org.jaga.individualRepresentation.proteinLocation
Class Blosum62

java.lang.Object
  org.jaga.individualRepresentation.proteinLocation.SubstitutionScoringMatrix
      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)