Class NucleotideModel

java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.NucleotideModel
All Implemented Interfaces:
Serializable, Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix
Direct Known Subclasses:
F81, F84, GTR, HKY, TN

public abstract class NucleotideModel extends AbstractRateMatrix implements RateMatrix, Serializable
base class for nucleotide rate matrices
Version:
$Id: NucleotideModel.java,v 1.10 2003/11/30 05:29:22 matt Exp $
Author:
Korbinian Strimmer
See Also:
  • Constructor Details

    • NucleotideModel

      protected NucleotideModel(double[] f)
  • Method Details

    • getInstance

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

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

      protected void printRatios(PrintWriter out)