Interface SubstitutionModel

    • Method Detail

      • getNumberOfTransitionCategories

        int getNumberOfTransitionCategories()
      • getTransitionCategoryProbability

        double getTransitionCategoryProbability​(int category)
      • getTransitionCategoryProbabilities

        double[] getTransitionCategoryProbabilities()
        Returns:
        all the category probabilites for each category respectively.
      • getTransitionProbabilities

        void getTransitionProbabilities​(double branchLength,
                                        double[][][] tableStore)
        Table is organized as [transition_group][from][to]
      • getTransitionProbabilitiesTranspose

        void getTransitionProbabilitiesTranspose​(double branchLength,
                                                 double[][][] tableStore)
        Table is organized as [transition_group][to][from]
      • getTransitionProbabilities

        void getTransitionProbabilities​(double branchLength,
                                        int category,
                                        double[][] tableStore)
        Table is organized as [transition_group][from][to]
      • getTransitionProbabilitiesTranspose

        void getTransitionProbabilitiesTranspose​(double branchLength,
                                                 int category,
                                                 double[][] tableStore)
        Table is organized as [transition_group][to][from]
      • getEquilibriumFrequencies

        double[] getEquilibriumFrequencies()
        Should return a double[] array of the related equilibrium frequencies. As a rule, callers should not alter the returned array (it may be used internally)
      • clone

        java.lang.Object clone()