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Ensembl Model v1.09 |
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Packages that use Species | |
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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 |
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Methods in uk.ac.roslin.ensembl.model.compara that return types with arguments of type Species | |
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List<? extends Species> |
HomologyRelationship.getSpecies()
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Uses of Species in uk.ac.roslin.ensembl.model.core |
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Subinterfaces of Species in uk.ac.roslin.ensembl.model.core | |
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interface |
CollectionSpecies
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Methods in uk.ac.roslin.ensembl.model.core that return Species | |
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Species |
CoreObject.getSpecies()
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Methods in uk.ac.roslin.ensembl.model.core with parameters of type Species | |
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List<? extends HomologyPairRelationship> |
Gene.getHomologies(EnsemblComparaDivision speciesGroup,
Species sp)
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List<? extends HomologyPairRelationship> |
Gene.getHomologies(Species sp)
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HashMap<? extends DNASequence,? extends MappingSet> |
Chromosome.getRegionsOfConservedSynteny(Coordinate range,
Species target)
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void |
CoreObject.setSpecies(Species species)
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Uses of Species in uk.ac.roslin.ensembl.model.database |
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Methods in uk.ac.roslin.ensembl.model.database that return Species | |
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Species |
SingleSpeciesDatabase.getSpecies()
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Species |
Registry.getSpeciesByAlias(String alias_or_name)
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Species |
Registry.getSpeciesByEnsemblName(String ensemblName)
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Methods in uk.ac.roslin.ensembl.model.database that return types with arguments of type Species | |
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Collection<? extends Species> |
Registry.getSpecies()
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Methods in uk.ac.roslin.ensembl.model.database with parameters of type Species | |
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void |
CollectionCoreDatabase.addFeatureCS(String featureType,
Integer csID,
Integer maxLength,
Species sp)
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void |
Registry.addSpecies(String dbStyleName,
Species species)
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CoordinateSystem |
CollectionCoreDatabase.getBuildCoordSystem(Species species,
String featureType)
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String |
CollectionCoreDatabase.getBuildLevel(Species species,
String featureKey)
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Chromosome |
CollectionCoreDatabase.getChromosomeByName(Species species,
String name)
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CoordinateSystem |
CollectionCoreDatabase.getChromosomeLevelCS(Species species)
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List<? extends Chromosome> |
CollectionCoreDatabase.getChromosomes(Species species)
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Object |
CollectionCoreDatabase.getCoreFactory(Species species)
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CoordinateSystem |
CollectionCoreDatabase.getCSByID(Species species,
Integer id)
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Set<? extends CoordinateSystem> |
CollectionCoreDatabase.getCSForFeature(Species sp,
ObjectType feature)
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List<? extends ObjectType> |
CollectionCoreDatabase.getFeaturesForCS(Species sp,
CoordinateSystem coordSys)
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Integer |
CollectionCoreDatabase.getMaxLengthForFeature(Species sp,
ObjectType feature,
CoordinateSystem cs)
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CoordinateSystem |
CollectionCoreDatabase.getSequenceLevelCS(Species species)
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CoordinateSystem |
CollectionCoreDatabase.getTopLevelCS(Species species)
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void |
CollectionCoreDatabase.setBuildLevels(Species species,
HashMap<String,String> keyedValues)
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void |
SingleSpeciesDatabase.setSpecies(Species species)
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Ensembl Model v1.09 |
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