Uses of Class
util.bio.annotation.ExonIntron

Packages that use ExonIntron

gata.main	Main app, utility, and params for GATAPlotter.
trans.main	Principle classes and scripts used in TiMAT2 analysis.
util.bio.annotation	For representing gene annotation.
util.bio.parsers	Parsers and extractors, fasta, quality, text, gff....

Uses of ExonIntron in gata.main

Methods in gata.main with parameters of type ExonIntron

static java.util.ArrayList	GATAUtil.extractStartEnds(ExonIntron[] exons) Deep copies start stops from ExonIntron objects to an ArrayList
static int[][]	GATAUtil.extractStartEndsInts(ExonIntron[] exons)

Uses of ExonIntron in trans.main

Methods in trans.main with parameters of type ExonIntron

int[][]

ScanGenes.convertToIndexPositions(ExonIntron[] exons) Converts an array of ExonIntron to an int[exon number][start index in bp positions array, stop index]

Uses of ExonIntron in util.bio.annotation

Methods in util.bio.annotation that return ExonIntron

ExonIntron[]

TransGroup.getExons()

Methods in util.bio.annotation with parameters of type ExonIntron

static int[][]	GeneGroup.extractStartEndsInts(ExonIntron[] exons)
static java.util.ArrayList	GeneGroup.extractStartEnds(ExonIntron[] exons)

Constructors in util.bio.annotation with parameters of type ExonIntron

TransGroup(Transcript transcript, Translation translation, ExonIntron[] exons)

Uses of ExonIntron in util.bio.parsers

Methods in util.bio.parsers that return ExonIntron

ExonIntron[]

UCSCGeneLine.getExons()