broad.core.siphy.PiHMM Member List

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

addConservedPi(Matrix pi, String name)	broad.core.siphy.PiHMM
computePathLogLikelihood(MultipleAlignment alignment, short[] path, int initialStateIdx, int endStateIdx)	broad.core.siphy.PiHMM
createDefaultTwoStateChain(double l, double gamma, EvolutionaryModel model)	broad.core.siphy.PiHMM	static
createTwoStateChain(double l, double gamma, EvolutionaryModel model, Matrix otherPi)	broad.core.siphy.PiHMM	static
generateAlignment(List< Integer > emittedPath, String format)	broad.core.siphy.PiHMM	protected
main(String[] args)	broad.core.siphy.PiHMM	static
PiHMM(EvolutionaryModel neutral, int stateNumber)	broad.core.siphy.PiHMM
PiHMM(EvolutionaryModel neutral, double minExpectedElementLength, double expectedCoverage)	broad.core.siphy.PiHMM
runBackwardAlgorithm(MultipleAlignment alignment, ForwardResult< Map< String, Matrix >> forwardData)	broad.core.siphy.PiHMM
runForwardAlgorithm(MultipleAlignment alignment)	broad.core.siphy.PiHMM
USAGE	broad.core.siphy.PiHMM	static
viterbiMostLikelyEstimation(MultipleAlignment alignment)	broad.core.siphy.PiHMM