Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09

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

Packages that use Species
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.model.compara
 

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

Methods in uk.ac.roslin.ensembl.model.core that return Species
 Species CoreObject.getSpecies()
           
 

Methods in uk.ac.roslin.ensembl.model.core with parameters of type Species
 List<? extends HomologyPairRelationship> Gene.getHomologies(EnsemblComparaDivision speciesGroup, Species sp)
           
 List<? extends HomologyPairRelationship> Gene.getHomologies(Species sp)
           
 HashMap<? extends DNASequence,? extends MappingSet> Chromosome.getRegionsOfConservedSynteny(Coordinate range, Species target)
           
 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
 Species SingleSpeciesDatabase.getSpecies()
           
 Species Registry.getSpeciesByAlias(String alias_or_name)
           
 Species Registry.getSpeciesByEnsemblName(String ensemblName)
           
 

Methods in uk.ac.roslin.ensembl.model.database that return types with arguments of type Species
 Collection<? extends Species> Registry.getSpecies()
           
 

Methods in uk.ac.roslin.ensembl.model.database with parameters of type Species
 void CollectionCoreDatabase.addFeatureCS(String featureType, Integer csID, Integer maxLength, Species sp)
           
 void Registry.addSpecies(String dbStyleName, Species species)
           
 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)
           
 Integer CollectionCoreDatabase.getMaxLengthForFeature(Species sp, ObjectType feature, CoordinateSystem cs)
           
 CoordinateSystem CollectionCoreDatabase.getSequenceLevelCS(Species species)
           
 CoordinateSystem CollectionCoreDatabase.getTopLevelCS(Species species)
           
 void CollectionCoreDatabase.setBuildLevels(Species species, HashMap<String,String> keyedValues)
           
 void SingleSpeciesDatabase.setSpecies(Species species)
           
 


Ensembl Model
v1.09

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3