Collaboration diagram for broad.core.siphy.TreeScalerIO:

Public Member Functions
	TreeScalerIO (int windowSize)

void	loadIntoDistribution (File source, EmpiricalDistribution ed, boolean shortFormat) throws IOException

	TreeScalerIO ()

void	parse (File source, int shift, String chr) throws IOException

void	load (InputStream is, int shift, String chr) throws IOException

void	load (File source, int shift, String chr) throws IOException

void	load (InputStream is) throws IOException

void	loadIntegrated (File source, double minPVal) throws IOException

void	loadOldIntegrated (File source, int shift, String chr, double minPVal) throws IOException

void	addListener (ScaledWindowParserListener listener)

void	loadAtMostRandom (File source, String chr, int maxNeutralOmegas) throws IOException

void	stitch (int window, int skip)

void	writeFull (BufferedWriter bw, List< ScaledWindow > windows) throws IOException

void	writeFull (BufferedWriter bw) throws IOException

void	writeFullAsGenomeGraphUsingLogPval (BufferedWriter bw) throws IOException

void	addWindow (ScaledWindow sw)

List< ScaledWindow >	getScaledWindows ()

void	clear ()

void	setNumberFormatter (DecimalFormat formatter)

int	getEstimationWindow ()

void	setEstimationWindow (int estimationWindow)

int	getTotalInSources ()

void	permute ()

Constructor & Destructor Documentation

broad.core.siphy.TreeScalerIO.TreeScalerIO ( int windowSize )

broad.core.siphy.TreeScalerIO.TreeScalerIO ( )

Member Function Documentation

void broad.core.siphy.TreeScalerIO.addListener ( ScaledWindowParserListener listener )

void broad.core.siphy.TreeScalerIO.addWindow ( ScaledWindow sw )

void broad.core.siphy.TreeScalerIO.clear ( )

int broad.core.siphy.TreeScalerIO.getEstimationWindow ( )

List<ScaledWindow> broad.core.siphy.TreeScalerIO.getScaledWindows ( )

Here is the caller graph for this function:

int broad.core.siphy.TreeScalerIO.getTotalInSources ( )

void broad.core.siphy.TreeScalerIO.load	(	InputStream	is,
		int	shift,
		String	chr
	)		throws IOException

Here is the caller graph for this function:

void broad.core.siphy.TreeScalerIO.load	(	File	source,
		int	shift,
		String	chr
	)		throws IOException

Here is the call graph for this function:

void broad.core.siphy.TreeScalerIO.load ( InputStream is ) throws IOException

Here is the call graph for this function:

void broad.core.siphy.TreeScalerIO.loadAtMostRandom	(	File	source,
		String	chr,
		int	maxNeutralOmegas
	)		throws IOException

void broad.core.siphy.TreeScalerIO.loadIntegrated	(	File	source,
		double	minPVal
	)		throws IOException

void broad.core.siphy.TreeScalerIO.loadIntoDistribution	(	File	source,
		EmpiricalDistribution	ed,
		boolean	shortFormat
	)		throws IOException

void broad.core.siphy.TreeScalerIO.loadOldIntegrated	(	File	source,
		int	shift,
		String	chr,
		double	minPVal
	)		throws IOException

void broad.core.siphy.TreeScalerIO.parse	(	File	source,
		int	shift,
		String	chr
	)		throws IOException

void broad.core.siphy.TreeScalerIO.permute ( )

void broad.core.siphy.TreeScalerIO.setEstimationWindow ( int estimationWindow )

void broad.core.siphy.TreeScalerIO.setNumberFormatter ( DecimalFormat formatter )

void broad.core.siphy.TreeScalerIO.stitch	(	int	window,
		int	skip
	)

void broad.core.siphy.TreeScalerIO.writeFull	(	BufferedWriter	bw,
		List< ScaledWindow >	windows
	)		throws IOException

Here is the caller graph for this function:

void broad.core.siphy.TreeScalerIO.writeFull ( BufferedWriter bw ) throws IOException

Here is the call graph for this function:

void broad.core.siphy.TreeScalerIO.writeFullAsGenomeGraphUsingLogPval ( BufferedWriter bw ) throws IOException

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