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Class Blosum62

  extended by org.jaga.individualRepresentation.proteinLocation.SubstitutionScoringMatrix
      extended by org.jaga.individualRepresentation.proteinLocation.Blosum62

public class Blosum62
extends SubstitutionScoringMatrix

TODO: Complete these comments.

Project: JAGA - Java API for Genetic Algorithms.

Company: University College London and JAGA.Org (http://www.jaga.org).

Copyright: (c) 2004 by G. Paperin.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, ONLY if you include a note of the original author(s) in any redistributed/modified copy.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA or see http://www.gnu.org/licenses/gpl.html

JAGA public release 1.0 beta
Greg Paperin (greg@jaga.org)

Field Summary
private  java.util.HashMap actualScores
private static java.lang.String dataFile
private  java.util.HashMap logScores
Constructor Summary
Method Summary
 double getActualScore(AminoAcid aminoAcid1, AminoAcid aminoAcid2)
 int getLogScore(AminoAcid aminoAcid1, AminoAcid aminoAcid2)
static void main(java.lang.String[] args)
Methods inherited from class org.jaga.individualRepresentation.proteinLocation.SubstitutionScoringMatrix
chooseProbabalisticMutation, chooseProbabalisticMutation, getActualScore, getLogScore
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail


private static final java.lang.String dataFile
See Also:
Constant Field Values


private java.util.HashMap logScores


private java.util.HashMap actualScores
Constructor Detail


public Blosum62()
Method Detail


public int getLogScore(AminoAcid aminoAcid1,
                       AminoAcid aminoAcid2)
Specified by:
getLogScore in class SubstitutionScoringMatrix


public double getActualScore(AminoAcid aminoAcid1,
                             AminoAcid aminoAcid2)
Specified by:
getActualScore in class SubstitutionScoringMatrix


public static void main(java.lang.String[] args)

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