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

Packages that use DADNASequence

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

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

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

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

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

Modifier and Type	Method and Description
DADNASequence	DBDNASequenceDAO.SequenceRowHandler.getObjectResult()
DADNASequence	DBDNASequenceDAO.getSequenceByID(Integer id)
DADNASequence	DBDNASequenceDAO.getValidatedSequence(DNASequence seq)

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

Modifier and Type	Method and Description
List<DADNASequence>	DBDNASequenceDAO.SequenceRowHandler.getListResult()

Constructors in uk.ac.roslin.ensembl.dao.database.coreaccess with parameters of type DADNASequence

Constructor and Description
DBGeneDAO.GeneMappingRowHandler(List<HashMap> results, DADNASequence parent)
DBGeneDAO.MappingRowHandler(List<HashMap> results, DADNASequence parent)

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

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

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

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

Modifier and Type	Field and Description
protected DADNASequence	DAEnsemblDNASequenceReader.dASequence
protected DADNASequence	DAEnsemblDNASequenceReader.parent
protected DADNASequence	DAFeature.thisSequence

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

Modifier and Type	Method and Description
DADNASequence	DAEnsemblDNASequenceReader.getParent()
DADNASequence	DATranscript.getPrimaryTranscript() Returns a DADNASequence object representing the unprocessed primary Transcript.
DADNASequence	DATranscript.getProcessedTranscript() Returns a DADNASequence object representing the processed (spliced exons) version of this Transcript.
DADNASequence	DAFeature.getSequence() Returns the sequence covered by this feature (i.e. a new DADNASequence object representing this region of the genome, it might be a GAPSequence if no sequence info is available).
DADNASequence	DAFeature.getTargetSequence() Returns the (genomic) sequence that this feature is annotated upon (at 'top level').
DADNASequence	DAFeature.getTopLevelTargetSequence()

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

Modifier and Type	Method and Description
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.

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

Modifier and Type	Method and Description
void	DAEnsemblDNASequenceReader.setParent(DADNASequence parent)