Class VT

    • Constructor Detail

      • VT

        public VT​(double[] f)
        constructor
        Parameters:
        f - amino acid 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
        Specified by:
        report in class AminoAcidModel
        Parameters:
        out - output stream
      • getOriginalFrequencies

        public static void getOriginalFrequencies​(double[] f)
        get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
        Parameters:
        f - array where amino acid frequencies will be stored
      • getOriginalFrequencies

        public static double[] getOriginalFrequencies()
        Returns:
        the frequencies of the original data set that formed the basis for the estimation of the rate matrix
      • getUniqueName

        public java.lang.String getUniqueName()
        Specified by:
        getUniqueName in interface RateMatrix
        Returns:
        a short unique human-readable identifier for this rate matrix.