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

Packages that use Coordinate

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
uk.ac.roslin.ensembl.model.compara
uk.ac.roslin.ensembl.model.core

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 Coordinate in uk.ac.roslin.ensembl.datasourceaware.core

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

Modifier and Type	Method and Description
Coordinate	DAFeature.convertToTargetCoordinate(Integer start, Integer stop) Converts a given range (relative to the annotation start site) to the Coordinates on the annotated target TopLevel (genomic) sequence.
Coordinate	DATranslation.getChromosomePositionFromAA(Integer aminoAcidPosition) Returns the mapped chromosomal coordinates of an amino acid position.
Coordinate	DATranslation.getPrimaryTranscriptPositionFromAA(Integer aminoAcidPosition) Returns the mapped coordinates of an amino acid position on the unprocessed primary transcript that provides this translation.
Coordinate	DATranslation.getProcessedTranscriptPositionFromAA(Integer aminoAcidPosition) Returns the mapped coordinates of an amino acid position on the (spliced) processed transcript that provides this translation.
Coordinate	DAFeature.getTopLevelTargetCoordinates()

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

Modifier and Type	Method and Description
List<DAGene>	DADNASequence.getGenesOnRegion(Coordinate coord) Returns a List of Genes on the specified Coordinate region.
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.
List<? extends Mapping>	DADNASequence.getVariationMappingsOnRegion(Coordinate coord) Returns List of Mappings of Variations on specified Coordinate Region.
List<DAVariation>	DADNASequence.getVariationsOnRegion(Coordinate coord) Returns list of Variations on specified Coordinate Region.

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

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

Modifier and Type	Field and Description
protected Coordinate	Mapping.sourceCoordinates
protected Coordinate	Mapping.targetCoordinates

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

Modifier and Type	Method and Description
Coordinate	MappingSet.getExtent() Returns a Coordinate representing the extent or range of this MappingSet.
Coordinate	Coordinate.getOverlap(Coordinate test) Returns the overlap extent (as a Coordinate) between this Coordinate and a test Coordinate.
Coordinate	CoordinateSet.getRange() Returns a Coordinate representing the extent or range of this CoordinateSet
Coordinate	Mapping.getSourceCoordinates()
Coordinate	Mapping.getTargetCoordinates()

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

Modifier and Type	Method and Description
int	Coordinate.compareTo(Coordinate o) Implements compareTo(another Coordinate) method for the Comparable interface.
Boolean	CoordinateSet.containsCoordinateWithoutGaps(Coordinate test) Returns whether a test Coordinate is contained in this CoordinateSet range WITHOUT any gaps.
Coordinate	Coordinate.getOverlap(Coordinate test) Returns the overlap extent (as a Coordinate) between this Coordinate and a test Coordinate.
CoordinateSet	CoordinateSet.getUncoveredRegions(Coordinate test) Returns the CoordinateSet (ordered set of Coordinates) that define regions of the test Coordinate not represented (covered) in this CoordinateSet.
Boolean	Coordinate.liesWithinCoordinate(Coordinate test) Tests whether this Coordinate lies TOTALLY within the range of another test Coordinate.
Boolean	Coordinate.overlaps(Coordinate test) Returns whether this Coordinate overlaps with the extent of a test Coordinate.
void	Mapping.setSourceCoordinates(Coordinate coord)
void	Mapping.setTargetCoordinates(Coordinate coord)

Uses of Coordinate in uk.ac.roslin.ensembl.model.compara

Methods in uk.ac.roslin.ensembl.model.compara that return Coordinate

Modifier and Type	Method and Description
Coordinate	HomologyAlignmentProperties.getCoords()

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

Modifier and Type	Method and Description
void	HomologyAlignmentProperties.setCoords(Coordinate coords)

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

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

Modifier and Type	Method and Description
List<? extends Gene>	DNASequence.getGenesOnRegion(Coordinate coord)
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.
List<? extends Mapping>	DNASequence.getVariationMappingsOnRegion(Coordinate coord)
List<? extends Variation>	DNASequence.getVariationsOnRegion(Coordinate coord)