabaseType) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
setDBVersion(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
setEnsemblSchemaVersion(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
setGenus_Species(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesFactory
 
setMybatisSchemaFilePath(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory
 
setSpecies(Species) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSpeciesFactory
 

T

TranscriptDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 
TranslationDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess
 

U

uk.ac.roslin.ensembl.dao - package uk.ac.roslin.ensembl.dao
 
uk.ac.roslin.ensembl.dao.compara - package uk.ac.roslin.ensembl.dao.compara
 
uk.ac.roslin.ensembl.dao.coreaccess - package uk.ac.roslin.ensembl.dao.coreaccess
 
uk.ac.roslin.ensembl.dao.factory - package uk.ac.roslin.ensembl.dao.factory
 

A C D E G H P R S T U
Ensembl Data Access Interface
v1.09

Ensembl Data Access Interface v1.09
© Roslin Institute 2010. GNU General Public License, version3