Uses of Class
uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

Packages that use DAAssembledDNASequence

Package	Description
uk.ac.roslin.ensembl.dao.database
uk.ac.roslin.ensembl.dao.database.coreaccess
uk.ac.roslin.ensembl.datasourceaware.core
uk.ac.roslin.ensembl.mapper.core

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

Fields in uk.ac.roslin.ensembl.dao.database with type parameters of type DAAssembledDNASequence

Modifier and Type	Field and Description
protected TreeMap<String,TreeMap<String,DAAssembledDNASequence>>	DBSpecies.fragments

Methods in uk.ac.roslin.ensembl.dao.database that return DAAssembledDNASequence

Modifier and Type	Method and Description
DAAssembledDNASequence	DBSpecies.getCachedFragment(DAAssembledDNASequence frag_in)
DAAssembledDNASequence	DBCollectionCoreDatabase.getFragmentByName(Species species, String name)
DAAssembledDNASequence	DBSpecies.getFragmentByName(String name)
DAAssembledDNASequence	DBSingleSpeciesCoreDatabase.getFragmentByName(String name) a Fragment is TopLevelAssembledDNASequence ( where there are no chromosomes )
DAAssembledDNASequence	DBSpecies.getFragmentByName(String name, String dbVersion)
DAAssembledDNASequence	DBCollectionSpecies.getFragmentByName(String name, String dbVersion)

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

Modifier and Type	Method and Description
TreeMap<String,DAAssembledDNASequence>	DBSpecies.getFragments()
List<DAAssembledDNASequence>	DBSingleSpeciesCoreDatabase.getFragments() Fragments are TopLevelAssembledDNASequences
List<DAAssembledDNASequence>	DBCollectionCoreDatabase.getFragments(Species species)
TreeMap<String,DAAssembledDNASequence>	DBSpecies.getFragments(String dbVersion)
TreeMap<String,DAAssembledDNASequence>	DBCollectionSpecies.getFragments(String dbVersion)

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

Modifier and Type	Method and Description
DAAssembledDNASequence	DBSpecies.getCachedFragment(DAAssembledDNASequence frag_in)

Uses of DAAssembledDNASequence in uk.ac.roslin.ensembl.dao.database.coreaccess

Methods in uk.ac.roslin.ensembl.dao.database.coreaccess that return DAAssembledDNASequence

Modifier and Type	Method and Description
DAAssembledDNASequence	DBChromosomeDAO.getFragmentByName(String name)

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

Modifier and Type	Method and Description
List<DAAssembledDNASequence>	DBChromosomeDAO.getFragments()

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

Subclasses of DAAssembledDNASequence in uk.ac.roslin.ensembl.datasourceaware.core

Modifier and Type	Class and Description
class	DAChromosome A DAChromosome is a particular type of DAAssembledDNASequence for representing whole chromosomes.

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

Modifier and Type	Method and Description
DAAssembledDNASequence	DAAssembly.getParent() Returns the DAAssembledDNASequence that this assembly holds (its 'Parent').

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

Modifier and Type	Method and Description
static DAAssembly	DAAssembly.getAssembly(DAAssembledDNASequence parent)
static DAAssembly	DAAssembly.getAssembly(DAAssembledDNASequence parent, Integer start, Integer stop)

Uses of DAAssembledDNASequence in uk.ac.roslin.ensembl.mapper.core

Methods in uk.ac.roslin.ensembl.mapper.core that return DAAssembledDNASequence

Modifier and Type	Method and Description
DAAssembledDNASequence	ChromosomeMapper.getTopLevelFragmentByName_CoordSysID(HashMap parameter)

Methods in uk.ac.roslin.ensembl.mapper.core that return types with arguments of type DAAssembledDNASequence

Modifier and Type	Method and Description
List<DAAssembledDNASequence>	ChromosomeMapper.getTopLevelFragmentsByCoordSysID(HashMap parameter)