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org.jaga.individualRepresentation.proteinLocation
Class SubstitutionScoringMatrix

java.lang.Object
  extended by org.jaga.individualRepresentation.proteinLocation.SubstitutionScoringMatrix
Direct Known Subclasses:
Blosum62

public abstract class SubstitutionScoringMatrix
extends java.lang.Object

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 static AminoAcid[] allAcids
           
 
Constructor Summary
SubstitutionScoringMatrix()
           
 
Method Summary
 AminoAcid chooseProbabalisticMutation(AminoAcid aminoAcid, GAParameterSet params)
           
 AminoAcid chooseProbabalisticMutation(java.lang.String aminoAcid, GAParameterSet params)
           
abstract  double getActualScore(AminoAcid aminoAcid1, AminoAcid aminoAcid2)
           
 double getActualScore(java.lang.String aminoAcid1, java.lang.String aminoAcid2)
           
abstract  int getLogScore(AminoAcid aminoAcid1, AminoAcid aminoAcid2)
           
 int getLogScore(java.lang.String aminoAcid1, java.lang.String aminoAcid2)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

allAcids

private static final AminoAcid[] allAcids
Constructor Detail

SubstitutionScoringMatrix

public SubstitutionScoringMatrix()
Method Detail

getLogScore

public abstract int getLogScore(AminoAcid aminoAcid1,
                                AminoAcid aminoAcid2)

getActualScore

public abstract double getActualScore(AminoAcid aminoAcid1,
                                      AminoAcid aminoAcid2)

getLogScore

public int getLogScore(java.lang.String aminoAcid1,
                       java.lang.String aminoAcid2)

getActualScore

public double getActualScore(java.lang.String aminoAcid1,
                             java.lang.String aminoAcid2)

chooseProbabalisticMutation

public AminoAcid chooseProbabalisticMutation(AminoAcid aminoAcid,
                                             GAParameterSet params)

chooseProbabalisticMutation

public AminoAcid chooseProbabalisticMutation(java.lang.String aminoAcid,
                                             GAParameterSet params)

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