org.biojavax.ga.impl

Class AbstractPopulation

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ga.impl.AbstractPopulation

All Implemented Interfaces:

Changeable, Population

Direct Known Subclasses:

SimplePopulation

public abstract class AbstractPopulation
extends AbstractChangeable
implements Population

Most Population implementations will want to inherit from here. This class doesn't define how Organims are stored or accessed so inheriting classes can define that themselves.

Since:

1.5

Version:

1.0

Author:

Mark Schreiber

Field Summary

Fields inherited from interface org.biojavax.ga.Population

NAME, ORGANISMS

Constructor Summary

Constructors

Constructor and Description
AbstractPopulation()
AbstractPopulation(String name)

Method Summary

Methods

Modifier and Type	Method and Description
void	addOrganism(Organism org) Adds an Organism to the Population
protected abstract void	addOrganismImpl(Organism org)
void	addOrganisms(Organism[] orgs) Adds several organisms to the population
void	addOrganisms(Population orgs) Adds the residents of one population to this one
void	addOrganisms(Set orgs) Adds several organisms to the population
String	getName()
void	removeAllOrganisms() Removes all the Organisms in this Population
protected abstract void	removeAllOrganismsImpl()
void	removeOrganism(Organism org) Kills off the organism
protected abstract void	removeOrganismImpl(Organism org)
void	removeOrganisms(Organism[] orgs) Removes all the Organisms in orgs
void	removeOrganisms(Set orgs) Removes all the Organisms in orgs
void	setName(String name) Sets the name of the population

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.Population

getOrganismByName, getOrganisms, organisms, size

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

AbstractPopulation

public AbstractPopulation()

AbstractPopulation

public AbstractPopulation(String name)

Method Detail

getName

public String getName()

Specified by:

getName in interface Population

Returns:

the name of the population

setName

public final void setName(String name)
                   throws ChangeVetoException

Description copied from interface: Population

Sets the name of the population

Specified by:

setName in interface Population

Parameters:

name - set the name to this.

Throws:

ChangeVetoException - if the name may not be changed

addOrganism

public final void addOrganism(Organism org)
                       throws ChangeVetoException,
                              IllegalOrganismException

Description copied from interface: Population

Adds an Organism to the Population

Specified by:

addOrganism in interface Population

Parameters:

org - the organism

Throws:

ChangeVetoException

IllegalOrganismException - if for some reason the organism is invalid

addOrganismImpl

protected abstract void addOrganismImpl(Organism org)
                                 throws IllegalOrganismException

Throws:

IllegalOrganismException

addOrganisms

public final void addOrganisms(Organism[] orgs)
                        throws ChangeVetoException,
                               IllegalOrganismException

Description copied from interface: Population

Adds several organisms to the population

Specified by:

addOrganisms in interface Population

Parameters:

orgs - the organisms to add

Throws:

ChangeVetoException

IllegalOrganismException - if for some reason the organism is invalid

addOrganisms

public final void addOrganisms(Set orgs)
                        throws ChangeVetoException,
                               IllegalOrganismException

Description copied from interface: Population

Adds several organisms to the population

Specified by:

addOrganisms in interface Population

Parameters:

orgs - the organisms to add

Throws:

ChangeVetoException

IllegalOrganismException - if for some reason the organism is invalid

addOrganisms

public final void addOrganisms(Population orgs)
                        throws ChangeVetoException,
                               IllegalOrganismException

Description copied from interface: Population

Adds the residents of one population to this one

Specified by:

addOrganisms in interface Population

Parameters:

orgs - the population to add

Throws:

ChangeVetoException

IllegalOrganismException - if for some reason the organism is invalid

removeOrganisms

public final void removeOrganisms(Organism[] orgs)
                           throws ChangeVetoException

Description copied from interface: Population

Removes all the Organisms in orgs

Specified by:

removeOrganisms in interface Population

Parameters:

orgs - the Organisms to remove.

Throws:

ChangeVetoException - if the change is vetoed

removeOrganisms

public final void removeOrganisms(Set orgs)
                           throws ChangeVetoException

Description copied from interface: Population

Removes all the Organisms in orgs

Specified by:

removeOrganisms in interface Population

Parameters:

orgs - the Organisms to remove.

Throws:

ChangeVetoException - if the change is vetoed

removeAllOrganisms

public final void removeAllOrganisms()
                              throws ChangeVetoException

Description copied from interface: Population

Removes all the Organisms in this Population

Specified by:

removeAllOrganisms in interface Population

Throws:

ChangeVetoException - if the change is vetoed

removeOrganism

public final void removeOrganism(Organism org)
                          throws ChangeVetoException

Description copied from interface: Population

Kills off the organism

Specified by:

removeOrganism in interface Population

Parameters:

org - the organism to kill

Throws:

ChangeVetoException

removeOrganismImpl

protected abstract void removeOrganismImpl(Organism org)

removeAllOrganismsImpl

protected abstract void removeAllOrganismsImpl()