Uses of Interface
uk.ac.roslin.ensembl.model.core.Species

Packages that use Species

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

Uses of Species in uk.ac.roslin.ensembl.dao

Methods in uk.ac.roslin.ensembl.dao that return Species

Modifier and Type	Method and Description
Species	DatabaseDAO.getSpeciesProperties(SingleSpeciesCoreDatabase database)

Uses of Species in uk.ac.roslin.ensembl.dao.compara

Methods in uk.ac.roslin.ensembl.dao.compara with parameters of type Species

Modifier and Type	Method and Description
List<? extends HomologyPairRelationship>	HomologyDAO.getHomologiesForGenesBySpecies(List<? extends Gene> genes, Species target_sp, String chrName) Specification of Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs.
HashMap<? extends DNASequence,? extends MappingSet>	HomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target) Specification of Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.
HashMap<? extends DNASequence,? extends MappingSet>	HomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target, String chrName) Specification of Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

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

Classes in uk.ac.roslin.ensembl.dao.database that implement Species

Modifier and Type	Class and Description
class	DBCollectionSpecies
class	DBSpecies

Methods in uk.ac.roslin.ensembl.dao.database that return types with arguments of type Species

Modifier and Type	Method and Description
Collection<? extends Species>	DBRegistry.getSetOfEverySpeciesByAlias(String alias_or_name) Returns a HashSet of all DBSpecies and old and newstyle CollectionSpecies matching the given alias.
Collection<? extends Species>	DBRegistry.getSetOfSpeciesByAlias(String alias_or_name) Returns a HashSet matching the given alias.
Set<? extends Species>	DBRegistry.getSpeciesForAliasBeginning(String alias)
Set<? extends Species>	DBRegistry.getSpeciesForAliasContaining(String alias)

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

Modifier and Type	Method and Description
void	DBCollectionCoreDatabase.addFeatureCS(String featureType, Integer csID, Integer maxLength, Species sp)
boolean	DBRegistry.addSessionAlias(Species sp, String alias)
DACoordinateSystem	DBCollectionCoreDatabase.getBuildCoordSystem(Species species, String featureType)
String	DBCollectionCoreDatabase.getBuildLevel(Species species, String featureKey)
DAChromosome	DBCollectionCoreDatabase.getChromosomeByName(Species species, String name)
DACoordinateSystem	DBCollectionCoreDatabase.getChromosomeLevelCS(Species species)
List<DAChromosome>	DBCollectionCoreDatabase.getChromosomes(Species species)
DBDAOCollectionCoreFactory	DBCollectionCoreDatabase.getCoreFactory(Species sp)
DACoordinateSystem	DBCollectionCoreDatabase.getCSByID(Species species, Integer id)
Set<DACoordinateSystem>	DBCollectionCoreDatabase.getCSForFeature(Species sp, ObjectType feature)
List<FeatureType>	DBCollectionCoreDatabase.getFeaturesForCS(Species sp, CoordinateSystem coordSys)
DAAssembledDNASequence	DBCollectionCoreDatabase.getFragmentByName(Species species, String name)
List<DAAssembledDNASequence>	DBCollectionCoreDatabase.getFragments(Species species)
Integer	DBCollectionCoreDatabase.getMaxLengthForFeature(Species sp, ObjectType feature, CoordinateSystem cs)
DACoordinateSystem	DBCollectionCoreDatabase.getSequenceLevelCS(Species species)
DACoordinateSystem	DBCollectionCoreDatabase.getTopLevelCS(Species species)
boolean	DBRegistry.isSpeciesInPanHomology(Species querySpecies, String dbVersion)
void	DBCollectionCoreDatabase.setBuildLevels(Species species, HashMap<String,String> keyedValues)
void	DBSingleSpeciesDatabase.setSpecies(Species species)

Uses of Species in uk.ac.roslin.ensembl.dao.database.compara

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

Modifier and Type	Method and Description
List<DAHomologyPairRelationship>	DBHomologyDAO.getHomologiesForGenesBySpecies(List<? extends Gene> genes, Species target_sp, String chrName) Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs.
HashMap<DADNASequence,MappingSet>	DBHomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target) Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.
HashMap<DADNASequence,MappingSet>	DBHomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target, String chrName) Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

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

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

Modifier and Type	Method and Description
void	DBDAOSpeciesFactory.setSpecies(Species species)

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

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

Modifier and Type	Method and Description
Species	DAOSpeciesFactory.getSpecies()

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

Modifier and Type	Method and Description
void	DAOSpeciesFactory.setSpecies(Species species)

Uses of Species in uk.ac.roslin.ensembl.datasourceaware.compara

Methods in uk.ac.roslin.ensembl.datasourceaware.compara that return types with arguments of type Species

Modifier and Type	Method and Description
List<Species>	InverseHomologyPairRelationshipView.getSpecies()
List<Species>	DAHomologyRelationship.getSpecies()
List<Species>	DAHomologyPairRelationship.getSpecies()

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

Fields in uk.ac.roslin.ensembl.datasourceaware.core declared as Species

Modifier and Type	Field and Description
protected Species	DADNASequence.species
protected Species	DACoreObject.species

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

Modifier and Type	Method and Description
Species	DADNASequence.getSpecies()
Species	DACoreObject.getSpecies()

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

Modifier and Type	Method and Description
List<DAHomologyPairRelationship>	DAGene.getHomologies(EnsemblComparaDivision comparaDivision, Species sp) Returns Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for the specified Species.
List<DAHomologyPairRelationship>	DAGene.getHomologies(Species sp) Returns Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene for the specified Species.
HashMap<DADNASequence,MappingSet>	DADNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target) Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species
HashMap<DADNASequence,MappingSet>	DADNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target, String chrName) Method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.
void	DADNASequence.setSpecies(Species species)
void	DACoreObject.setSpecies(Species species)

Uses of Species in uk.ac.roslin.ensembl.model.compara

Methods in uk.ac.roslin.ensembl.model.compara that return types with arguments of type Species

Modifier and Type	Method and Description
List<? extends Species>	HomologyRelationship.getSpecies()

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

Subinterfaces of Species in uk.ac.roslin.ensembl.model.core

Modifier and Type	Interface and Description
interface	CollectionSpecies

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

Modifier and Type	Method and Description
Species	CoreObject.getSpecies()

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

Modifier and Type	Method and Description
List<? extends HomologyPairRelationship>	Gene.getHomologies(EnsemblComparaDivision speciesGroup, Species sp)
List<? extends HomologyPairRelationship>	Gene.getHomologies(Species sp)
HashMap<? extends DNASequence,MappingSet>	DNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target) Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species
HashMap<? extends DNASequence,MappingSet>	DNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target, String chrName) Specifies method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.
void	CoreObject.setSpecies(Species species)

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

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

Modifier and Type	Method and Description
Species	Registry.getMostRecentSpeciesByAlias(String alias_or_name)
Species	SingleSpeciesDatabase.getSpecies()
Species	Registry.getSpeciesByAlias(String alias_or_name)
Species	Registry.getSpeciesByAlias(String alias_or_name, String version)
Species	Registry.getSpeciesByEnsemblName(String ensemblName)

Methods in uk.ac.roslin.ensembl.model.database that return types with arguments of type Species

Modifier and Type	Method and Description
Collection<? extends Species>	Registry.getSetOfEverySpeciesByAlias(String alias_or_name)
Collection<? extends Species>	Registry.getSetOfSpeciesByAlias(String alias_or_name)
Collection<? extends Species>	Registry.getSpecies()
Set<? extends Species>	Registry.getSpeciesForAliasBeginning(String alias)
Set<? extends Species>	Registry.getSpeciesForAliasContaining(String alias)

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

Modifier and Type	Method and Description
void	CollectionCoreDatabase.addFeatureCS(String featureType, Integer csID, Integer maxLength, Species sp)
boolean	Registry.addSessionAlias(Species sp, String alias)
CoordinateSystem	CollectionCoreDatabase.getBuildCoordSystem(Species species, String featureType)
String	CollectionCoreDatabase.getBuildLevel(Species species, String featureKey)
Chromosome	CollectionCoreDatabase.getChromosomeByName(Species species, String name)
CoordinateSystem	CollectionCoreDatabase.getChromosomeLevelCS(Species species)
List<? extends Chromosome>	CollectionCoreDatabase.getChromosomes(Species species)
Object	CollectionCoreDatabase.getCoreFactory(Species species)
CoordinateSystem	CollectionCoreDatabase.getCSByID(Species species, Integer id)
Set<? extends CoordinateSystem>	CollectionCoreDatabase.getCSForFeature(Species sp, ObjectType feature)
List<? extends ObjectType>	CollectionCoreDatabase.getFeaturesForCS(Species sp, CoordinateSystem coordSys)
AssembledDNASequence	CollectionCoreDatabase.getFragmentByName(Species species, String name)
List<? extends AssembledDNASequence>	CollectionCoreDatabase.getFragments(Species species)
Integer	CollectionCoreDatabase.getMaxLengthForFeature(Species sp, ObjectType feature, CoordinateSystem cs)
CoordinateSystem	CollectionCoreDatabase.getSequenceLevelCS(Species species)
CoordinateSystem	CollectionCoreDatabase.getTopLevelCS(Species species)
boolean	Registry.isSpeciesInPanHomology(Species querySpecies, String dbVersion)
void	CollectionCoreDatabase.setBuildLevels(Species species, HashMap<String,String> keyedValues)
void	SingleSpeciesDatabase.setSpecies(Species species)