Uses of Class
uk.ac.roslin.ensembl.model.Mapping

Packages that use Mapping

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

Uses of Mapping in uk.ac.roslin.ensembl.dao.coreaccess

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

Modifier and Type	Method and Description
List<? extends Mapping>	GeneDAO.getGeneMappingsOnRegion(DNASequence region, Coordinate coords)

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

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

Modifier and Type	Method and Description
Mapping	DBGeneDAO.MappingRowHandler.getObjectResult()
Mapping	DBAssemblyDAO.PARMappingHandler.getObjectResult()

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

Modifier and Type	Method and Description
List<Mapping>	DBGeneDAO.getGeneMappingsOnRegion(DNASequence region, Coordinate coords)
List<Mapping>	DBGeneDAO.MappingRowHandler.getListResult()
List<Mapping>	DBAssemblyDAO.PARMappingHandler.getListResult()

Uses of Mapping in uk.ac.roslin.ensembl.dao.variation

Methods in uk.ac.roslin.ensembl.dao.variation that return types with arguments of type Mapping

Modifier and Type	Method and Description
List<? extends Mapping>	VariationDAO.getVariationMappingsOnRegion(DNASequence region, Coordinate coords)

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

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

Modifier and Type	Method and Description
Mapping	DAFeature.getChromosomeMapping() Utility method to pull back a unique chromosomal mapping of this Feature.
Mapping	DAFeature.getChromosomeMapping(Chromosome chr) Utility method to pull back a single mapping of this Feature on a Given chromosome.

Methods in uk.ac.roslin.ensembl.datasourceaware.core that return types with arguments of type Mapping

Modifier and Type	Method and Description
List<? extends Mapping>	DADNASequence.getVariationMappingsOnRegion(Coordinate coord) Returns List of Mappings of Variations on specified Coordinate Region.
List<? extends Mapping>	DADNASequence.getVariationMappingsOnRegion(Integer start, Integer stop) Returns List of Mappings of Variations on specified Coordinate Region.

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

Modifier and Type	Method and Description
void	DAChromosome.addException(AssemblyExceptionType type, Mapping mapping) public method called by the DA infrastructure when adding an AssemblyException mapping of the indicated type.
Boolean	DAFeature.addMapping(Mapping mapping)
Boolean	DADNASequence.addMapping(Mapping mapping)

Uses of Mapping in uk.ac.roslin.ensembl.datasourceaware.variation

Subclasses of Mapping in uk.ac.roslin.ensembl.datasourceaware.variation

Modifier and Type	Class and Description
class	VariationMapping

Methods in uk.ac.roslin.ensembl.datasourceaware.variation that return Mapping

Modifier and Type	Method and Description
Mapping	DAVariation.getChromosomeMapping() Utility method to pull back a unique chromosomal mapping of this Feature.
Mapping	DAVariation.getChromosomeMapping(Chromosome chr) Utility method to pull back a single mapping of this Feature on a Given chromosome.

Methods in uk.ac.roslin.ensembl.datasourceaware.variation with parameters of type Mapping

Modifier and Type	Method and Description
Boolean	DAVariation.addMapping(Mapping mapping)

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

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

Modifier and Type	Method and Description
List<Mapping>	SequenceMapper.getComponentSequences(HashMap parameters)

Uses of Mapping in uk.ac.roslin.ensembl.model

Fields in uk.ac.roslin.ensembl.model declared as Mapping

Modifier and Type	Field and Description
protected Mapping	Mapping.reverseMapping

Methods in uk.ac.roslin.ensembl.model that return Mapping

Modifier and Type	Method and Description
Mapping	Mapping.getReverseMapping()

Methods in uk.ac.roslin.ensembl.model with parameters of type Mapping

Modifier and Type	Method and Description
Boolean	MappableObject.addMapping(Mapping mapping)
static boolean	Mapping.addReverseMapping(Mapping originalMapping)
void	Mapping.setReverseMapping(Mapping reverseMapping)

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

Methods in uk.ac.roslin.ensembl.model.core that return Mapping

Modifier and Type	Method and Description
Mapping	Feature.getChromosomeMapping()
Mapping	Feature.getChromosomeMapping(Chromosome chr)

Methods in uk.ac.roslin.ensembl.model.core that return types with arguments of type Mapping

Modifier and Type	Method and Description
List<? extends Mapping>	DNASequence.getVariationMappingsOnRegion(Coordinate coord)
List<? extends Mapping>	DNASequence.getVariationMappingsOnRegion(Integer start, Integer stop)