Public Member Functions
	NeighborAnalysis ()

	NeighborAnalysis (String setname, String refname) throws IOException

	NeighborAnalysis (BEDFileParser newGeneSet, BEDFileParser newRefSet) throws IOException

void	getNeighbors (BEDFileParser neighborsBed, BufferedWriter bw, boolean toWrite, double distThreshold) throws IOException

void	updateDistanceToNeighbors () throws IOException

GeneWithIsoforms[]	getNeighbors (Gene g) throws IOException

double[]	getNeighborDistance (Gene g) throws IOException

Static Public Member Functions
static void	main (String[] args) throws Exception

static GeneWithIsoforms	getLeftNeighbor (Gene g, BEDFileParser ref)

static GeneWithIsoforms	getRightNeighbor (Gene g, BEDFileParser ref)

Constructor & Destructor Documentation

broad.pda.gene.NeighborAnalysis.NeighborAnalysis ( )

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broad.pda.gene.NeighborAnalysis.NeighborAnalysis	(	String	setname,
		String	refname
	)		throws IOException

broad.pda.gene.NeighborAnalysis.NeighborAnalysis	(	BEDFileParser	newGeneSet,
		BEDFileParser	newRefSet
	)		throws IOException

Member Function Documentation

static GeneWithIsoforms broad.pda.gene.NeighborAnalysis.getLeftNeighbor	(	Gene	g,
		BEDFileParser	ref
	)

static

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double [] broad.pda.gene.NeighborAnalysis.getNeighborDistance ( Gene g ) throws IOException

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void broad.pda.gene.NeighborAnalysis.getNeighbors	(	BEDFileParser	neighborsBed,
		BufferedWriter	bw,
		boolean	toWrite,
		double	distThreshold
	)		throws IOException