Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Data Access Module
v1.09
A C D E F G H I K L M N P R S T U

A

addDatabase(Database) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
addDatabase(Database) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
addDatabases(TreeSet<? extends CollectionDatabase>) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
addDatabases(TreeSet<? extends Database>) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
addDatabases(TreeSet<? extends Database>) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
addFeatureCS(String, Integer, Integer, Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
addFeatureCS(String, Integer, Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
addGeneByIDOnParent(Integer, DNASequence) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
 
addGeneByStableIDOnParent(String, DNASequence) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
The gene returned has mapping to a sequence region - and the id for the coordinate system that this region belongs to
addSessionAlias(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
Method for an adhoc alias to be added by the user in this session.
addSpecies(Collection<? extends CollectionSpecies>) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
addSpecies(CollectionSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
addSpecies(String, Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
aliases - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
allDatabases - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
alreadyInitialized - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
assembly - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 
assemblyMap - Variable in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
 

C

collection - Variable in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
 
collectionDatabases - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
collectionName - Variable in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
 
collectionNameDBVersionHash - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
collections - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
collectionspeciesHash - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
collFactory - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 
commonName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
comparaDBByDivision - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
comparaName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
compareTo(CollectionSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
compareTo(Database) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
comparisonDatabases - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
configProperties - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
configuration - Variable in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO
 
configuration - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 

D

daoFactory - Variable in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO
 
database - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
databaseName - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
databaseStyleSpeciesName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
databaseType - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
DBAssemblyDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBAssemblyDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO
 
DBAssemblyDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO
 
DBAssemblyDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO
 
DBBaseDAO - Class in uk.ac.roslin.ensembl.dao.database
 
DBBaseDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBBaseDAO
 
DBBaseDAO(DAOFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBBaseDAO
Constructor for (subclasses of) this class.
DBBaseDAO(Properties) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBBaseDAO
Constructor for (subclasses of) this class.
DBChromosomeDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBChromosomeDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO
 
DBChromosomeDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO
 
DBChromosomeDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO
 
DBCollection - Class in uk.ac.roslin.ensembl.dao.database
 
DBCollection() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollection
 
DBCollection(DBCollectionCoreDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollection
 
DBCollectionCoreDatabase - Class in uk.ac.roslin.ensembl.dao.database
 
DBCollectionCoreDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
DBCollectionDatabase - Class in uk.ac.roslin.ensembl.dao.database
 
DBCollectionDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
 
DBCollectionSpecies - Class in uk.ac.roslin.ensembl.dao.database
 
DBCollectionSpecies() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
DBCollectionSpecies(DBCollectionDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
DBComparisonDatabase - Class in uk.ac.roslin.ensembl.dao.database
 
DBComparisonDatabase(String, EnsemblDBType, DBRegistry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBComparisonDatabase
 
dbConnection - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
DBCoordinateSystemDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBCoordinateSystemDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO
 
DBCoordinateSystemDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO
 
DBCoordinateSystemDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO
 
DBCoreObjectDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBCoreObjectDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 
DBCoreObjectDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 
DBCoreObjectDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 
DBDAOCollectionCoreFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOCollectionCoreFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
DBDAOCollectionCoreFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
DBDAOCollectionFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOCollectionFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory
 
DBDAOCollectionFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory
 
DBDAOCollectionFuncgenFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOCollectionFuncgenFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFuncgenFactory
 
DBDAOCollectionFuncgenFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFuncgenFactory
 
DBDAOCollectionVariationFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOCollectionVariationFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionVariationFactory
 
DBDAOCollectionVariationFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionVariationFactory
 
DBDAOComparaFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOComparaFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory
 
DBDAOComparaFactory(ComparisonDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory
 
DBDAOFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
DBDAOFactory(Database) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
DBDAOSingleSpeciesCoreFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOSingleSpeciesCoreFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
DBDAOSingleSpeciesCoreFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
DBDAOSingleSpeciesFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOSingleSpeciesFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory
 
DBDAOSingleSpeciesFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory
 
DBDAOSingleSpeciesFuncgenFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOSingleSpeciesFuncgenFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFuncgenFactory
 
DBDAOSingleSpeciesFuncgenFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFuncgenFactory
 
DBDAOSingleSpeciesVariationFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOSingleSpeciesVariationFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory
 
DBDAOSingleSpeciesVariationFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory
 
DBDAOSpeciesFactory - Class in uk.ac.roslin.ensembl.dao.database.factory
 
DBDAOSpeciesFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory
 
DBDAOSpeciesFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory
 
DBDAOSpeciesFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory
 
DBDatabase - Class in uk.ac.roslin.ensembl.dao.database
 
DBDatabase() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
DBDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
DBDNASequenceDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBDNASequenceDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO
 
DBDNASequenceDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO
 
DBDNASequenceDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO
 
DBDNASequenceDAO.SequenceRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBDNASequenceDAO.SequenceRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO.SequenceRowHandler
 
DBExonDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBExonDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO
 
DBExonDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO
 
DBExonDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO
 
DBExonDAO.ExonRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBExonDAO.ExonRowHandler(List<HashMap>, DATranscript) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler
 
DBExonDAO.ExonRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler
 
DBGeneDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBGeneDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
 
DBGeneDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
 
DBGeneDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
 
DBGeneDAO.GeneMappingRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBGeneDAO.GeneMappingRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler
 
DBGeneDAO.GeneMappingRowHandler(List<HashMap>, DADNASequence) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler
 
DBGeneDAO.MappingRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBGeneDAO.MappingRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler
 
DBGeneDAO.MappingRowHandler(List<HashMap>, DADNASequence) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler
 
DBHomologyDAO - Class in uk.ac.roslin.ensembl.dao.database.compara
 
DBHomologyDAO(DAOComparaFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO
 
DBProteinFeatureDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBProteinFeatureDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBProteinFeatureDAO
 
DBProteinFeatureDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBProteinFeatureDAO
 
DBProteinFeatureDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBProteinFeatureDAO
 
DBRegistry - Class in uk.ac.roslin.ensembl.dao.database
 
DBRegistry() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBRegistry
Parameterless public constructor for DBRegistry object
DBRegistry(DBConnection.DataSource) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBRegistry
Public Constructor for default value DBRegistry object, using values in ensembl-config artifact.
DBRegistry(RegistryConfiguration, boolean) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBRegistry
Public Constructor for default value DBRegistry object, using values in ensembl-config artifact.
DBSingleSpeciesCoreDatabase - Class in uk.ac.roslin.ensembl.dao.database
 
DBSingleSpeciesCoreDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
DBSingleSpeciesDatabase - Class in uk.ac.roslin.ensembl.dao.database
 
DBSingleSpeciesDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 
DBSpecies - Class in uk.ac.roslin.ensembl.dao.database
 
DBSpecies() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
DBSpecies(DBSingleSpeciesCoreDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
dbSpeciesName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 
DBTranscriptDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBTranscriptDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO
 
DBTranscriptDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO
 
DBTranscriptDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO
 
DBTranscriptDAO.TranscriptRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBTranscriptDAO.TranscriptRowHandler(List<HashMap>, DAGene) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler
 
DBTranscriptDAO.TranscriptRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler
 
DBTranslationDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess
 
DBTranslationDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO
 
DBTranslationDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO
 
DBTranslationDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO
 
dBType - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
dbVersion - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 

E

ensemblNameForAliasHash - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
ensemblSchema - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
ensemblStablePrefix - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 

F

findMybatisSchemaForSchemaVersion(DatabaseType, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 

G

genus_species - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory
 
getAliases() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getAssemblies(CollectionDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getAssembly(CollectionSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
 
getAssembly() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getAssembly(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getAssembly(SingleSpeciesDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getAssembly() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 
getAssembly() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getAssembly(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getAssemblyDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getAssemblyDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getBriefRegistryReport() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getBuild() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
getBuildCoordSystem(Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getBuildCoordSystem(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getBuildLevel(Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getBuildLevel(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getBuildLevels(CollectionSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getBuildLevels() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getCachedChromosome(DAChromosome) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getChromosomeByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO
 
getChromosomeByName(Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getChromosomeByName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getChromosomeByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getChromosomeByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getChromosomeByName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getChromosomeDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getChromosomeDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getChromosomeLevelCoordSystem() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getChromosomeLevelCS(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getChromosomes() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO
 
getChromosomes(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getChromosomes(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getChromosomes() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getChromosomes() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getChromosomes(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getCollection() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
 
getCollection(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getCollectionName() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
getCollectionName() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
 
getCollectionRegistriesByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getCollections() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getCollectionsByDBVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getCollectionSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getCommonName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getComparaDatabase(EnsemblComparaDivision, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getComparaDivision() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getComparaDivision() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory
 
getComparaFactory() - Method in class uk.ac.roslin.ensembl.dao.database.DBComparisonDatabase
 
getComparaFactory(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getComparaFactory(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getComparaName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getComparisonDivision() - Method in class uk.ac.roslin.ensembl.dao.database.DBComparisonDatabase
 
getComponentMappingsByStartStop(DNASequence, Integer, Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO
 
getConfigProperties() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getConfiguration() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
getCoordinateSystemDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getCoordinateSystemDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getCoordinateSystems() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO
 
getCoreDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
getCoreFactory(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getCoreFactory() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getCSByID(Species, Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getCSByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getCSForFeature(Species, ObjectType) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getCSForFeature(ObjectType) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getCurrentCoreDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getCurrentCoreDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getDatabase(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getDatabase(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getDatabase(String, DatabaseType, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory
 
getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory
 
getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory
 
getDatabaseByTypeAndVersion(DatabaseType, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getDatabaseByTypeAndVersion(DatabaseType, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getDatabaseForFullName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getDatabaseName() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
getDatabases() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
getDatabases() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getDatabases() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getDatabasesByType(DatabaseType) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
getDatabasesByType(DatabaseType) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getDatabasesByType(DatabaseType) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getDatabasesByType(DatabaseType) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getDatabasesByVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getDatabasesByVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getDatabaseStyleName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getDatasourceType() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getdBName() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
getDBSpeciesID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getDBSpeciesID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getDBSpeciesID() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getDbSpeciesName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 
getDBType() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
getDBVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
getDBVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
getDBVersion() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
getDBVersions() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getEnsemblNameForAlias(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
Looks up the ensembl_genus_species_name for the given alias from the ensemblNameForAliasHash hash of aliases in this Registry.
getEnsemblSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
getEnsemblStablePrefix() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getExonByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO
 
getExonByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO
 
getExonDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getExonDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getExonsForTranscript(Transcript) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO
 
getFactory() - Method in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO
 
getFeaturesForCS(Species, CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getFeaturesForCS(CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getFullSequence(EnsemblDNASequenceReader) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO
 
getGeneByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
 
getGeneByID(Integer, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getGeneByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getGeneByID(Integer, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getGeneByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
 
getGeneByStableID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
getGeneByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getGeneByStableID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getGeneDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getGeneDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getGeneMappingsOnRegion(DNASequence, Coordinate) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
 
getGenus_Species() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory
 
getHighestDBVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getHighestEnsemblSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getHomologiesForGene(Gene) - Method in class uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO
 
getHomologyDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory
 
getIntDBVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
getIntSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
getKnownSchemaVersions() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO.SequenceRowHandler
 
getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler
 
getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler
 
getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler
 
getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler
 
getMaxLengthForFeature(Species, ObjectType, CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getMaxLengthForFeature(ObjectType, CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getMostRecentDBVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getMostRecentEnsemblVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getMybatisSchemaFilePath() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
getNewSqlSession() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
getNewSqlSession() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO.SequenceRowHandler
 
getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler
 
getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler
 
getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler
 
getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler
 
getProteinFeatureDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getProteinFeatureDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getProteinFeaturesByTranslationID(int) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBProteinFeatureDAO
 
getRegionsOfConservedSynteny(Chromosome, Coordinate, Species) - Method in class uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO
 
getRegistry() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
getRegistry() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
getSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
getSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
getSchemaVersions() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getSequenceByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO
 
getSequenceByStartStop(EnsemblDNASequenceReader, Integer, Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO
 
getSequenceDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getSequenceDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getSequenceLevelCoordSystem() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getSequenceLevelCS(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getShortName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 
getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 
getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory
 
getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory
 
getSpeciesBinomial() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getSpeciesByAlias(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getSpeciesByEnsemblName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
getTaxonomyID() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
getTopLevelCoordSystem() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
getTopLevelCS(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
getTranscriptByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO
 
getTranscriptByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO
 
getTranscriptDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getTranscriptDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getTranscriptsForGene(Gene) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO
 
getTranslationByTranscriptID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO
 
getTranslationDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory
 
getTranslationDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory
 
getType() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
getValidatedSequence(DNASequence) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO
 
getValidatedSequences(List<? extends DNASequence>) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO
 
getVersions() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 

H

handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO.SequenceRowHandler
 
handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler
 
handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler
 
handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler
 
handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler
 

I

ibatisSchemaFilePath - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
initialize() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
private initialisation method for the registry which connects to ensembl via a DBDatasourceDAO and retreives details on all the current tables and creates database objects of the appropriate type for each.
isSingleSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 

K

knownSchemaVersions - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 

L

lazyLoadAssembly() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 

M

makeDatabase(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
makeFactory(CollectionDatabase, CollectionSpecies) - Static method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory
 
makeFactory(SingleSpeciesDatabase) - Static method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory
 
mostRecentDBRelease - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
mostRecentEnsemblSchemaVersion - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
mybatisSchemaFilePath - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 

N

newline - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 

P

printRegistryReport() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 

R

reader - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
regConfig - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
registry - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
registry - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
reInitialize(CoreObject) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO
Uses the stableid of an object to fill in missing data
reInitialize(CoreObject) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
Uses the stableid of an object to fill in missing data that would have been present if the the gene had intially been made by a call to getGeneByStableID or getGeneByID.
reInitialize(CoreObject) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO
Uses the stableid of an object to fill in missing data

S

schemaVersion - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
schemaVersion - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
setBuild(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
setBuildLevel(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
 
setBuildLevels(Species, HashMap<String, String>) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
 
setCollection(CollectionOfSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
 
setCollectionName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
 
setCommonName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
setComparaDivision(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
setComparaName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
setConfiguration(Properties) - Method in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO
 
setConfiguration(RegistryConfiguration) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
setConfiguration(DBConnection.DataSource) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
setCoreDBBuildLevels(SingleSpeciesCoreDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
setCurrentCoreDatabase(DBCollectionCoreDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
setDatabase(DBCollectionDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
setDatabase(Database) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
setDatabaseName(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
setDatabaseStyleSpeciesName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
setdBName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
setDbSpeciesName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 
setDBType(DatabaseType) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
setDBVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
setDBVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
setEnsemblSchemaVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
setEnsemblStablePrefix(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
setFactory(DAOSingleSpeciesCoreFactory) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 
setFactory(DAOCollectionCoreFactory) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 
setFactory(DAOFactory) - Method in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO
 
setFeatureCS() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO
 
setGenus_Species(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory
 
setIDForVersion(Integer, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
setIntDBVersion(int) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
setIntSchemaVersion(int) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
setMybatisSchemaFilePath(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
setPrimaryCoreDatabase(DBCollectionCoreDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
setProperty(String, HashMap) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
setProperty(HashMap) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
 
setProperty(HashMap) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
setRegistry(Registry) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
setSchemaVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
setShortName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
setSpecies(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 
setSpecies(Species) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory
 
setSpeciesBinomial(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
setTaxonomyID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
setType(EnsemblDBType) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
shortName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
singleSpecies - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 
singleSpeciesDatabases - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
species - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 
species - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
 
species - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory
 
speciesBinomial - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
speciesHash - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
sqlMapper - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
sqlSessionFactory - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
ssFactory - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
 

T

taxonomyID - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 
thisDBUrl - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory
 
tooNewDB - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 
toString() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection
 
toString() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase
 
toString() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies
 

U

uk.ac.roslin.ensembl.dao.database - package uk.ac.roslin.ensembl.dao.database
 
uk.ac.roslin.ensembl.dao.database.compara - package uk.ac.roslin.ensembl.dao.database.compara
 
uk.ac.roslin.ensembl.dao.database.coreaccess - package uk.ac.roslin.ensembl.dao.database.coreaccess
 
uk.ac.roslin.ensembl.dao.database.factory - package uk.ac.roslin.ensembl.dao.database.factory
 
unknownDB - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry
 

A C D E F G H I K L M N P R S T U
Ensembl Data Access Module
v1.09

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