org.biojavax.ga

Interface Organism

All Superinterfaces:

Changeable

All Known Implementing Classes:

AbstractOrganism, SimpleOrganism

public interface Organism
extends Changeable

A GA 'organism' contains one or more Chromosomes

Since:

1.5

Version:

1.0

Author:

Mark Schreiber, Susanne Merz, Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	CHROMOSOMES
static ChangeType	NAME

Method Summary

Methods

Modifier and Type	Method and Description
SymbolList[]	getChromosomes() Gets the organisms 'chromosome' sequences
double[]	getFitness() Returns the current fitness of this organism.
String	getName() Gets the organisms name
boolean	isHaploid() Is the organism Haploid?
Organism	replicate(String name) Creates a replica of this Organism with a new name.
void	setChromosomes(SymbolList[] chromosomes) Sets the organisms 'chromosome' sequences.
void	setFitness(double[] fitness) This method allows to set the fitness of this organism to the specified value.
void	setName(String name) Sets the organisms name

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

CHROMOSOMES

static final ChangeType CHROMOSOMES

NAME

static final ChangeType NAME

Method Detail

setFitness

void setFitness(double[] fitness)

This method allows to set the fitness of this organism to the specified value. Generally this will be an array, which in the most cases contains just a single entry. In cases where we want to have multi-objective optimization we may want to make use of a more general fitness array with mutliple entries.

Parameters:

fitness -

getFitness

double[] getFitness()

Returns the current fitness of this organism. This is an array. Note that in the most cases this array may only contain one single value, but for multi-objective optimization it is necessary to store multiple fitness values.

Returns:

the fitness of the organism

getChromosomes

SymbolList[] getChromosomes()

Gets the organisms 'chromosome' sequences

Returns:

a SymbolList[]

setChromosomes

void setChromosomes(SymbolList[] chromosomes)
                    throws ChangeVetoException

Sets the organisms 'chromosome' sequences.

Parameters:

chromosomes - a SymbolList[]

Throws:

ChangeVetoException - if the Chromosome collection of the Organism is unchangable

getName

String getName()

Gets the organisms name

Returns:

the name String

setName

void setName(String name)
             throws ChangeVetoException

Sets the organisms name

Parameters:

name - the name of the organism.

Throws:

ChangeVetoException - if the name may not be changed.

replicate

Organism replicate(String name)

Creates a replica of this Organism with a new name.

Parameters:

name - the new name for the sequence.

Returns:

the replicated organism.

isHaploid

boolean isHaploid()

Is the organism Haploid?

Returns:

true if it is.