broad.core.siphy.TreeScaler Member List

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

encodeAsMatrix()	broad.core.siphy.TreeScaler
fitPI(Phylogeny alnTree, int i)	broad.core.siphy.TreeScaler
getLogLikelihood(double omega, Phylogeny alnTree, int startPosition, int window)	broad.core.siphy.TreeScaler
getMinimumTreeLength()	broad.core.siphy.TreeScaler
getModel()	broad.core.siphy.TreeScaler
getTotalDistanceFromNode(PhylogenyNode n)	broad.core.siphy.TreeScaler
main(String[] args)	broad.core.siphy.TreeScaler	static
scaleRegion(List< String > ignoreList, GenomicAnnotation region)	broad.core.siphy.TreeScaler
scaleRegion(Annotation region)	broad.core.siphy.TreeScaler
scaleTree(int window, BufferedWriter bw, List< String > ignoreList, int overlap)	broad.core.siphy.TreeScaler
scaleTree(int window, List< String > ignoreList, int overlap)	broad.core.siphy.TreeScaler
scaleTreeWithSampling(int window, BufferedWriter bw, List< String > ignoreList, int numberToAverage)	broad.core.siphy.TreeScaler
setAlignment(String alnFile, String alnFileFormat)	broad.core.siphy.TreeScaler
setAlignment(MultipleAlignment alignment)	broad.core.siphy.TreeScaler
setMinimumTreeLength(double minimumTreeLength)	broad.core.siphy.TreeScaler
setModel(EvolutionaryModel model)	broad.core.siphy.TreeScaler
setNeutralModel(File modelFile)	broad.core.siphy.TreeScaler
slidePWM(PositionWeightMatrix pwm, double minSeedScore, short[] encodedRef, List< int[]> ungappedChunks, int numPermutations)	broad.core.siphy.TreeScaler
slidePWM(PositionWeightMatrix pwm, double minSeedScore, int numPermutations)	broad.core.siphy.TreeScaler
TreeScaler()	broad.core.siphy.TreeScaler
TreeScaler(Annotation region, File modelFile, String alnFile, String alnFileFormat)	broad.core.siphy.TreeScaler
USAGE	broad.core.siphy.TreeScaler	static