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

Uses of Class
uk.ac.roslin.ensembl.exception.DAOException

Packages that use DAOException
uk.ac.roslin.ensembl.model.core   
uk.ac.roslin.ensembl.model.database   
 

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

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()
           
 

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

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)
           
 


Ensembl Model
v1.09

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