Uses of Class
org.biojava.nbio.core.sequence.AccessionID

Packages that use AccessionID

Package	Description
org.biojava.nbio.core.alignment
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.location
org.biojava.nbio.core.sequence.location.template
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template

Uses of AccessionID in org.biojava.nbio.core.alignment

Methods in org.biojava.nbio.core.alignment that return AccessionID

Modifier and Type	Method	Description
AccessionID	SimpleAlignedSequence.getAccession()

Uses of AccessionID in org.biojava.nbio.core.sequence

Methods in org.biojava.nbio.core.sequence with parameters of type AccessionID

Modifier and Type	Method	Description
CDSSequence	TranscriptSequence.addCDS(AccessionID accession, int begin, int end, int phase)	Add a Coding Sequence region with phase to the transcript sequence
ExonSequence	GeneSequence.addExon(AccessionID accession, int begin, int end)	Add an ExonSequence mainly used to mark as a feature
GeneSequence	ChromosomeSequence.addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand)	Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.
IntronSequence	GeneSequence.addIntron(AccessionID accession, int begin, int end)	Add an Intron Currently used to mark an IntronSequence as a feature
void	TranscriptSequence.addStartCodonSequence(AccessionID accession, int begin, int end)	Sets the start codon sequence at given begin / end location.
void	TranscriptSequence.addStopCodonSequence(AccessionID accession, int begin, int end)	Sets the stop codon sequence at given begin / end location.
TranscriptSequence	GeneSequence.addTranscript(AccessionID accession, int begin, int end)	Add a transcription sequence to a gene which describes a ProteinSequence

Constructors in org.biojava.nbio.core.sequence with parameters of type AccessionID

Constructor	Description
GeneSequence(ChromosomeSequence parentSequence, AccessionID accessionId, int begin, int end, Strand strand)	A class that keeps track of the details of a GeneSequence which is difficult to properly model.
TranscriptSequence(GeneSequence parentDNASequence, AccessionID accessionID, int begin, int end)

Uses of AccessionID in org.biojava.nbio.core.sequence.loader

Methods in org.biojava.nbio.core.sequence.loader that return AccessionID

Modifier and Type	Method	Description
AccessionID	SequenceFileProxyLoader.getAccession()
AccessionID	StringProxySequenceReader.getAccession()
AccessionID	UniprotProxySequenceReader.getAccession()

Methods in org.biojava.nbio.core.sequence.loader that return types with arguments of type AccessionID

Modifier and Type	Method	Description
ArrayList<AccessionID>	UniprotProxySequenceReader.getAccessions()	Pull uniprot accessions associated with this sequence

Uses of AccessionID in org.biojava.nbio.core.sequence.location

Constructors in org.biojava.nbio.core.sequence.location with parameters of type AccessionID

Constructor	Description
SimpleLocation(Point start, Point end, Strand strand, boolean betweenCompounds, AccessionID accession)
SimpleLocation(Point start, Point end, Strand strand, AccessionID accession)

Uses of AccessionID in org.biojava.nbio.core.sequence.location.template

Methods in org.biojava.nbio.core.sequence.location.template that return AccessionID

Modifier and Type	Method	Description
AccessionID	AbstractLocation.getAccession()

Methods in org.biojava.nbio.core.sequence.location.template with parameters of type AccessionID

Modifier and Type	Method	Description
void	AbstractLocation.setAccession(AccessionID accession)

Constructors in org.biojava.nbio.core.sequence.location.template with parameters of type AccessionID

Constructor	Description
AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, List<Location> subLocations)	Default constructor

Uses of AccessionID in org.biojava.nbio.core.sequence.storage

Methods in org.biojava.nbio.core.sequence.storage that return AccessionID

Modifier and Type	Method	Description
AccessionID	ArrayListSequenceReader.getAccession()
AccessionID	BitSequenceReader.getAccession()
AccessionID	JoiningSequenceReader.getAccession()
AccessionID	SingleCompoundSequenceReader.getAccession()	Unsupoorted

Constructors in org.biojava.nbio.core.sequence.storage with parameters of type AccessionID

Constructor	Description
BitSequenceReader(BitSequenceReader.BitArrayWorker<C> worker, AccessionID accession)	Instance which allows you to supply a different @{BitArrayWorker} object.
FourBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession)
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C> worker, AccessionID accession)
TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession)
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker, AccessionID accession)

Uses of AccessionID in org.biojava.nbio.core.sequence.template

Methods in org.biojava.nbio.core.sequence.template that return AccessionID

Modifier and Type	Method	Description
AccessionID	AbstractSequence.getAccession()
AccessionID	Accessioned.getAccession()	Returns the AccessionID this location is currently bound with
AccessionID	SequenceProxyView.getAccession()

Methods in org.biojava.nbio.core.sequence.template with parameters of type AccessionID

Modifier and Type	Method	Description
void	AbstractSequence.setAccession(AccessionID accession)