Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Datasource Aware Module
v1.09
A C D F G H I L M N O P R S T U V X

A

addExon(Exon) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
addHomology(EnsemblComparaDivision, DAHomologyPairRelationship) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
addMappedObjectType(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
addMapping(Mapping) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
addMapping(Mapping) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
addTranscript(Transcript) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
addXRefs(List<DAXRef>) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
assemblyStart - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
assemblyStop - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 

C

clearAllMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
clearAllMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
comparaFactories - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
comparaFactories - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
compare(DAObject, DAObject) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject.DAComparator
 
componentMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
compoundSet - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
coordSystem - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
coordSystemID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
countCompounds(NucleotideCompound...) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
creationDate - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
current - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 

D

DAAnalysis - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAAnalysis() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAAnalysis
 
DAAssembledDNASequence - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAAssembledDNASequence() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
 
DAAssembledDNASequence(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
 
DAAssembly - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAAssembly() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
DAChromosome - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAChromosome() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome
 
DAChromosome(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome
 
daComparator - Static variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
DACoordinateSystem - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DACoordinateSystem() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
DACoreObject - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DACoreObject() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
DACoreObject(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
DADNASequence - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DADNASequence() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
DADNASequence(DAEnsemblDNASequenceReader) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
DADNASequence(String) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
DADNASequence(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
DAEnsemblDNASequenceReader - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAEnsemblDNASequenceReader() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
DAEnsemblDNASequenceReader(Integer, Integer, Integer, String, DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
DAEnsemblDNASequenceReader.EmptyIterator<NucleotideCompound> - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAEnsemblDNASequenceReader.EmptyIterator() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader.EmptyIterator
 
DAExon - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAExon() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
DAExon(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
DAExternalDB - Class in uk.ac.roslin.ensembl.datasourceaware
 
DAExternalDB() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
DAFeature - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAFeature() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
DAFeature(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
DAFeature.Status - Enum in uk.ac.roslin.ensembl.datasourceaware.core
 
DAGene - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAGene() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
DAGene(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
DAHomologyPairRelationship - Class in uk.ac.roslin.ensembl.datasourceaware.compara
 
DAHomologyPairRelationship() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
DAHomologyRelationship - Class in uk.ac.roslin.ensembl.datasourceaware.compara
 
DAHomologyRelationship() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship
 
DAObject - Class in uk.ac.roslin.ensembl.datasourceaware
 
DAObject() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
DAObject(DAOFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
DAObject.DAComparator - Class in uk.ac.roslin.ensembl.datasourceaware
 
DAObject.DAComparator() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAObject.DAComparator
 
daoFactory - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
daoFactory - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
DAProteinFeature - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DAProteinFeature() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
DAProteinFeature(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
dASequence - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
DATranscript - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DATranscript() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
DATranscript(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
DATranslation - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
DATranslation() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation
 
DAXRef - Class in uk.ac.roslin.ensembl.datasourceaware
 
DAXRef() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
DBSeqLength - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
dbSpeciesName - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
dbVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
dbVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
defaultVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
description - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
displayName - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
displayXRef - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 

F

factory - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 

G

GapSequence - Class in uk.ac.roslin.ensembl.datasourceaware.core
 
getAccession() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getAnalysis() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
getAnalysisID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getAnnotationLevelMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getAsList() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getAssembly(DAAssembledDNASequence) - Static method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getAssembly(DAAssembledDNASequence, Integer, Integer) - Static method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getAssembly() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
getAssembly() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getAssemblyStart() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getAssemblyStop() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getBinaryRelationship() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getBioEnd() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getBiotype() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
getBiotype() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
getBuildLevelMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getCanonicalTranscript() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
getCanonicalTranscriptID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
getCanonicalTranslation() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
getChromosomeMapping(Chromosome) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
Utility method to pull back a single mapping of this Feature on a Given chromosome.
getChromosomeName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome
 
getComparaDivision() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
getComparaDivision() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getComparaFactory(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
getComparaFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
getComparaFactory(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getComparaFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getCompleteAssembly() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
 
getCompoundAt(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getCompoundSet() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getCoordSystem() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getCoordSystemID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getCreationDate() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getDaoFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
getDaoFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getDaoFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
getDB() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
getDBDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
getDBName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getDBName() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
getDBName() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
getDBRelease() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
getDBSeqLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getDBStatus() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
getDBType() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
getDBVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getDBVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
getDescription() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getDescription() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
getDisplayID() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
getDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
getDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
getDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
getDisplayXRef() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getEndPhase() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
getEValue() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getExons() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
getFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getGene() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
getGeneID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
getGenesOnRegion(Coordinate) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getGenesOnRegion(Integer, Integer, Coordinate.Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getGenesOnRegion(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getHashID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getHashID() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
getHomologies() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
Returns all Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene.
getHomologies(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
Returns all Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for this Gene.
getHomologies(Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
Returns Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene for the specified Species.
getHomologies(EnsemblComparaDivision, Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
Returns Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for the specified Species.
getHomologiesWithoutLazyLoad() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
Utility method to get all of the current DAHomologyPairRelationships for this Gene
getId() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Get the value of id
getId() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getId() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
getIndexOf(NucleotideCompound) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getInfo() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
getInfoType() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
getInverse() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getLastCommonAncestor() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship
 
getLastCommonAncestor() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getLastIndexOf(NucleotideCompound) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence
 
getLengthInteger() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getMappedRegions() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getMappings(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getMappings(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getMembers() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
getMembers() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship
 
getMembers() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getModificationDate() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getObjectTypeMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getParent() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getParent() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getPercentIdentity() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getPhase() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
getProteinFeatures() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation
 
getRank() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Get the value of rank
getRank() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
getRegionsOfConservedSynteny(Coordinate, Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome
 
getRegistry() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getRegistry() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
getRelationshipType() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship
 
getRelationshipType() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
 
getReverseComplementSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getReverseComplementSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getReverseComplementSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence
 
getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence
 
getSchemaVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getSchemaVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
getScore() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getSeqRegionID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
 
getSequenceAsString(Integer, Integer, Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
 
getSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
getSequenceAsString(Integer, Integer, Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getSequenceAsString(Integer, Integer, Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence
 
getSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence
 
getSequenceAsString(Integer, Integer, Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence
 
getSource() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
getSource() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getSourceEnd() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getSourceProperties() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
getSourceProperties() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getSourceStart() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship
 
getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getSpeciesID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Get the value of speciesID
getStableID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
getStableID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
getStableID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
getStatus() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getStitchedMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getStitchedMappings(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
getSubSequence(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
getTarget() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
getTarget() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getTargetEnd() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getTargetName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getTargetProperties() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
getTargetProperties() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getTargetStart() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getTopLevelMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
getTranscript() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
getTranscript() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation
 
getTranscriptID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
getTranscripts() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
getTranslation() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
getTranslationID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAnalysis
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Get the value of type
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
getVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Get the value of version
getVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
getXRefs() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 

H

hasNext() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader.EmptyIterator
 

I

id - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
id - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
id - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
InverseHomologyPairRelationshipView - Class in uk.ac.roslin.ensembl.datasourceaware.compara
 
InverseHomologyPairRelationshipView(DAHomologyPairRelationship) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView
 
isCanonical() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
isConstitutive() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
isCurrent() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
isDefaultVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
isObjectTypeMapped(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
isSequenceLevel() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
isTopLevel() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
iterator() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 

L

length - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 

M

makeGap(Integer) - Static method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence
 
mappedObjectTypes - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
mappedRegions - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
mappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
mappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
modificationDate - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 

N

name - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
name - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
next() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader.EmptyIterator
 

O

objectTypeMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
objectTypeMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 

P

parent - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 

R

rank - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
registry - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
registry - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
remove() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader.EmptyIterator
 

S

schemaVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
schemaVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
seqRegionID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
seqRegionID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
sequence - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
sequenceLevel - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
setAnalysis(Analysis) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
setAnalysisID(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setAssemblyStart(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
setAssemblyStop(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
setBiotype(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
setBiotype(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
setCanonical(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
setCanonicalTranscriptID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
setChromosomeName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome
 
setCompoundSet(CompoundSet) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
setConstitutive(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
setContents(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
setCoordSystem(CoordinateSystem) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
setCoordSystemID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
setCreationDate(Date) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
setCurrent(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
setDaoFactory(DAOFactory) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
setDaoFactory(DAOFactory) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
setDB(DAExternalDB) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
setDBDisplayName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
setDBName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
setDBName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
setDBRelease(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
setDBSeqLength(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
setDBStatus(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
setDBType(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB
 
setDBVersion(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
setDefaultVersion(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
setDescription(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
setDescription(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
setDisplayID(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
setDisplayName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
setDisplayXRef(DAXRef) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
setEndPhase(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
setEValue(Double) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setFactory(DAOCoreFactory) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
setGene(DAGene) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
setGeneID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
setId(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Set the value of id
setId(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
setId(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
setInfo(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
setInfoType(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
setLastCommonAncestor(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship
 
setLength(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
setModificationDate(Date) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
setName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
setName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
setParent(AssembledDNASequence) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 
setParent(DADNASequence) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
setPercentIdentity(Double) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setPhase(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
setRank(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Set the value of rank
setRank(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
setRegistry(Registry) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
setRegistry(Registry) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject
 
setRelationshipType(RelationshipType) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship
 
setScore(Double) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setSearchedHomologies(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
setSeqRegionID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
 
setSequenceLevel(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
setSequenceStorage(DAEnsemblDNASequenceReader) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
setSource(DAGene) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
setSourceEnd(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setSourceProperties(HomologyAlignmentProperties) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
setSourceStart(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setSpecies(Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
setSpecies(Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
setSpeciesID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Set the value of speciesID
setStableID(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
setStableID(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene
 
setStableID(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript
 
setStatus(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 
setTarget(DAGene) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
setTargetEnd(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setTargetName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setTargetProperties(HomologyAlignmentProperties) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship
 
setTargetStart(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setTranscript(Transcript) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
setTranscript(DATranscript) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation
 
setTranscriptID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon
 
setTranslationID(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature
 
setType(HomologyType) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship
 
setType(CoordSystemType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Set the value of type
setVersion(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
Set the value of version
setVersion(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef
 
species - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
 
species - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
speciesID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 
stitchedComponentMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
 

T

toString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome
 
toString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
 
toString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence
 
type - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 

U

uk.ac.roslin.ensembl.datasourceaware - package uk.ac.roslin.ensembl.datasourceaware
 
uk.ac.roslin.ensembl.datasourceaware.compara - package uk.ac.roslin.ensembl.datasourceaware.compara
 
uk.ac.roslin.ensembl.datasourceaware.core - package uk.ac.roslin.ensembl.datasourceaware.core
 

V

valueOf(String) - Static method in enum uk.ac.roslin.ensembl.datasourceaware.core.DAFeature.Status
Returns the enum constant of this type with the specified name.
values() - Static method in enum uk.ac.roslin.ensembl.datasourceaware.core.DAFeature.Status
Returns an array containing the constants of this enum type, in the order they are declared.
version - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem
 

X

xrefs - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
 

A C D F G H I L M N O P R S T U V X
Ensembl Datasource Aware Module
v1.09

Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3