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

Packages that use ChromosomeSequence

Package	Description
org.biojava.nbio.core.sequence
org.biojava.nbio.genome
org.biojava.nbio.genome.parsers.gff

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

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

Modifier and Type	Method and Description
ChromosomeSequence	GeneSequence.getParentChromosomeSequence() The parent ChromosomeSequence which contains the actual DNA sequence data

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

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

Uses of ChromosomeSequence in org.biojava.nbio.genome

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

Modifier and Type	Method and Description
static LinkedHashMap<String,ChromosomeSequence>	GeneFeatureHelper.getChromosomeSequenceFromDNASequence(LinkedHashMap<String,DNASequence> dnaSequenceList)
static LinkedHashMap<String,ChromosomeSequence>	GeneFeatureHelper.loadFastaAddGeneFeaturesFromGeneIDGFF2(File fastaSequenceFile, File gffFile) Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm
static LinkedHashMap<String,ChromosomeSequence>	GeneFeatureHelper.loadFastaAddGeneFeaturesFromGeneMarkGTF(File fastaSequenceFile, File gffFile)
static LinkedHashMap<String,ChromosomeSequence>	GeneFeatureHelper.loadFastaAddGeneFeaturesFromGlimmerGFF3(File fastaSequenceFile, File gffFile)
static LinkedHashMap<String,ChromosomeSequence>	GeneFeatureHelper.loadFastaAddGeneFeaturesFromGmodGFF3(File fastaSequenceFile, File gffFile, boolean lazyloadsequences) Lots of variations in the ontology or descriptors that can be used in GFF3 which requires writing a custom parser to handle a GFF3 generated or used by a specific application.
static LinkedHashMap<String,ChromosomeSequence>	GeneFeatureHelper.loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File fastaSequenceFile, File uppercaseFastaFile, boolean throwExceptionGeneNotFound)

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

Modifier and Type	Method and Description
static void	GeneFeatureHelper.addGeneIDGFF2GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences
static void	GeneFeatureHelper.addGeneMarkGTFGeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
static void	GeneFeatureHelper.addGlimmerGFF3GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
static void	GeneFeatureHelper.addGmodGFF3GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete
static LinkedHashMap<String,GeneSequence>	GeneFeatureHelper.getGeneSequences(Collection<ChromosomeSequence> chromosomeSequences)
static LinkedHashMap<String,ProteinSequence>	GeneFeatureHelper.getProteinSequences(Collection<ChromosomeSequence> chromosomeSequences)

Uses of ChromosomeSequence in org.biojava.nbio.genome.parsers.gff

Method parameters in org.biojava.nbio.genome.parsers.gff with type arguments of type ChromosomeSequence

Modifier and Type	Method and Description
void	GFF3Writer.write(OutputStream outputStream, LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList) Output gff3 format for a DNA Sequence