Package pal.substmodel

Class CodonModel

java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.CodonModel
All Implemented Interfaces:
Serializable, Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix
Direct Known Subclasses:
YangCodonModel
public abstract class CodonModel extends AbstractRateMatrix implements RateMatrix, Serializable
base class for nucleotide rate matrices
Version:
$Id: CodonModel.java,v 1.5 2003/11/13 04:05:39 matt Exp $
Author:
Andrew Rambaut
See Also:

  • Constructor Details

    • CodonModel

      protected CodonModel(double[] f)

  • Method Details

    • getInstance

      public static CodonModel getInstance(int modelID, double[] params, double[] freq)
      Create codon substitution model according to model type
      Parameters:
      modelID - model code
      params - model parameters
      freq - model frequencies
      Returns:
      codon rate matrix

    • printFrequencies

      protected void printFrequencies(PrintWriter out)
      Overrides:
      printFrequencies in class AbstractRateMatrix

    • printRatios

      protected void printRatios(PrintWriter out)