Class F84

    • Field Detail

      • EXPECTED_TS_TV_PARAMETER_INDEX

        public static final int EXPECTED_TS_TV_PARAMETER_INDEX
        See Also:
        Constant Field Values
    • Constructor Detail

      • F84

        public F84​(double expectedTsTv,
                   double[] freq)
        constructor 1
        Parameters:
        expectedTsTv - expected transition-transversion ratio
        freq - nucleotide frequencies
      • F84

        public F84​(double[] params,
                   double[] freq)
        Constructor 2
        Parameters:
        params - parameter list
        freq - nucleotide frequencies
    • Method Detail

      • report

        public void report​(java.io.PrintWriter out)
        Description copied from interface: Report
        print human readable report (e.g., on parameters and associated model)
        Specified by:
        report in interface Report
        Parameters:
        out - output stream
      • getNumParameters

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

        public java.lang.String getUniqueName()
        Specified by:
        getUniqueName in interface RateMatrix
        Returns:
        the name of this rate matrix
      • getParameterName

        public java.lang.String getParameterName​(int i)
        Specified by:
        getParameterName in interface NamedParameterized
        Returns:
        a short identifier for this parameter type. Should be the same for all instances of a given class!
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object