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

Packages that use GeneSequence

Package	Description
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.io
org.biojava.nbio.genome
org.biojava.nbio.genome.homology

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

Methods in org.biojava.nbio.core.sequence that return GeneSequence

Modifier and Type	Method and Description
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.
GeneSequence	ChromosomeSequence.getGene(String accession) Get the gene based on accession.
GeneSequence	ChromosomeSequence.removeGeneSequence(String accession)

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

Modifier and Type	Method and Description
LinkedHashMap<String,GeneSequence>	ChromosomeSequence.getGeneSequences() Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.

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

Constructor and Description
ExonSequence(GeneSequence parentGeneSequence, int bioBegin, int bioEnd) Need a parent gene sequence and the bioBegin and bioEnd.
IntronSequence(GeneSequence parentGeneSequence, int begin, int end) Place holder for Intron sequence features
TranscriptSequence(GeneSequence parentDNASequence, int begin, int end)

Uses of GeneSequence in org.biojava.nbio.core.sequence.io

Method parameters in org.biojava.nbio.core.sequence.io with type arguments of type GeneSequence

Modifier and Type	Method and Description
static void	FastaWriterHelper.writeGeneSequence(File file, Collection<GeneSequence> geneSequences, boolean showExonUppercase) Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
static void	FastaWriterHelper.writeGeneSequence(OutputStream outputStream, Collection<GeneSequence> geneSequences, boolean showExonUppercase) Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence

Constructor parameters in org.biojava.nbio.core.sequence.io with type arguments of type GeneSequence

Constructor and Description
FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase)
FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase)
FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase, int lineLength)
FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase, int lineLength)

Uses of GeneSequence in org.biojava.nbio.genome

Methods in org.biojava.nbio.genome that return types with arguments of type GeneSequence

Modifier and Type	Method and Description
static LinkedHashMap<String,GeneSequence>	GeneFeatureHelper.getGeneSequences(Collection<ChromosomeSequence> chromosomeSequences)

Uses of GeneSequence in org.biojava.nbio.genome.homology

Method parameters in org.biojava.nbio.genome.homology with type arguments of type GeneSequence

Modifier and Type	Method and Description
void	GFF3FromUniprotBlastHits.process(File xmlBlastHits, double ecutoff, LinkedHashMap<String,GeneSequence> geneSequenceHashMap, OutputStream gff3Output)
void	GFF3FromUniprotBlastHits.process(LinkedHashMap<String,ArrayList<String>> hits, LinkedHashMap<String,GeneSequence> geneSequenceHashMap, OutputStream gff3Output)