Public Member Functions
	ComputeConservedMotifs (Alignments region, String pwmFile, String saveDir, String alignDir, String alignFormat, File modelFile) throws Exception

Static Public Member Functions
static String[]	getMotifNames (String pwmFile) throws Exception

static List< BED >[]	scoreMotifs (Alignments region, TreeScaler scaler, String alnFormat, String alignFile, String pwmFile, boolean reverseCompliment) throws Exception

static void	main (String[] args) throws Exception

Constructor & Destructor Documentation

broad.core.motif.misc.ComputeConservedMotifs.ComputeConservedMotifs	(	Alignments	region,
		String	pwmFile,
		String	saveDir,
		String	alignDir,
		String	alignFormat,
		File	modelFile
	)		throws Exception

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Member Function Documentation

static String [] broad.core.motif.misc.ComputeConservedMotifs.getMotifNames ( String pwmFile ) throws Exception

static

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static void broad.core.motif.misc.ComputeConservedMotifs.main ( String[] args ) throws Exception

static

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static List<BED> [] broad.core.motif.misc.ComputeConservedMotifs.scoreMotifs	(	Alignments	region,
		TreeScaler	scaler,
		String	alnFormat,
		String	alignFile,
		String	pwmFile,
		boolean	reverseCompliment
	)		throws Exception

static

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