Collaboration diagram for broad.core.siphy.ConservedPWMScanner:

Public Member Functions
	ConservedPWMScanner (String pwmFile) throws IOException, ParseException

	ConservedPWMScanner (List< PositionWeightMatrix > matrices)

Iterator< PositionWeightMatrix >	getPWMiterator ()

void	setBackgroundModel (AnnotationReader<?extends GenomicAnnotation > reader, Map< String, Sequence > org) throws IOException

void	setModel (EvolutionaryModel model)

int	getAlignmentChunkSize ()

void	setAlignmentChunkSize (int alignmentChunkSize)

Map< PositionWeightMatrix, GenomicAnnotation >	scan (MAFIO chrMafIO, List< BED > annotations, int shuffles, float seedMinScore) throws IOException, ParseException

void	setIgnoreList (List< String > ignoreList)

Protected Member Functions
List< BED >	slidePWM (PositionWeightMatrix pwm, double minSeedScore, short[] encodedRef, List< int[]> ungappedChunks, int numPermutations)

Constructor & Destructor Documentation

broad.core.siphy.ConservedPWMScanner.ConservedPWMScanner ( String pwmFile ) throws IOException, ParseException

broad.core.siphy.ConservedPWMScanner.ConservedPWMScanner ( List< PositionWeightMatrix > matrices )

Member Function Documentation

int broad.core.siphy.ConservedPWMScanner.getAlignmentChunkSize ( )

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Iterator<PositionWeightMatrix> broad.core.siphy.ConservedPWMScanner.getPWMiterator ( )

Map<PositionWeightMatrix, GenomicAnnotation> broad.core.siphy.ConservedPWMScanner.scan	(	MAFIO	chrMafIO,
		List< BED >	annotations,
		int	shuffles,
		float	seedMinScore
	)		throws IOException, ParseException

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void broad.core.siphy.ConservedPWMScanner.setAlignmentChunkSize ( int alignmentChunkSize )

void broad.core.siphy.ConservedPWMScanner.setBackgroundModel	(	AnnotationReader<?extends GenomicAnnotation >	reader,
		Map< String, Sequence >	org
	)		throws IOException

void broad.core.siphy.ConservedPWMScanner.setIgnoreList ( List< String > ignoreList )

void broad.core.siphy.ConservedPWMScanner.setModel ( EvolutionaryModel model )

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

protected

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