broad.pda.seq.graph.Path Member List

This is the complete list of members for broad.pda.seq.graph.Path, including all inherited members.

addEdge(BubbleEdge edge)	broad.pda.seq.graph.Path
addEdges(Collection< BubbleEdge > edges)	broad.pda.seq.graph.Path
addPairedEnd(Alignment align)	broad.pda.seq.graph.Path
addPairedEndEdges(Collection< Alignment > pairedEndEdges2)	broad.pda.seq.graph.Path
compareTo(Path b)	broad.pda.seq.graph.Path
copy()	broad.pda.seq.graph.Path
equals(Object o)	broad.pda.seq.graph.Path
getAlignment()	broad.pda.seq.graph.Path
getChromosome()	broad.pda.seq.graph.Path
getCoverage()	broad.pda.seq.graph.Path
getEdgeList()	broad.pda.seq.graph.Path
getEdges()	broad.pda.seq.graph.Path
getEnd()	broad.pda.seq.graph.Path
getEndVertex()	broad.pda.seq.graph.Path
getGraph()	broad.pda.seq.graph.Path
getLocalLambda()	broad.pda.seq.graph.Path
getNodeCount(Annotation v1)	broad.pda.seq.graph.Path
getNumberOfEdges()	broad.pda.seq.graph.Path
getOrientation()	broad.pda.seq.graph.Path
getOverlappingNodes(Alignment read)	broad.pda.seq.graph.Path
getPairedEndEdges()	broad.pda.seq.graph.Path
getPercentConsistent(EmpiricalDistribution pairedInsertDistribution)	broad.pda.seq.graph.Path
getScore()	broad.pda.seq.graph.Path
getSize()	broad.pda.seq.graph.Path
getSortedNodes()	broad.pda.seq.graph.Path
getSpliceWeight()	broad.pda.seq.graph.Path
getStart()	broad.pda.seq.graph.Path
getStartVertex()	broad.pda.seq.graph.Path
getWeight()	broad.pda.seq.graph.Path
hashCode()	broad.pda.seq.graph.Path
isToComplex()	broad.pda.seq.graph.Path
overlaps(Path leftPath)	broad.pda.seq.graph.Path
overlapsLeft(Alignment read)	broad.pda.seq.graph.Path
overlapsRight(Alignment read)	broad.pda.seq.graph.Path
Path(Collection< BubbleEdge > edges, double spliceWeight)	broad.pda.seq.graph.Path
Path(Collection< BubbleEdge > edges, Transformer< BubbleEdge, Number > transformer, double spliceWeight)	broad.pda.seq.graph.Path
Path(double spliceWeight)	broad.pda.seq.graph.Path
Path()	broad.pda.seq.graph.Path
Path(Gene gene, ChromosomeWithBubblesJGraphT graph)	broad.pda.seq.graph.Path
removeEdge(BubbleEdge edge)	broad.pda.seq.graph.Path
setIsToComplex(boolean isToComplex)	broad.pda.seq.graph.Path
setLocalLambda(double localLambda)	broad.pda.seq.graph.Path
setSpliceWeight(double weight)	broad.pda.seq.graph.Path
toFilledInGene()	broad.pda.seq.graph.Path
toGene()	broad.pda.seq.graph.Path
toGene(double[] extraFields)	broad.pda.seq.graph.Path
toString()	broad.pda.seq.graph.Path