Class SimpleRateMatrixGroup

    • Constructor Detail

      • SimpleRateMatrixGroup

        public SimpleRateMatrixGroup​(NeoRateMatrix[] baseMatrices,
                                     double[] equilibriumFrequencies,
                                     double[] initialClassProbabilities,
                                     DataType dataType)
    • Method Detail

      • getNumberOfParameters

        public int getNumberOfParameters()
      • getLowerLimit

        public double getLowerLimit​(int n)
      • getUpperLimit

        public double getUpperLimit​(int n)
      • getDefaultValue

        public double getDefaultValue​(int n)
      • setParameters

        public void setParameters​(double[] parameters,
                                  double[] categoryProbabilities)
      • getTransitionProbabilities

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

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