org.biojavax.ga.impl

Class AbstractGeneticAlgorithm

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ga.impl.AbstractGeneticAlgorithm

All Implemented Interfaces:

Changeable, GeneticAlgorithm

Direct Known Subclasses:

SimpleGeneticAlgorithm

public abstract class AbstractGeneticAlgorithm
extends AbstractChangeable
implements GeneticAlgorithm

Base class from which most implementations of GeneticAlgorithm will inherit.

Since:

1.5

Version:

1.1

Author:

Mark Schreiber, Susanne Merz, Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and Description
protected Population	population

Fields inherited from interface org.biojavax.ga.GeneticAlgorithm

CROSS_OVER_FUNCTION, FITNESS_FUNCTION, FUNCTION, MUTATION_FUNCTION, POPULATION, SELECTION_FUNCTION

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractGeneticAlgorithm()

Method Summary

Modifier and Type	Method and Description
CrossOverFunction	getCrossOverFunction()
FitnessFunction	getFitnessFunction() Returns the fitness function, i.e. the class that computes the fitness of each organism in a population.
MutationFunction	getMutationFunction()
Population	getPopulation() The registered Population
SelectionFunction	getSelectionFunction()
void	initPopulation() Assigns a fitness value to each organism within the population according to the currently set fitness function.
void	setCrossOverFunction(CrossOverFunction function) Changes the CrossOverFunction used to CrossOver Chromosomes
void	setFitnessFunction(FitnessFunction func) The fitness function that will be used to compute the fitness of each organism.
void	setMutationFunction(MutationFunction function) Sets the current MutationFunction
void	setPopulation(Population pop) Sets the Population of Organisms to the Algorithm.
void	setSelectionFunction(SelectionFunction function) Changes the SelectionFunction used to select candidates for the next generation

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.biojavax.ga.GeneticAlgorithm

getGeneration, run

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

population

protected Population population

Constructor Detail

AbstractGeneticAlgorithm

protected AbstractGeneticAlgorithm()

Method Detail

getCrossOverFunction

public final CrossOverFunction getCrossOverFunction()

Specified by:

getCrossOverFunction in interface GeneticAlgorithm

Returns:

the current CrossOverFunction

getFitnessFunction

public FitnessFunction getFitnessFunction()

Description copied from interface: GeneticAlgorithm

Returns the fitness function, i.e. the class that computes the fitness of each organism in a population.

Specified by:

getFitnessFunction in interface GeneticAlgorithm

Returns:

the fitness function

getMutationFunction

public final MutationFunction getMutationFunction()

Specified by:

getMutationFunction in interface GeneticAlgorithm

Returns:

the current MutationFunction

getPopulation

public final Population getPopulation()

Description copied from interface: GeneticAlgorithm

The registered Population

Specified by:

getPopulation in interface GeneticAlgorithm

Returns:

the Population being operated on.

getSelectionFunction

public final SelectionFunction getSelectionFunction()

Specified by:

getSelectionFunction in interface GeneticAlgorithm

Returns:

the current SelectionFunction

initPopulation

public void initPopulation()

Assigns a fitness value to each organism within the population according to the currently set fitness function. If no population or no fitness function is set, nothing will happen.

setCrossOverFunction

public final void setCrossOverFunction(CrossOverFunction function)
                                throws ChangeVetoException

Description copied from interface: GeneticAlgorithm

Changes the CrossOverFunction used to CrossOver Chromosomes

Specified by:

setCrossOverFunction in interface GeneticAlgorithm

Parameters:

function - a CrossOverFunction

Throws:

ChangeVetoException - if the CrossOverFunction is not allowed to be changed

setFitnessFunction

public final void setFitnessFunction(FitnessFunction func)
                              throws ChangeVetoException

Description copied from interface: GeneticAlgorithm

The fitness function that will be used to compute the fitness of each organism.

Specified by:

setFitnessFunction in interface GeneticAlgorithm

Parameters:

func - the FitnessFunction to be used

Throws:

ChangeVetoException - if the change is vetoed.

setMutationFunction

public final void setMutationFunction(MutationFunction function)
                               throws ChangeVetoException

Description copied from interface: GeneticAlgorithm

Sets the current MutationFunction

Specified by:

setMutationFunction in interface GeneticAlgorithm

Parameters:

function - a MutationFunction

Throws:

ChangeVetoException - if the MutationFunction change is Vetoed by a listener.

setPopulation

public final void setPopulation(Population pop)
                         throws ChangeVetoException

Description copied from interface: GeneticAlgorithm

Sets the Population of Organisms to the Algorithm.

Specified by:

setPopulation in interface GeneticAlgorithm

Parameters:

pop - the population to add.

Throws:

ChangeVetoException - if new populations are not allowed.

setSelectionFunction

public final void setSelectionFunction(SelectionFunction function)
                                throws ChangeVetoException

Description copied from interface: GeneticAlgorithm

Changes the SelectionFunction used to select candidates for the next generation

Specified by:

setSelectionFunction in interface GeneticAlgorithm

Parameters:

function - a SelectionFunction

Throws:

ChangeVetoException - if the SelectionFunction is not allowed to be changed