| changeBackground(double pA, double pC, double pG, double pT) | broad.core.siphy.EvolutionaryModel | |
| changeBackground(Matrix newPi) | broad.core.siphy.EvolutionaryModel | |
| computeJMatrix(PhylogenyNode node) | broad.core.siphy.EvolutionaryModel | |
| computeLikelihood(Map< String, Matrix > leafValues, PhylogenyNode root, int site) | broad.core.siphy.EvolutionaryModel | |
| computeTransitions(double branchLength) | broad.core.siphy.EvolutionaryModel | |
| copy() | broad.core.siphy.EvolutionaryModel | |
| EvolutionaryModel(EvolutionaryModelParameters parameters) | broad.core.siphy.EvolutionaryModel | |
| evolve(String sequence) | broad.core.siphy.EvolutionaryModel | |
| fitOmega(Map< String, Matrix > leafValues, Phylogeny tree, int window) | broad.core.siphy.EvolutionaryModel | |
| fitPI(Map< String, Matrix > alignmentColumn, Phylogeny tree) | broad.core.siphy.EvolutionaryModel | |
| getAlphabetSize() | broad.core.siphy.EvolutionaryModel | |
| getModelParameters() | broad.core.siphy.EvolutionaryModel | |
| getNodeLikelihoodParameterMap() | broad.core.siphy.EvolutionaryModel | |
| getParameters() | broad.core.siphy.EvolutionaryModel | |
| getPi() | broad.core.siphy.EvolutionaryModel | |
| getPVal(OmegaFit fit, boolean useLogOddsLikelihood) | broad.core.siphy.EvolutionaryModel | |
| getRateMatrix() | broad.core.siphy.EvolutionaryModel | protected |
| getTree() | broad.core.siphy.EvolutionaryModel | |
| omegaEMIteration(Map< String, Matrix > leafValues, PhylogenyNode root, double newOmega, int window) | broad.core.siphy.EvolutionaryModel | |
| piEMIteration(Map< String, Matrix > column, PhylogenyNode root, Matrix newPI) | broad.core.siphy.EvolutionaryModel | |
| pruneAndPeel(Map< String, Matrix > leafValues, PhylogenyNode root, int site) | broad.core.siphy.EvolutionaryModel | |
| pruneTree(List< String > ignoreList) | broad.core.siphy.EvolutionaryModel | |
| resetPI() | broad.core.siphy.EvolutionaryModel | |
| RPIDecomposition() | broad.core.siphy.EvolutionaryModel | |
| sample() | broad.core.siphy.EvolutionaryModel | |
| sample(PhylogenyNode node, short parentState) | broad.core.siphy.EvolutionaryModel | |
| setAlphabetSize(int alphabetSize) | broad.core.siphy.EvolutionaryModel | |
| setModelParameters(EvolutionaryModelParameters parameters) | broad.core.siphy.EvolutionaryModel | |
| setNeutralOmegaDistribution(String neutralOmegaFile) | broad.core.siphy.EvolutionaryModel | |
| setOmega(double omega) | broad.core.siphy.EvolutionaryModel | |
| setOmegaDistByTreeLength(String neutralOmegaDistributionByTreeLengthFile) | broad.core.siphy.EvolutionaryModel | |
| setParameters(EvolutionaryModelParameters parameters) | broad.core.siphy.EvolutionaryModel | |
| setPi(Matrix pi) | broad.core.siphy.EvolutionaryModel | |
1.8.7
