Interface RateMatrixGroup

    • Method Detail

      • getEquilibriumFrequencies

        double[] getEquilibriumFrequencies()
      • updateParameters

        void updateParameters​(double[] categoryProbabilities)
        Update internal representation based on any parameters (that are specified externally) and the given category probablitilies. The controller (user of this class) should be calling this method after the parameters of an external parameterization object have been set.
        Parameters:
        categoryProbabilities - the probabilities (summing to one) of each category (class) of substitution
      • getNumberOfTransitionCategories

        int getNumberOfTransitionCategories()
      • getTransitionProbabilities

        void getTransitionProbabilities​(double branchLength,
                                        double[][][] tableStore)
      • getTransitionProbabilitiesTranspose

        void getTransitionProbabilitiesTranspose​(double branchLength,
                                                 double[][][] tableStore)
      • getTransitionProbabilities

        void getTransitionProbabilities​(double branchLength,
                                        int category,
                                        double[][] tableStore)
      • getTransitionProbabilitiesTranspose

        void getTransitionProbabilitiesTranspose​(double branchLength,
                                                 int category,
                                                 double[][] tableStore)
      • getSummary

        java.lang.String getSummary​(double[] categoryProbabilities)