Class RateMatrixHandler

    • Constructor Detail

      • RateMatrixHandler

        public RateMatrixHandler​(NeoRateMatrix rateMatrix,
                                 double[] equilibriumFrequencies)
    • Method Detail

      • getEquilibriumFrequencies

        public final double[] getEquilibriumFrequencies()
      • getTransitionProbabilities

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

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

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

        public int getNumParameters()
        Description copied from interface: Parameterized
        get number of parameters
        Specified by:
        getNumParameters in interface Parameterized
        Returns:
        number of parameters
      • setParameter

        public void setParameter​(double param,
                                 int n)
        Description copied from interface: Parameterized
        set model parameter
        Specified by:
        setParameter in interface Parameterized
        Parameters:
        param - parameter value
        n - parameter number
      • getParameter

        public double getParameter​(int n)
        Description copied from interface: Parameterized
        get model parameter
        Specified by:
        getParameter in interface Parameterized
        Parameters:
        n - parameter number
        Returns:
        parameter value
      • setParameterSE

        public void setParameterSE​(double paramSE,
                                   int n)
        Description copied from interface: Parameterized
        set standard errors for model parameter
        Specified by:
        setParameterSE in interface Parameterized
        Parameters:
        paramSE - standard error of parameter value
        n - parameter number
      • getLowerLimit

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

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

        public double getDefaultValue​(int n)
        Description copied from interface: Parameterized
        get default value of parameter
        Specified by:
        getDefaultValue in interface Parameterized
        Parameters:
        n - parameter number
        Returns:
        default value