Collaboration diagram for broad.core.siphy.ConservationUtils:

Static Public Member Functions
static void	setUninformativeNodes (Map< String, Matrix > column, List< String > sequences)

static void	setUninformativeNodes (Map< String, Matrix > column, List< String > sequences, int colIdx)

static Phylogeny	pruneTree (List< String > toPrune, Phylogeny tree)

static Phylogeny	pruneTree (String toPrune, Phylogeny tree)

static List< String >	getGappedSeqsInWindowMatrix (int window, Map< String, Matrix > alignmentMatrix, int start)

static MultipleAlignment	setUpAlignment (ArgumentMap argMap, String alnFile, String alnFileFormat, List< String > ignoreList, EvolutionaryModel model) throws IOException, ParseException, FileNotFoundException

static MultipleAlignment	setUpMAF (String alnFile, List< String > ignoreList, EvolutionaryModel model, int start, int end) throws IOException, ParseException, FileNotFoundException

static MultipleAlignment	setUpMAF (MAFIO mafio, List< String > ignoreList, EvolutionaryModel model, int start, int end) throws IOException, ParseException, FileNotFoundException

static MultipleAlignment	setUpMAF (MAFIO mafio, List< String > ignoreList, Phylogeny guideTree, int start, int end) throws IOException, ParseException, FileNotFoundException

static List< String >	commaSeparatedStringToList (String csvListStr)

Member Function Documentation

static List<String> broad.core.siphy.ConservationUtils.commaSeparatedStringToList ( String csvListStr )

static

static List<String> broad.core.siphy.ConservationUtils.getGappedSeqsInWindowMatrix	(	int	window,
		Map< String, Matrix >	alignmentMatrix,
		int	start
	)

static

static Phylogeny broad.core.siphy.ConservationUtils.pruneTree	(	List< String >	toPrune,
		Phylogeny	tree
	)

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static Phylogeny broad.core.siphy.ConservationUtils.pruneTree	(	String	toPrune,
		Phylogeny	tree
	)

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static void broad.core.siphy.ConservationUtils.setUninformativeNodes	(	Map< String, Matrix >	column,
		List< String >	sequences
	)

static

static void broad.core.siphy.ConservationUtils.setUninformativeNodes	(	Map< String, Matrix >	column,
		List< String >	sequences,
		int	colIdx
	)

static

static MultipleAlignment broad.core.siphy.ConservationUtils.setUpAlignment	(	ArgumentMap	argMap,
		String	alnFile,
		String	alnFileFormat,
		List< String >	ignoreList,
		EvolutionaryModel	model
	)		throws IOException, ParseException, FileNotFoundException

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static MultipleAlignment broad.core.siphy.ConservationUtils.setUpMAF	(	String	alnFile,
		List< String >	ignoreList,
		EvolutionaryModel	model,
		int	start,
		int	end
	)		throws IOException, ParseException, FileNotFoundException

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static MultipleAlignment broad.core.siphy.ConservationUtils.setUpMAF	(	MAFIO	mafio,
		List< String >	ignoreList,
		EvolutionaryModel	model,
		int	start,
		int	end
	)		throws IOException, ParseException, FileNotFoundException

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static MultipleAlignment broad.core.siphy.ConservationUtils.setUpMAF	(	MAFIO	mafio,
		List< String >	ignoreList,
		Phylogeny	guideTree,
		int	start,
		int	end
	)		throws IOException, ParseException, FileNotFoundException

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

Static Public Member Functions