Package org.biojavax.ga.impl

Class SimpleGeneticAlgorithm

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ga.impl.AbstractGeneticAlgorithm

org.biojavax.ga.impl.SimpleGeneticAlgorithm

All Implemented Interfaces:

Changeable, GeneticAlgorithm

public final class SimpleGeneticAlgorithm
extends AbstractGeneticAlgorithm

A simple implementation of the GeneticAlgorithm interface it is not intended that this class be overidden, hence it is final. It is much better to overide AbstractGeneticAlgorithm.

Since:

1.5

Version:

1.1

Author:

Mark Schreiber, Susanne Merz, Andreas Dräger

Field Summary

Fields inherited from class org.biojavax.ga.impl.AbstractGeneticAlgorithm

population

Fields inherited from interface org.biojavax.ga.GeneticAlgorithm

CROSS_OVER_FUNCTION, FITNESS_FUNCTION, FUNCTION, MUTATION_FUNCTION, POPULATION, SELECTION_FUNCTION

Constructor Summary

Constructors

Constructor	Description
SimpleGeneticAlgorithm()
SimpleGeneticAlgorithm(Population pop, MutationFunction mutFunc, CrossOverFunction xFunc, SelectionFunction selFunc)

Method Summary

Modifier and Type	Method	Description
List	getCrossResults()	Get a List containing details of all the cross over events during the run.
int	getGeneration()	The current generation
void	run(GAStoppingCriteria stoppingCriteria)	Iterates the Algorithm until the stopping criteria are met.

Methods inherited from class org.biojavax.ga.impl.AbstractGeneticAlgorithm

getCrossOverFunction, getFitnessFunction, getMutationFunction, getPopulation, getSelectionFunction, initPopulation, setCrossOverFunction, setFitnessFunction, setMutationFunction, setPopulation, setSelectionFunction

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SimpleGeneticAlgorithm

public SimpleGeneticAlgorithm()

SimpleGeneticAlgorithm

public SimpleGeneticAlgorithm(Population pop,
                              MutationFunction mutFunc,
                              CrossOverFunction xFunc,
                              SelectionFunction selFunc)

Method Detail

getGeneration

public int getGeneration()

The current generation

Returns:

an int giving the generation number

getCrossResults

public List getCrossResults()

Get a List containing details of all the cross over events during the run. If run(GAStoppingCriteria stoppingCriteria) has not yet been called the list will be empty. This implementation only stores a buffer of the last 100 crosses for memory reasons.

Returns:

a List of GACrossResult objects.

run

public void run(GAStoppingCriteria stoppingCriteria)
         throws ChangeVetoException,
                IllegalAlphabetException,
                IllegalSymbolException

Description copied from interface: GeneticAlgorithm

Iterates the Algorithm until the stopping criteria are met. For saftey implementations should synchronize on this method.

Parameters:

stoppingCriteria - determines when to stop.

Throws:

ChangeVetoException - if the Population being modified is locked

IllegalAlphabetException - if the MutationFunction chosen attempts to modify a Symbol from one of the Chromosomes to a Symbol outside of its Alphabet.

IllegalSymbolException - if the MutationFunction chosen is using the wrong Alphabet.