Uses of Class
org.biojava3.core.sequence.AccessionID

Packages that use AccessionID

org.biojava3.core.sequence
org.biojava3.core.sequence.loader
org.biojava3.core.sequence.location
org.biojava3.core.sequence.location.template
org.biojava3.core.sequence.storage
org.biojava3.core.sequence.template

Uses of AccessionID in org.biojava3.core.sequence

Methods in org.biojava3.core.sequence with parameters of type AccessionID

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)
void	TranscriptSequence.addStopCodonSequence(AccessionID accession, int begin, int end)
TranscriptSequence	GeneSequence.addTranscript(AccessionID accession, int begin, int end) Add a transcription sequence to a gene which describes a ProteinSequence

Uses of AccessionID in org.biojava3.core.sequence.loader

Methods in org.biojava3.core.sequence.loader that return AccessionID

AccessionID	SequenceFileProxyLoader.getAccession()
AccessionID	StringProxySequenceReader.getAccession()
AccessionID	UniprotProxySequenceReader.getAccession()

Uses of AccessionID in org.biojava3.core.sequence.location

Methods in org.biojava3.core.sequence.location that return AccessionID

protected AccessionID

InsdcParser.getAccession(String accession)

Constructors in org.biojava3.core.sequence.location with parameters of type AccessionID

SimpleLocation(Point start, Point end, Strand strand, AccessionID accession)

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

Uses of AccessionID in org.biojava3.core.sequence.location.template

Methods in org.biojava3.core.sequence.location.template that return AccessionID

AccessionID

AbstractLocation.getAccession()

Methods in org.biojava3.core.sequence.location.template with parameters of type AccessionID

protected void

AbstractLocation.setAccession(AccessionID accession)

Constructors in org.biojava3.core.sequence.location.template with parameters of type AccessionID

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

Uses of AccessionID in org.biojava3.core.sequence.storage

Methods in org.biojava3.core.sequence.storage that return AccessionID

AccessionID	SingleCompoundSequenceReader.getAccession() Unsupoorted
AccessionID	BitSequenceReader.getAccession()
AccessionID	ArrayListSequenceReader.getAccession()
AccessionID	JoiningSequenceReader.getAccession()

Constructors in org.biojava3.core.sequence.storage with parameters of type AccessionID

BitSequenceReader(BitSequenceReader.BitArrayWorker<C> worker, AccessionID accession)
Instance which allows you to supply a different @{BitArrayWorker} object.

FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C> worker, AccessionID accession)

FourBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession)

TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession)

TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker, AccessionID accession)

Uses of AccessionID in org.biojava3.core.sequence.template

Methods in org.biojava3.core.sequence.template that return AccessionID

AccessionID	AbstractSequence.getAccession()
AccessionID	SequenceProxyView.getAccession()
AccessionID	Accessioned.getAccession() Returns the AccessionID this location is currently bound with

Methods in org.biojava3.core.sequence.template with parameters of type AccessionID

void	AbstractSequence.setAccession(AccessionID accession)