broad.pda.gene.GeneWithIsoforms Member List

This is the complete list of members for broad.pda.gene.GeneWithIsoforms, including all inherited members.

AddAllIsoforms(GeneWithIsoforms overlapper)	broad.pda.gene.GeneWithIsoforms
AddAllIsoforms(GeneWithIsoforms overlapper, boolean updateMainIsoform)	broad.pda.gene.GeneWithIsoforms
AddAllIsoNotIncludedforms(GeneWithIsoforms other)	broad.pda.gene.GeneWithIsoforms
addContainedIsoform(Gene isoform)	broad.pda.gene.GeneWithIsoforms
AddIsoform(Gene gene)	broad.pda.gene.GeneWithIsoforms
AddIsoform(Gene gene, boolean updateMainIsoform)	broad.pda.gene.GeneWithIsoforms
addSuffixToName(String refName)	broad.pda.gene.GeneWithIsoforms
allIsoformsToBED()	broad.pda.gene.GeneWithIsoforms
almostContains(Gene other, int exonFudgeFactor)	broad.pda.gene.GeneWithIsoforms
almostContains(GeneWithIsoforms other, int exonFudgeFactor)	broad.pda.gene.GeneWithIsoforms
cleanIsoforms()	broad.pda.gene.GeneWithIsoforms
colapse(int exonFudgeFactor)	broad.pda.gene.GeneWithIsoforms
constituentIntrons()	broad.pda.gene.GeneWithIsoforms
constituentIsoform()	broad.pda.gene.GeneWithIsoforms
dedup()	broad.pda.gene.GeneWithIsoforms
expandUtrs(Integer utr1, Integer utr2)	broad.pda.gene.GeneWithIsoforms
findCompatibleGenes(IntervalTree< GeneWithIsoforms > overlapTree, int[] numIntrons)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(Collection<?extends LightweightGenomicAnnotation > exons)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(LightweightGenomicAnnotation align)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(String pslString)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(String chrString, int start, int end)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(String chr, int start, int end, String name, Strand orientation, Collection< Annotation > exons)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd, int blockStart, int blockEnd)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd, int blockStart, int blockEnd, String[] extraData)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd, String[] extraData)	broad.pda.gene.GeneWithIsoforms
GeneWithIsoforms(Gene gene)	broad.pda.gene.GeneWithIsoforms
getAllIsoformExonSet()	broad.pda.gene.GeneWithIsoforms
getAllIsoformIntronSet()	broad.pda.gene.GeneWithIsoforms
getAllIsoforms()	broad.pda.gene.GeneWithIsoforms
getAllIsoforms(boolean includeContainingIsoform)	broad.pda.gene.GeneWithIsoforms
getMerged()	broad.pda.gene.GeneWithIsoforms
getNumberOfIsoforms()	broad.pda.gene.GeneWithIsoforms
getScoredExons()	broad.pda.gene.GeneWithIsoforms
hasOverlapping3PUTR(GeneWithIsoforms other)	broad.pda.gene.GeneWithIsoforms
hasOverlapping5PUTR(GeneWithIsoforms other)	broad.pda.gene.GeneWithIsoforms
IsExactOverlappingIsoform(Gene gene)	broad.pda.gene.GeneWithIsoforms
overlaps(Gene other)	broad.pda.gene.GeneWithIsoforms
overlapsByGenomicRegion(IntervalTree< GeneWithIsoforms > otherTree, boolean considerOrientation)	broad.pda.gene.GeneWithIsoforms
overlapsExon(LightweightGenomicAnnotation exon)	broad.pda.gene.GeneWithIsoforms
overlapsExon(Gene gene)	broad.pda.gene.GeneWithIsoforms
selectRandIsoSubset(Integer maxIsoPerLoci)	broad.pda.gene.GeneWithIsoforms
setBedScore(double scr)	broad.pda.gene.GeneWithIsoforms
setExtraFields(double[] scores)	broad.pda.gene.GeneWithIsoforms
standardizeOreintation()	broad.pda.gene.GeneWithIsoforms
toString(String name)	broad.pda.gene.GeneWithIsoforms
updateScrToBedScore(double score)	broad.pda.gene.GeneWithIsoforms