Class MultiRateMatrixHandler

    • Constructor Detail

      • MultiRateMatrixHandler

        public MultiRateMatrixHandler​(NeoRateMatrix[] rateMatrices,
                                      double[] equilibriumFrequencies,
                                      double[] initialClassProportions)
    • Method Detail

      • setSubstitutionClassProbabilities

        public void setSubstitutionClassProbabilities​(double[] classProportions)
      • setSubstitutionClassProbabilities

        public void setSubstitutionClassProbabilities​(double[] classProportions,
                                                      int startIndex)
      • getNumberOfSubstitutionClasses

        public final int getNumberOfSubstitutionClasses()
      • getEquilibriumFrequencies

        public final double[] getEquilibriumFrequencies()
      • getTransitionProbabilities

        public void getTransitionProbabilities​(double distance,
                                               double[][][] store)
      • getTransitionProbabilities

        public void getTransitionProbabilities​(double distance,
                                               int category,
                                               double[][] store)
      • getTransitionProbabilitiesTranspose

        public void getTransitionProbabilitiesTranspose​(double distance,
                                                        double[][][] store)
      • getTransitionProbabilitiesTranspose

        public void getTransitionProbabilitiesTranspose​(double distance,
                                                        int category,
                                                        double[][] store)
      • report

        public void report​(java.io.PrintWriter out)
        Reporting stuff
        Parameters:
        out - where to report too
      • getSubstitutionClassLowerLimit

        public final double getSubstitutionClassLowerLimit()
      • getSubstitutionClassUpperLimit

        public final double getSubstitutionClassUpperLimit()
      • getSubstitutionClassDefaultValue

        public final double getSubstitutionClassDefaultValue()
      • getLowerLimit

        public double getLowerLimit​(int n)
        Description copied from interface: NeoParameterized
        get lower parameter limit
        Specified by:
        getLowerLimit in interface NeoParameterized
        Parameters:
        n - parameter number
        Returns:
        lower bound
      • getUpperLimit

        public double getUpperLimit​(int n)
        Description copied from interface: NeoParameterized
        get upper parameter limit
        Specified by:
        getUpperLimit in interface NeoParameterized
        Parameters:
        n - parameter number
        Returns:
        upper bound
      • getDefaultValue

        public double getDefaultValue​(int n)
      • setAllParameters

        public void setAllParameters​(double[] rateParameters,
                                     double[] classProportions)
      • setParameters

        public void setParameters​(double[] parameters,
                                  int startIndex)
        Description copied from interface: NeoParameterized
        set model parameter
        Specified by:
        setParameters in interface NeoParameterized
        Parameters:
        parameters - the array holding the parameters
        startIndex - the index into the array that the related parameters start at
      • getParameters

        public void getParameters​(double[] parameterStore,
                                  int startIndex)
        Description copied from interface: NeoParameterized
        get model parameter
        Specified by:
        getParameters in interface NeoParameterized
        startIndex - the index into the array that the related parameters start at