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