Class NeutralSelectionRateMatrixGroup

    • Constructor Detail

      • NeutralSelectionRateMatrixGroup

        public NeutralSelectionRateMatrixGroup​(MutableDouble kappaStore,
                                               double[] freqs,
                                               CodonTable table)
    • Method Detail

      • updateParameters

        public void updateParameters​(double[] categoryProbabilities)
        Description copied from interface: RateMatrixGroup
        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.
        Specified by:
        updateParameters in interface RateMatrixGroup
        Parameters:
        categoryProbabilities - the probabilities (summing to one) of each category (class) of substitution
      • getTransitionProbabilities

        public void getTransitionProbabilities​(double branchLength,
                                               int category,
                                               double[][] tableStore)
        Specified by:
        getTransitionProbabilities in interface RateMatrixGroup
      • getSummary

        public java.lang.String getSummary​(double[] categoryProbabilities)
        Specified by:
        getSummary in interface RateMatrixGroup