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()