org.biojavax.ga
Interface GeneticAlgorithm

All Superinterfaces:

Changeable

All Known Implementing Classes:

AbstractGeneticAlgorithm, SimpleGeneticAlgorithm

public interface GeneticAlgorithm
extends Changeable

The class that runs the cycles of reproduction, evolution and selection, potentially on multiple Populations

Since:

1.5

Version:

1.1

Author:

Mark Schreiber, Susanne Merz, Andreas Dräger

Field Summary

static ChangeType	CROSS_OVER_FUNCTION
static ChangeType	FITNESS_FUNCTION
static ChangeType	FUNCTION
static ChangeType	MUTATION_FUNCTION
static ChangeType	POPULATION
static ChangeType	SELECTION_FUNCTION

Method Summary

CrossOverFunction	getCrossOverFunction()
FitnessFunction	getFitnessFunction() Returns the fitness function, i.e.
int	getGeneration()
MutationFunction	getMutationFunction()
Population	getPopulation() The registered Population
SelectionFunction	getSelectionFunction()
void	run(GAStoppingCriteria stoppingCriteria) Iterates the Algorithm until the stopping criteria are met.
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 interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

FITNESS_FUNCTION

static final ChangeType FITNESS_FUNCTION

POPULATION

static final ChangeType POPULATION

FUNCTION

static final ChangeType FUNCTION

CROSS_OVER_FUNCTION

static final ChangeType CROSS_OVER_FUNCTION

MUTATION_FUNCTION

static final ChangeType MUTATION_FUNCTION

SELECTION_FUNCTION

static final ChangeType SELECTION_FUNCTION

Method Detail

setFitnessFunction

void setFitnessFunction(FitnessFunction func)
                        throws ChangeVetoException

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

Parameters:

func - the FitnessFunction to be used

Throws:

ChangeVetoException - if the change is vetoed.

getFitnessFunction

FitnessFunction getFitnessFunction()

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

Returns:

the fitness function

setPopulation

void setPopulation(Population pop)
                   throws ChangeVetoException

Sets the Population of Organisms to the Algorithm.

Parameters:

pop - the population to add.

Throws:

ChangeVetoException - if new populations are not allowed.

getPopulation

Population getPopulation()

The registered Population

Returns:

the Population being operated on.

setSelectionFunction

void setSelectionFunction(SelectionFunction function)
                          throws ChangeVetoException

Changes the SelectionFunction used to select candidates for the next generation

Parameters:

function - a SelectionFunction

Throws:

ChangeVetoException - if the SelectionFunction is not allowed to be changed

getSelectionFunction

SelectionFunction getSelectionFunction()

Returns:

the current SelectionFunction

setCrossOverFunction

void setCrossOverFunction(CrossOverFunction function)
                          throws ChangeVetoException

Changes the CrossOverFunction used to CrossOver Chromosomes

Parameters:

function - a CrossOverFunction

Throws:

ChangeVetoException - if the CrossOverFunction is not allowed to be changed

getCrossOverFunction

CrossOverFunction getCrossOverFunction()

Returns:

the current CrossOverFunction

setMutationFunction

void setMutationFunction(MutationFunction function)
                         throws ChangeVetoException

Sets the current MutationFunction

Parameters:

function - a MutationFunction

Throws:

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

getMutationFunction

MutationFunction getMutationFunction()

Returns:

the current MutationFunction

getGeneration

int getGeneration()

Returns:

the Current generation number

run

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

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.