org.jaga.individualRepresentation.proteinLocation
Class SubstitutionScoringMatrix

java.lang.Object
  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)