Uses of Class
uk.ac.roslin.ensembl.config.EnsemblComparaDivision

Packages that use EnsemblComparaDivision

Package	Description
uk.ac.roslin.ensembl.config
uk.ac.roslin.ensembl.dao.database
uk.ac.roslin.ensembl.dao.database.factory
uk.ac.roslin.ensembl.dao.factory
uk.ac.roslin.ensembl.datasourceaware.core
uk.ac.roslin.ensembl.model.core
uk.ac.roslin.ensembl.model.database

Uses of EnsemblComparaDivision in uk.ac.roslin.ensembl.config

Fields in uk.ac.roslin.ensembl.config declared as EnsemblComparaDivision

Modifier and Type	Field and Description
static EnsemblComparaDivision	EnsemblComparaDivision.BACTERIA
static EnsemblComparaDivision	EnsemblComparaDivision.FUNGI
static EnsemblComparaDivision	EnsemblComparaDivision.INCOMPLETE_SEARCH
static EnsemblComparaDivision	EnsemblComparaDivision.METAZOA
static EnsemblComparaDivision	EnsemblComparaDivision.MULTI
static EnsemblComparaDivision	EnsemblComparaDivision.PAN_HOMOLOGY
static EnsemblComparaDivision	EnsemblComparaDivision.PLANTS
static EnsemblComparaDivision	EnsemblComparaDivision.PROTISTS

Methods in uk.ac.roslin.ensembl.config that return EnsemblComparaDivision

Modifier and Type	Method and Description
static EnsemblComparaDivision	EnsemblComparaDivision.getEnsemblComparaDivision(String value)
static EnsemblComparaDivision	EnsemblComparaDivision.getEnsemblComparaDivisionByMetaValue(String value)

Methods in uk.ac.roslin.ensembl.config that return types with arguments of type EnsemblComparaDivision

Modifier and Type	Method and Description
static Collection<EnsemblComparaDivision>	EnsemblComparaDivision.getAllTypes()

Methods in uk.ac.roslin.ensembl.config with parameters of type EnsemblComparaDivision

Modifier and Type	Method and Description
int	EnsemblComparaDivision.compareTo(EnsemblComparaDivision other)

Uses of EnsemblComparaDivision in uk.ac.roslin.ensembl.dao.database

Fields in uk.ac.roslin.ensembl.dao.database with type parameters of type EnsemblComparaDivision

Modifier and Type	Field and Description
protected HashMap<EnsemblComparaDivision,HashMap<String,DBComparisonDatabase>>	DBRegistry.comparaDBByDivision

Methods in uk.ac.roslin.ensembl.dao.database that return EnsemblComparaDivision

Modifier and Type	Method and Description
EnsemblComparaDivision	DBSpecies.getComparaDivision()
EnsemblComparaDivision	DBComparisonDatabase.getComparisonDivision()

Methods in uk.ac.roslin.ensembl.dao.database with parameters of type EnsemblComparaDivision

Modifier and Type	Method and Description
ComparisonDatabase	DBRegistry.getComparaDatabase(EnsemblComparaDivision comparaDivision, String db_version)
void	DBSpecies.setComparaDivision(EnsemblComparaDivision speciesDivision)

Uses of EnsemblComparaDivision in uk.ac.roslin.ensembl.dao.database.factory

Methods in uk.ac.roslin.ensembl.dao.database.factory that return EnsemblComparaDivision

Modifier and Type	Method and Description
EnsemblComparaDivision	DBDAOComparaFactory.getComparaDivision()

Methods in uk.ac.roslin.ensembl.dao.database.factory with parameters of type EnsemblComparaDivision

Modifier and Type	Method and Description
DBDAOComparaFactory	DBDAOSingleSpeciesCoreFactory.getComparaFactory(EnsemblComparaDivision comparaDivision)
DBDAOComparaFactory	DBDAOCollectionCoreFactory.getComparaFactory(EnsemblComparaDivision comparaDivision)

Uses of EnsemblComparaDivision in uk.ac.roslin.ensembl.dao.factory

Methods in uk.ac.roslin.ensembl.dao.factory that return EnsemblComparaDivision

Modifier and Type	Method and Description
EnsemblComparaDivision	DAOComparaFactory.getComparaDivision()

Methods in uk.ac.roslin.ensembl.dao.factory with parameters of type EnsemblComparaDivision

Modifier and Type	Method and Description
DAOComparaFactory	DAOCoreFactory.getComparaFactory(EnsemblComparaDivision comparaDivision)

Uses of EnsemblComparaDivision in uk.ac.roslin.ensembl.datasourceaware.core

Fields in uk.ac.roslin.ensembl.datasourceaware.core with type parameters of type EnsemblComparaDivision

Modifier and Type	Field and Description
protected HashMap<EnsemblComparaDivision,DAOComparaFactory>	DADNASequence.comparaFactories
protected HashMap<EnsemblComparaDivision,DAOComparaFactory>	DACoreObject.comparaFactories

Methods in uk.ac.roslin.ensembl.datasourceaware.core that return EnsemblComparaDivision

Modifier and Type	Method and Description
EnsemblComparaDivision	DAGene.getComparaDivision() Note the special case for Bacteria in collections in DB >16
EnsemblComparaDivision	DADNASequence.getComparaDivision() Note the special case for Bacteria in collections in DB >16
EnsemblComparaDivision	DACoreObject.getComparaDivision()

Methods in uk.ac.roslin.ensembl.datasourceaware.core with parameters of type EnsemblComparaDivision

Modifier and Type	Method and Description
void	DAGene.addHomology(EnsemblComparaDivision division, DAHomologyPairRelationship homology)
DAOComparaFactory	DADNASequence.getComparaFactory(EnsemblComparaDivision comparaDivision)
DAOComparaFactory	DACoreObject.getComparaFactory(EnsemblComparaDivision comparaDivision)
List<DAHomologyPairRelationship>	DAGene.getHomologies(EnsemblComparaDivision comparaDivision) Returns all Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for this Gene.
List<DAHomologyPairRelationship>	DAGene.getHomologies(EnsemblComparaDivision comparaDivision, Species sp) Returns Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for the specified Species.
boolean	DAGene.setSearchedHomologies(EnsemblComparaDivision comparaDivision)

Uses of EnsemblComparaDivision in uk.ac.roslin.ensembl.model.core

Methods in uk.ac.roslin.ensembl.model.core that return EnsemblComparaDivision

Modifier and Type	Method and Description
EnsemblComparaDivision	Species.getComparaDivision()

Methods in uk.ac.roslin.ensembl.model.core with parameters of type EnsemblComparaDivision

Modifier and Type	Method and Description
List<? extends HomologyPairRelationship>	Gene.getHomologies(EnsemblComparaDivision speciesGroup)
List<? extends HomologyPairRelationship>	Gene.getHomologies(EnsemblComparaDivision speciesGroup, Species sp)

Uses of EnsemblComparaDivision in uk.ac.roslin.ensembl.model.database

Methods in uk.ac.roslin.ensembl.model.database that return EnsemblComparaDivision

Modifier and Type	Method and Description
EnsemblComparaDivision	ComparisonDatabase.getComparisonDivision()

Methods in uk.ac.roslin.ensembl.model.database with parameters of type EnsemblComparaDivision

Modifier and Type	Method and Description
ComparisonDatabase	Registry.getComparaDatabase(EnsemblComparaDivision comparaDivision, String db_version)