Methods in uk.ac.roslin.ensembl.model.core that throw DAOException |
Chromosome |
Species.getChromosomeByName(String name)
|
Chromosome |
Species.getChromosomeByName(String name,
String dbVersion)
|
TreeMap<String,? extends Chromosome> |
Species.getChromosomes()
|
TreeMap<String,? extends Chromosome> |
Species.getChromosomes(String dbVersion)
|
Gene |
Species.getGeneByID(Integer id)
|
Gene |
Species.getGeneByID(Integer id,
String dbVersion)
|
Gene |
Species.getGeneByStableID(String stableID)
|
Gene |
Species.getGeneByStableID(String stableID,
String dbVersion)
|
List<? extends Gene> |
DNASequence.getGenesOnRegion(Coordinate coord)
|
List<? extends Gene> |
DNASequence.getGenesOnRegion(Integer start,
Integer stop)
|
List<? extends Gene> |
DNASequence.getGenesOnRegion(Integer start,
Integer stop,
Coordinate.Strand strand)
|
MappingSet |
Assembly.getMappings()
|
HashMap<? extends DNASequence,? extends MappingSet> |
Chromosome.getRegionsOfConservedSynteny(Coordinate range,
Species target)
|
MappingSet |
Assembly.getStitchedMappings()
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Methods in uk.ac.roslin.ensembl.model.database that throw DAOException |
HashMap<CollectionSpecies,String> |
Registry.getAssemblies(CollectionDatabase database)
|
String |
Registry.getAssembly(SingleSpeciesDatabase database)
|
CoordinateSystem |
CollectionCoreDatabase.getBuildCoordSystem(Species species,
String featureType)
|
CoordinateSystem |
SingleSpeciesCoreDatabase.getBuildCoordSystem(String featureType)
|
String |
CollectionCoreDatabase.getBuildLevel(Species species,
String featureKey)
|
String |
SingleSpeciesCoreDatabase.getBuildLevel(String featureType)
|
Chromosome |
CollectionCoreDatabase.getChromosomeByName(Species species,
String name)
|
Chromosome |
SingleSpeciesCoreDatabase.getChromosomeByName(String name)
|
CoordinateSystem |
SingleSpeciesCoreDatabase.getChromosomeLevelCoordSystem()
|
CoordinateSystem |
CollectionCoreDatabase.getChromosomeLevelCS(Species species)
|
List<? extends Chromosome> |
SingleSpeciesCoreDatabase.getChromosomes()
|
List<? extends Chromosome> |
CollectionCoreDatabase.getChromosomes(Species species)
|
CoordinateSystem |
SingleSpeciesCoreDatabase.getCSByID(Integer id)
|
CoordinateSystem |
CollectionCoreDatabase.getCSByID(Species species,
Integer id)
|
Set<? extends CoordinateSystem> |
SingleSpeciesCoreDatabase.getCSForFeature(ObjectType featureType)
|
Set<? extends CoordinateSystem> |
CollectionCoreDatabase.getCSForFeature(Species sp,
ObjectType feature)
|
List<? extends ObjectType> |
SingleSpeciesCoreDatabase.getFeaturesForCS(CoordinateSystem coordSys)
|
List<? extends ObjectType> |
CollectionCoreDatabase.getFeaturesForCS(Species sp,
CoordinateSystem coordSys)
|
Integer |
SingleSpeciesCoreDatabase.getMaxLengthForFeature(ObjectType featureType,
CoordinateSystem cs)
|
Integer |
CollectionCoreDatabase.getMaxLengthForFeature(Species sp,
ObjectType feature,
CoordinateSystem cs)
|
Object |
Database.getNewSqlSession()
|
CoordinateSystem |
SingleSpeciesCoreDatabase.getSequenceLevelCoordSystem()
|
CoordinateSystem |
CollectionCoreDatabase.getSequenceLevelCS(Species species)
|
CoordinateSystem |
SingleSpeciesCoreDatabase.getTopLevelCoordSystem()
|
CoordinateSystem |
CollectionCoreDatabase.getTopLevelCS(Species species)
|
void |
Registry.setCoreDBBuildLevels(SingleSpeciesCoreDatabase database)
|