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org.jaga.individualRepresentation.proteinLocation
Class Blosum62

java.lang.Object
  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

Version:
JAGA public release 1.0 beta
Author:
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
Blosum62()
           
 
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

dataFile

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

logScores

private java.util.HashMap logScores

actualScores

private java.util.HashMap actualScores
Constructor Detail

Blosum62

public Blosum62()
Method Detail

getLogScore

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

getActualScore

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

main

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

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