Package pal.substmodel

Class BLOSUM62

java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.AminoAcidModel
pal.substmodel.BLOSUM62
All Implemented Interfaces:
Serializable, Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants
public class BLOSUM62 extends AminoAcidModel implements XMLConstants
BLOSUM62 model of amino acid evolution
Version:
$Id: BLOSUM62.java,v 1.7 2003/11/13 04:05:39 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:

  • Constructor Details

    • BLOSUM62

      public BLOSUM62(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