Public Member Functions
	EstimateOmegaPerExon (File BEDFile, File modelFile, String alnDir, String alnFileFormat, String save) throws Exception

	EstimateOmegaPerExon (Collection< Gene > genes, File modelFile, String alnDir, String alnFileFormat, String save) throws Exception

Static Public Member Functions
static OmegaFit	fitOmega (Annotation align, File modelFile, String alnFile, String alnFileFormat) throws Exception

static ArrayList< OmegaFit >	slideWindowComputeOmega (Annotation align, File modelFile, String alnFile, String alnFileFormat, int windowSize, int overlap) throws Exception

static OmegaFit	fitOmega (Alignments align, TreeScaler scaler) throws Exception

static ArrayList< OmegaFit >	slideWindowComputeOmega (Alignments align, TreeScaler scaler, int windowSize, int overlap) throws Exception

static void	main (String[] args) throws Exception

Constructor & Destructor Documentation

broad.core.siphy.tools.conservation.EstimateOmegaPerExon.EstimateOmegaPerExon	(	File	BEDFile,
		File	modelFile,
		String	alnDir,
		String	alnFileFormat,
		String	save
	)		throws Exception

Here is the caller graph for this function:

broad.core.siphy.tools.conservation.EstimateOmegaPerExon.EstimateOmegaPerExon	(	Collection< Gene >	genes,
		File	modelFile,
		String	alnDir,
		String	alnFileFormat,
		String	save
	)		throws Exception

Member Function Documentation

static OmegaFit broad.core.siphy.tools.conservation.EstimateOmegaPerExon.fitOmega	(	Annotation	align,
		File	modelFile,
		String	alnFile,
		String	alnFileFormat
	)		throws Exception

static

static OmegaFit broad.core.siphy.tools.conservation.EstimateOmegaPerExon.fitOmega	(	Alignments	align,
		TreeScaler	scaler
	)		throws Exception

static

static void broad.core.siphy.tools.conservation.EstimateOmegaPerExon.main ( String[] args ) throws Exception

static

Here is the call graph for this function:

static ArrayList<OmegaFit> broad.core.siphy.tools.conservation.EstimateOmegaPerExon.slideWindowComputeOmega	(	Annotation	align,
		File	modelFile,
		String	alnFile,
		String	alnFileFormat,
		int	windowSize,
		int	overlap
	)		throws Exception

static

static ArrayList<OmegaFit> broad.core.siphy.tools.conservation.EstimateOmegaPerExon.slideWindowComputeOmega	(	Alignments	align,
		TreeScaler	scaler,
		int	windowSize,
		int	overlap
	)		throws Exception

static

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