broad.core.siphy.TreeScaler Class Reference

Collaboration diagram for broad.core.siphy.TreeScaler:

Public Member Functions
	TreeScaler ()
	TreeScaler (Annotation region, File modelFile, String alnFile, String alnFileFormat) throws Exception
void	setAlignment (String alnFile, String alnFileFormat) throws Exception
void	encodeAsMatrix ()
double	getLogLikelihood (double omega, Phylogeny alnTree, int startPosition, int window)
PiFit	fitPI (Phylogeny alnTree, int i)
List< BED >	slidePWM (PositionWeightMatrix pwm, double minSeedScore, short[] encodedRef, List< int[]> ungappedChunks, int numPermutations)
List< BED >	slidePWM (PositionWeightMatrix pwm, double minSeedScore, int numPermutations)
OmegaFit	scaleRegion (List< String > ignoreList, GenomicAnnotation region)
OmegaFit	scaleRegion (Annotation region)
void	scaleTree (int window, BufferedWriter bw, List< String > ignoreList, int overlap) throws IOException
ArrayList< OmegaFit >	scaleTree (int window, List< String > ignoreList, int overlap) throws IOException
void	scaleTreeWithSampling (int window, BufferedWriter bw, List< String > ignoreList, int numberToAverage) throws IOException
void	setAlignment (MultipleAlignment alignment)
double	getTotalDistanceFromNode (PhylogenyNode n)
void	setNeutralModel (File modelFile) throws IOException, ParseException
double	getMinimumTreeLength ()
void	setMinimumTreeLength (double minimumTreeLength)
EvolutionaryModel	getModel ()
void	setModel (EvolutionaryModel model)

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

Static Public Attributes
static final String	USAGE

Constructor & Destructor Documentation

broad.core.siphy.TreeScaler.TreeScaler

(

)

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broad.core.siphy.TreeScaler.TreeScaler	(	Annotation	region,
		File	modelFile,
		String	alnFile,
		String	alnFileFormat
	)		throws Exception

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Member Function Documentation

void broad.core.siphy.TreeScaler.encodeAsMatrix

(

)

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PiFit broad.core.siphy.TreeScaler.fitPI	(	Phylogeny	alnTree,
		int	i
	)

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double broad.core.siphy.TreeScaler.getLogLikelihood	(	double	omega,
		Phylogeny	alnTree,
		int	startPosition,
		int	window
	)

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double broad.core.siphy.TreeScaler.getMinimumTreeLength

(

)

EvolutionaryModel broad.core.siphy.TreeScaler.getModel

(

)

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double broad.core.siphy.TreeScaler.getTotalDistanceFromNode

(

PhylogenyNode

n

)

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static void broad.core.siphy.TreeScaler.main ( String[]  args ) throws Exception

static

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OmegaFit broad.core.siphy.TreeScaler.scaleRegion	(	List< String >	ignoreList,
		GenomicAnnotation	region
	)

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OmegaFit broad.core.siphy.TreeScaler.scaleRegion

(

Annotation

region

)

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void broad.core.siphy.TreeScaler.scaleTree	(	int	window,
		BufferedWriter	bw,
		List< String >	ignoreList,
		int	overlap
	)		throws IOException

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ArrayList<OmegaFit> broad.core.siphy.TreeScaler.scaleTree	(	int	window,
		List< String >	ignoreList,
		int	overlap
	)		throws IOException

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void broad.core.siphy.TreeScaler.scaleTreeWithSampling	(	int	window,
		BufferedWriter	bw,
		List< String >	ignoreList,
		int	numberToAverage
	)		throws IOException

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void broad.core.siphy.TreeScaler.setAlignment	(	String	alnFile,
		String	alnFileFormat
	)		throws Exception

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void broad.core.siphy.TreeScaler.setAlignment

(

MultipleAlignment

alignment

)

void broad.core.siphy.TreeScaler.setMinimumTreeLength

(

double

minimumTreeLength

)

void broad.core.siphy.TreeScaler.setModel

(

EvolutionaryModel

model

)

void broad.core.siphy.TreeScaler.setNeutralModel

(

File

modelFile

)

throws IOException, ParseException

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List<BED> broad.core.siphy.TreeScaler.slidePWM	(	PositionWeightMatrix	pwm,
		double	minSeedScore,
		short[]	encodedRef,
		List< int[]>	ungappedChunks,
		int	numPermutations
	)

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List<BED> broad.core.siphy.TreeScaler.slidePWM	(	PositionWeightMatrix	pwm,
		double	minSeedScore,
		int	numPermutations
	)

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Member Data Documentation

final String broad.core.siphy.TreeScaler.USAGE

static

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

• java/broad/core/siphy/TreeScaler.java