org.biojavax.ga.impl

Class AbstractOrganism

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ga.impl.AbstractOrganism

All Implemented Interfaces:

Changeable, Organism

Direct Known Subclasses:

SimpleOrganism

public abstract class AbstractOrganism
extends AbstractChangeable
implements Organism

Abstract implementation of Organism. Most implementations would want to inherit from here.

Since:

1.5

Version:

1.0

Author:

Mark Schreiber

Field Summary

Fields

Modifier and Type	Field and Description
protected SymbolList[]	chromosomes

Fields inherited from interface org.biojavax.ga.Organism

CHROMOSOMES, NAME

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractOrganism()
protected	AbstractOrganism(Organism org, String name)

Method Summary

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
abstract boolean	isHaploid() Is the organism Haploid?
protected abstract void	setChromImpl(SymbolList[] chromosomes)
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 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.Organism

replicate

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

chromosomes

protected SymbolList[] chromosomes

Constructor Detail

AbstractOrganism

protected AbstractOrganism()

AbstractOrganism

protected AbstractOrganism(Organism org,
                           String name)

Method Detail

getChromosomes

public final SymbolList[] getChromosomes()

Description copied from interface: Organism

Gets the organisms 'chromosome' sequences

Specified by:

getChromosomes in interface Organism

Returns:

a SymbolList[]

getFitness

public final double[] getFitness()

Description copied from interface: Organism

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.

Specified by:

getFitness in interface Organism

Returns:

the fitness of the organism

getName

public String getName()

Description copied from interface: Organism

Gets the organisms name

Specified by:

getName in interface Organism

Returns:

the name String

isHaploid

public abstract boolean isHaploid()

Description copied from interface: Organism

Is the organism Haploid?

Specified by:

isHaploid in interface Organism

Returns:

true if it is.

setChromImpl

protected abstract void setChromImpl(SymbolList[] chromosomes)

setChromosomes

public final void setChromosomes(SymbolList[] chromosomes)
                          throws ChangeVetoException

Description copied from interface: Organism

Sets the organisms 'chromosome' sequences.

Specified by:

setChromosomes in interface Organism

Parameters:

chromosomes - a SymbolList[]

Throws:

ChangeVetoException - if the Chromosome collection of the Organism is unchangable

setFitness

public final void setFitness(double[] fitness)

Description copied from interface: Organism

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.

Specified by:

setFitness in interface Organism

setName

public final void setName(String name)
                   throws ChangeVetoException

Description copied from interface: Organism

Sets the organisms name

Specified by:

setName in interface Organism

Parameters:

name - the name of the organism.

Throws:

ChangeVetoException - if the name may not be changed.