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

Packages that use MappingSet

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

Uses of MappingSet in uk.ac.roslin.ensembl.dao.compara

Methods in uk.ac.roslin.ensembl.dao.compara that return types with arguments of type MappingSet

Modifier and Type	Method and Description
HashMap<? extends DNASequence,? extends MappingSet>	HomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target) Specification of Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.
HashMap<? extends DNASequence,? extends MappingSet>	HomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target, String chrName) Specification of Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

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

Methods in uk.ac.roslin.ensembl.dao.coreaccess that return MappingSet

Modifier and Type	Method and Description
MappingSet	AssemblyDAO.getComponentMappingsByStartStop(DNASequence assembledSequence, Integer start, Integer stop)
MappingSet	AssemblyDAO.getPARMappingsByStartStop(Chromosome chr, Integer start, Integer stop)

Uses of MappingSet in uk.ac.roslin.ensembl.dao.database.compara

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

Modifier and Type	Method and Description
HashMap<DADNASequence,MappingSet>	DBHomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target) Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.
HashMap<DADNASequence,MappingSet>	DBHomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target, String chrName) Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

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

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

Modifier and Type	Method and Description
MappingSet	DBAssemblyDAO.getComponentMappingsByStartStop(DNASequence assembledSequence, Integer begin, Integer stop)
MappingSet	DBAssemblyDAO.getPARMappingsByStartStop(Chromosome chr, Integer begin, Integer stop)

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

Fields in uk.ac.roslin.ensembl.datasourceaware.core declared as MappingSet

Modifier and Type	Field and Description
protected MappingSet	DAAssembly.componentMappings
protected MappingSet	DAFeature.mappings
protected MappingSet	DADNASequence.mappings
protected MappingSet	DAAssembly.pARMappings
protected MappingSet	DAAssembly.stitchedComponentMappings

Fields in uk.ac.roslin.ensembl.datasourceaware.core with type parameters of type MappingSet

Modifier and Type	Field and Description
protected HashMap<ObjectType,MappingSet>	DAFeature.objectTypeMappings
protected HashMap<ObjectType,MappingSet>	DADNASequence.objectTypeMappings

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

Modifier and Type	Method and Description
MappingSet	DAFeature.getAnnotationLevelMappings()
MappingSet	DAChromosome.getAssemblyExceptions(AssemblyExceptionType type) Returns a MappingSet of AssemblyExceptions of the indicated AssemblyExceptionType.
MappingSet	DAFeature.getBuildLevelMappings()
MappingSet	DAFeature.getChromosomeMappings() Method to return all chromosomal mappings for this feature.
MappingSet	DAFeature.getLoadedMappings()
MappingSet	DADNASequence.getLoadedMappings()
MappingSet	DAFeature.getLoadedMappings(ObjectType targetType)
MappingSet	DADNASequence.getLoadedMappings(ObjectType targetType)
MappingSet	DAAssembly.getMappings() Returns the MappingSet 'componentMappings' of all of the mappings of all of the DNASequences that make up this assembly.
MappingSet	DAChromosome.getPseudoAutosomalRegion()
MappingSet	DAAssembly.getStitchedMappings() Returns the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly.
MappingSet	DAAssembly.getStitchedMappings(Integer start, Integer stop) For a given range, returns a subset of the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly.
MappingSet	DAFeature.getTopLevelMappings()
MappingSet	DATranslation.getTranslationMappings() Returns the Set of Mappings between coordinates on this Translation and the Primary transcript.
protected MappingSet	DAAssembly.stitchComponents() Protected method to join together (stitch) all of the component sub-sequences of the assembly, together with GapSequences to form a single continuous ungapped assembly, held in the MappingSet 'stitchedComponentMappings';

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

Modifier and Type	Method and Description
HashMap<ObjectType,MappingSet>	DADNASequence.getObjectTypeMappings()
HashMap<DADNASequence,MappingSet>	DADNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target) Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species
HashMap<DADNASequence,MappingSet>	DADNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target, String chrName) Method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.

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

Fields in uk.ac.roslin.ensembl.datasourceaware.variation declared as MappingSet

Modifier and Type	Field and Description
protected MappingSet	DAVariation.mappings

Fields in uk.ac.roslin.ensembl.datasourceaware.variation with type parameters of type MappingSet

Modifier and Type	Field and Description
protected HashMap<ObjectType,MappingSet>	DAVariation.objectTypeMappings

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

Modifier and Type	Method and Description
MappingSet	DAVariation.getChromosomeMappings() Method to return all chromosomal mappings for this feature.
MappingSet	DAVariation.getLoadedMappings()
MappingSet	DAVariation.getLoadedMappings(ObjectType targetType)
MappingSet	DAVariation.getMappings()

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

Modifier and Type	Method and Description
void	DAVariation.setMappings(MappingSet mappings)

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

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

Modifier and Type	Method and Description
MappingSet	MappableObject.getLoadedMappings()
MappingSet	MappableObject.getLoadedMappings(ObjectType targetType)

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

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

Modifier and Type	Method and Description
MappingSet	Feature.getChromosomeMappings()
MappingSet	Assembly.getMappings()
MappingSet	Chromosome.getPseudoAutosomalRegion()
MappingSet	Assembly.getStitchedMappings()

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

Modifier and Type	Method and Description
HashMap<ObjectType,? extends MappingSet>	DNASequence.getObjectTypeMappings()
HashMap<? extends DNASequence,MappingSet>	DNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target) Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species
HashMap<? extends DNASequence,MappingSet>	DNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target, String chrName) Specifies method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.