Class Dayhoff

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants

    public class Dayhoff
    extends AminoAcidModel
    implements XMLConstants
    Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978) A model of evolutionary change in proteins. Dayhoff, M.O. (ed.) Atlas of Protein Sequence Structur., Vol5, Suppl. 3, National Biomedical Research Foundation, Washington DC, pp. 345-352.
    Version:
    $Id: Dayhoff.java,v 1.7 2003/11/13 04:05:39 matt Exp $
    Author:
    Korbinian Strimmer
    See Also:
    Serialized Form
    • Constructor Detail

      • Dayhoff

        public Dayhoff​(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.