broad.core.siphy.ConservationUtils Member List

This is the complete list of members for broad.core.siphy.ConservationUtils, including all inherited members.

commaSeparatedStringToList(String csvListStr)	broad.core.siphy.ConservationUtils	static
getGappedSeqsInWindowMatrix(int window, Map< String, Matrix > alignmentMatrix, int start)	broad.core.siphy.ConservationUtils	static
pruneTree(List< String > toPrune, Phylogeny tree)	broad.core.siphy.ConservationUtils	static
pruneTree(String toPrune, Phylogeny tree)	broad.core.siphy.ConservationUtils	static
setUninformativeNodes(Map< String, Matrix > column, List< String > sequences)	broad.core.siphy.ConservationUtils	static
setUninformativeNodes(Map< String, Matrix > column, List< String > sequences, int colIdx)	broad.core.siphy.ConservationUtils	static
setUpAlignment(ArgumentMap argMap, String alnFile, String alnFileFormat, List< String > ignoreList, EvolutionaryModel model)	broad.core.siphy.ConservationUtils	static
setUpMAF(String alnFile, List< String > ignoreList, EvolutionaryModel model, int start, int end)	broad.core.siphy.ConservationUtils	static
setUpMAF(MAFIO mafio, List< String > ignoreList, EvolutionaryModel model, int start, int end)	broad.core.siphy.ConservationUtils	static
setUpMAF(MAFIO mafio, List< String > ignoreList, Phylogeny guideTree, int start, int end)	broad.core.siphy.ConservationUtils	static