Uses of Class
org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

Packages that use GeneChromosomePosition

Package	Description
org.biojava.nbio.genome.parsers.genename
org.biojava.nbio.genome.util

Uses of GeneChromosomePosition in org.biojava.nbio.genome.parsers.genename

Methods in org.biojava.nbio.genome.parsers.genename that return types with arguments of type GeneChromosomePosition

Modifier and Type	Method and Description
static java.util.List<GeneChromosomePosition>	GeneChromosomePositionParser.getChromosomeMappings()
static java.util.List<GeneChromosomePosition>	GeneChromosomePositionParser.getChromosomeMappings(java.io.InputStream inStream)

Methods in org.biojava.nbio.genome.parsers.genename with parameters of type GeneChromosomePosition

Modifier and Type	Method and Description
int	GeneChromosomePosition.compareTo(GeneChromosomePosition o)

Uses of GeneChromosomePosition in org.biojava.nbio.genome.util

Methods in org.biojava.nbio.genome.util with parameters of type GeneChromosomePosition

Modifier and Type	Method and Description
static java.lang.String	ChromosomeMappingTools.formatExonStructure(GeneChromosomePosition chromosomePosition) Pretty print the details of a GeneChromosomePosition to a String
static java.util.List<com.google.common.collect.Range<java.lang.Integer>>	ChromosomeMappingTools.getCDSExonRanges(GeneChromosomePosition chromPos) Extracts the exon boundaries in CDS coordinates.
static int	ChromosomeMappingTools.getCDSLength(GeneChromosomePosition chromPos) Get the length of the CDS in nucleotides.
static int	ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosomePosition chromosomePosition) I have a genomic coordinate, where is it on the mRNA
static java.util.List<com.google.common.collect.Range<java.lang.Integer>>	ChromosomeMappingTools.getChromosomalRangesForCDS(GeneChromosomePosition chromPos) Extracts the boundaries of the coding regions in chromosomal coordinates
static ChromPos	ChromosomeMappingTools.getChromosomePosForCDScoordinate(int cdsNucleotidePosition, GeneChromosomePosition chromPos) Maps the position of a CDS nucleotide back to the genome
static DNASequence	ChromosomeMappingTools.getTranscriptDNASequence(TwoBitFacade twoBitFacade, GeneChromosomePosition gcp) Extracts the DNA sequence transcribed from the input genetic coordinates.