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

Description

AbstractPopulation()

AbstractPopulation(String name)
Method Summary

Modifier and Type

Method

Description

final void

addOrganism(Organism org)

Adds an Organism to the Population

protected abstract void

addOrganismImpl(Organism org)

final void

addOrganisms(Set orgs)

Adds several organisms to the population

final void

addOrganisms(Organism[] orgs)

Adds several organisms to the population

final void

addOrganisms(Population orgs)

Adds the residents of one population to this one

String

getName()

final void

removeAllOrganisms()

Removes all the Organisms in this Population

protected abstract void

removeAllOrganismsImpl()

final void

removeOrganism(Organism org)

Kills off the organism

protected abstract void

removeOrganismImpl(Organism org)

final void

removeOrganisms(Set orgs)

Removes all the Organisms in orgs

final void

removeOrganisms(Organism[] orgs)

Removes all the Organisms in orgs

final 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.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojavax.ga.Population
getOrganismByName, getOrganisms, organisms, size

Constructor Details
- AbstractPopulation
  
  public AbstractPopulation()
- AbstractPopulation
  
  public AbstractPopulation(String name)
Method Details
- 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()

Class AbstractPopulation

Field Summary

Fields inherited from interface org.biojavax.ga.Population

Constructor Summary

Method Summary

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.utils.Changeable

Methods inherited from interface org.biojavax.ga.Population

Constructor Details

AbstractPopulation

AbstractPopulation

Method Details

getName

setName

addOrganism

addOrganismImpl

addOrganisms

addOrganisms

addOrganisms

removeOrganisms

removeOrganisms

removeAllOrganisms

removeOrganism

removeOrganismImpl

removeAllOrganismsImpl