Uses of Interface
uk.ac.roslin.ensembl.model.core.DNASequence

Packages that use DNASequence

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.dao.database.variation
uk.ac.roslin.ensembl.dao.variation
uk.ac.roslin.ensembl.datasourceaware.core
uk.ac.roslin.ensembl.model.core

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

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

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.

Methods in uk.ac.roslin.ensembl.dao.compara with parameters of type DNASequence

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 DNASequence in uk.ac.roslin.ensembl.dao.coreaccess

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

Modifier and Type	Method and Description
DNASequence	DNASequenceDAO.getSequenceByID(Integer id)
DNASequence	DNASequenceDAO.getValidatedSequence(DNASequence seq)

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

Modifier and Type	Method and Description
List<? extends DNASequence>	DNASequenceDAO.getValidatedSequences(List<? extends DNASequence> sequences)

Methods in uk.ac.roslin.ensembl.dao.coreaccess with parameters of type DNASequence

Modifier and Type	Method and Description
Gene	GeneDAO.addGeneByIDOnParent(Integer id, DNASequence parent)
Gene	GeneDAO.addGeneByStableIDOnParent(String stableID, DNASequence parent)
MappingSet	AssemblyDAO.getComponentMappingsByStartStop(DNASequence assembledSequence, Integer start, Integer stop)
List<? extends Mapping>	GeneDAO.getGeneMappingsOnRegion(DNASequence region, Coordinate coords)
DNASequence	DNASequenceDAO.getValidatedSequence(DNASequence seq)

Method parameters in uk.ac.roslin.ensembl.dao.coreaccess with type arguments of type DNASequence

Modifier and Type	Method and Description
List<? extends DNASequence>	DNASequenceDAO.getValidatedSequences(List<? extends DNASequence> sequences)

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

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

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 DNASequence in uk.ac.roslin.ensembl.dao.database.coreaccess

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

Modifier and Type	Method and Description
List<? extends DNASequence>	DBDNASequenceDAO.getValidatedSequences(List<? extends DNASequence> in_sequences)

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

Modifier and Type	Method and Description
DAGene	DBGeneDAO.addGeneByIDOnParent(Integer id, DNASequence parent)
DAGene	DBGeneDAO.addGeneByStableIDOnParent(String stableID, DNASequence parent) The gene returned has mapping to a sequence region - and the id for the coordinate system that this region belongs to
MappingSet	DBAssemblyDAO.getComponentMappingsByStartStop(DNASequence assembledSequence, Integer begin, Integer stop)
List<Mapping>	DBGeneDAO.getGeneMappingsOnRegion(DNASequence region, Coordinate coords)
DADNASequence	DBDNASequenceDAO.getValidatedSequence(DNASequence seq)

Method parameters in uk.ac.roslin.ensembl.dao.database.coreaccess with type arguments of type DNASequence

Modifier and Type	Method and Description
List<? extends DNASequence>	DBDNASequenceDAO.getValidatedSequences(List<? extends DNASequence> in_sequences)

Uses of DNASequence in uk.ac.roslin.ensembl.dao.database.variation

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

Modifier and Type	Method and Description
List<VariationMapping>	DBVariationDAO.getVariationMappingsOnRegion(DNASequence region, Coordinate coords)
List<DAVariation>	DBVariationDAO.getVariationsOnRegion(DNASequence region, Coordinate coords)

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

Methods in uk.ac.roslin.ensembl.dao.variation with parameters of type DNASequence

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

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

Classes in uk.ac.roslin.ensembl.datasourceaware.core that implement DNASequence

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

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

Subinterfaces of DNASequence in uk.ac.roslin.ensembl.model.core

Modifier and Type	Interface and Description
interface	AssembledDNASequence
interface	Chromosome

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

Modifier and Type	Method and Description
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.