Class JTT

All Implemented Interfaces:
Serializable, Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants

public class JTT extends AminoAcidModel implements XMLConstants
JTT model of amino acid evolution Jones, D. T., Taylor, W. R. and Thornton, J. M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Applic. Biosci., 8, 275-282.
Version:
$Id: JTT.java,v 1.7 2003/11/13 04:05:39 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:
  • Constructor Details

    • JTT

      public JTT(double[] f)
      constructor
      Parameters:
      f - amino acid frequencies
  • Method Details

    • getModelID

      public int getModelID()
      Description copied from class: AbstractRateMatrix
      get numerical code describing the model type
      Specified by:
      getModelID in interface RateMatrix
      Specified by:
      getModelID in class AbstractRateMatrix
      Returns:
      integer code identifying a substitution model
    • report

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

      protected void rebuildRateMatrix(double[][] rate, double[] parameters)
      Specified by:
      rebuildRateMatrix in class AbstractRateMatrix