org.jaga.fitnessEvaluation.proteinLocation
Class ProteinLocationTrainer

java.lang.Object
  org.jaga.fitnessEvaluation.proteinLocation.ProteinLocationTrainer

All Implemented Interfaces:

FitnessEvaluationAlgorithm

public class ProteinLocationTrainer

extends java.lang.Object

implements FitnessEvaluationAlgorithm

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 ProteinLocationClassifier	best
private int	minOverlap
private ProteinGroup	negativeGroup
private ProteinGroup	positiveGroup

Constructor Summary

private	ProteinLocationTrainer()
	ProteinLocationTrainer(ProteinGroup positiveGroup, ProteinGroup negativeGroup, int minOverlap)

Method Summary

Fitness	evaluateFitness(Individual individual, int age, Population population, GAParameterSet params) Evaluates the fitness of a spscified individual.
java.lang.Class	getApplicableClass() Returns the class of individuals handled by this selection algorithm.
int	getMinOverlap()
ProteinGroup	getNegativeGroup()
ProteinGroup	getPositiveGroup()
void	setMinOverlap(int minOverlap)
void	setNegativeGroup(ProteinGroup nGroup)
void	setPositiveGroup(ProteinGroup pGroup)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

positiveGroup

private ProteinGroup positiveGroup

negativeGroup

private ProteinGroup negativeGroup

minOverlap

private int minOverlap

best

private ProteinLocationClassifier best

Constructor Detail

ProteinLocationTrainer

private ProteinLocationTrainer()

ProteinLocationTrainer

public ProteinLocationTrainer(ProteinGroup positiveGroup,
                              ProteinGroup negativeGroup,
                              int minOverlap)

Method Detail

getApplicableClass

public java.lang.Class getApplicableClass()

Description copied from interface: FitnessEvaluationAlgorithm

Returns the class of individuals handled by this selection algorithm.

Specified by:

getApplicableClass in interface FitnessEvaluationAlgorithm

Returns:

The required type the individual passed to the method evaluateFitness.

setPositiveGroup

public void setPositiveGroup(ProteinGroup pGroup)

getPositiveGroup

public ProteinGroup getPositiveGroup()

setNegativeGroup

public void setNegativeGroup(ProteinGroup nGroup)

getNegativeGroup

public ProteinGroup getNegativeGroup()

getMinOverlap

public int getMinOverlap()

setMinOverlap

public void setMinOverlap(int minOverlap)

evaluateFitness

public Fitness evaluateFitness(Individual individual,
                               int age,
                               Population population,
                               GAParameterSet params)

Description copied from interface: FitnessEvaluationAlgorithm

Evaluates the fitness of a spscified individual.

Specified by:

evaluateFitness in interface FitnessEvaluationAlgorithm

Parameters:

individual - The Individual to be evaluated.

age - The generation of the individual and its population.

population - The population from which the individual was drawn.

params - The experiment-parameters

Returns:

The fitness of the specified individual