Public Member Functions
	NeighborsNullModel ()

	NeighborsNullModel (String setname, String refname, int binsize, int permnum) throws IOException

	NeighborsNullModel (BEDFileParser setname, BEDFileParser refname, int binsize, int permnum) throws IOException

void	makeBinnedIntervalModel (boolean UseCustomBins)

void	makeNaiveRandModel (String chrSizeF) throws IOException

void	makeDartThrowingModel ()

ArrayList< GeneWithIsoforms[]>	getGeneRandNeighbors (Gene gene)

void	printRandNeighborsInfo ()

int	getPermNum ()

HashMap< Gene, ArrayList < GeneWithIsoforms[]> >	getGeneRandNeighbors ()

Collection< Gene >	getUniqueNeighbors ()

Constructor & Destructor Documentation

broad.pda.gene.NeighborsNullModel.NeighborsNullModel ( )

broad.pda.gene.NeighborsNullModel.NeighborsNullModel	(	String	setname,
		String	refname,
		int	binsize,
		int	permnum
	)		throws IOException

broad.pda.gene.NeighborsNullModel.NeighborsNullModel	(	BEDFileParser	setname,
		BEDFileParser	refname,
		int	binsize,
		int	permnum
	)		throws IOException

Member Function Documentation

ArrayList<GeneWithIsoforms[]> broad.pda.gene.NeighborsNullModel.getGeneRandNeighbors ( Gene gene )

HashMap<Gene, ArrayList<GeneWithIsoforms[]> > broad.pda.gene.NeighborsNullModel.getGeneRandNeighbors ( )

int broad.pda.gene.NeighborsNullModel.getPermNum ( )

Collection<Gene> broad.pda.gene.NeighborsNullModel.getUniqueNeighbors ( )

void broad.pda.gene.NeighborsNullModel.makeBinnedIntervalModel ( boolean UseCustomBins )

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void broad.pda.gene.NeighborsNullModel.makeDartThrowingModel ( )

void broad.pda.gene.NeighborsNullModel.makeNaiveRandModel ( String chrSizeF ) throws IOException

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void broad.pda.gene.NeighborsNullModel.printRandNeighborsInfo ( )

The documentation for this class was generated from the following file: