java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ga.impl.AbstractGeneticAlgorithm

All Implemented Interfaces:: Changeable, GeneticAlgorithm

Direct Known Subclasses:: SimpleGeneticAlgorithm

public abstract class AbstractGeneticAlgorithm extends AbstractChangeable implements GeneticAlgorithm

Base class from which most implementations of GeneticAlgorithm will inherit.

Since:: 1.5
Version:: 1.1
Author:: Mark Schreiber, Susanne Merz, Andreas Dräger

Field Summary

Fields

Modifier and Type

Field

Description

protected Population

population

Fields inherited from interface org.biojavax.ga.GeneticAlgorithm
CROSS_OVER_FUNCTION, FITNESS_FUNCTION, FUNCTION, MUTATION_FUNCTION, POPULATION, SELECTION_FUNCTION
Constructor Summary

Constructors

Modifier

Constructor

Description

protected

AbstractGeneticAlgorithm()
Method Summary

Modifier and Type

Method

Description

final CrossOverFunction

getCrossOverFunction()

FitnessFunction

getFitnessFunction()

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

final MutationFunction

getMutationFunction()

final Population

getPopulation()

The registered Population

final SelectionFunction

getSelectionFunction()

void

initPopulation()

Assigns a fitness value to each organism within the population according to the currently set fitness function.

final void

setCrossOverFunction(CrossOverFunction function)

Changes the CrossOverFunction used to CrossOver Chromosomes

final void

setFitnessFunction(FitnessFunction func)

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

final void

setMutationFunction(MutationFunction function)

Sets the current MutationFunction

final void

setPopulation(Population pop)

Sets the Population of Organisms to the Algorithm.

final void

setSelectionFunction(SelectionFunction function)

Changes the SelectionFunction used to select candidates for the next generation

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.GeneticAlgorithm
getGeneration, run

Field Details
- population
  
  protected Population population
Constructor Details
- AbstractGeneticAlgorithm
  
  protected AbstractGeneticAlgorithm()
Method Details
- getCrossOverFunction
  
  public final CrossOverFunction getCrossOverFunction()
  
  Specified by:
  
  getCrossOverFunction in interface GeneticAlgorithm
  
  Returns:
  
  the current CrossOverFunction
- getFitnessFunction
  
  public FitnessFunction getFitnessFunction()
  
  Description copied from interface: GeneticAlgorithm
  
  Returns the fitness function, i.e. the class that computes the fitness of each organism in a population.
  
  Specified by:
  
  getFitnessFunction in interface GeneticAlgorithm
  
  Returns:
  
  the fitness function
- getMutationFunction
  
  public final MutationFunction getMutationFunction()
  
  Specified by:
  
  getMutationFunction in interface GeneticAlgorithm
  
  Returns:
  
  the current MutationFunction
- getPopulation
  
  public final Population getPopulation()
  
  Description copied from interface: GeneticAlgorithm
  
  The registered Population
  
  Specified by:
  
  getPopulation in interface GeneticAlgorithm
  
  Returns:
  
  the Population being operated on.
- getSelectionFunction
  
  public final SelectionFunction getSelectionFunction()
  
  Specified by:
  
  getSelectionFunction in interface GeneticAlgorithm
  
  Returns:
  
  the current SelectionFunction
- initPopulation
  
  public void initPopulation()
  
  Assigns a fitness value to each organism within the population according to the currently set fitness function. If no population or no fitness function is set, nothing will happen.
- setCrossOverFunction
  
  public final void setCrossOverFunction(CrossOverFunction function) throws ChangeVetoException
  
  Description copied from interface: GeneticAlgorithm
  
  Changes the CrossOverFunction used to CrossOver Chromosomes
  
  Specified by:
  
  setCrossOverFunction in interface GeneticAlgorithm
  
  Parameters:
  
  function - a CrossOverFunction
  
  Throws:
  
  ChangeVetoException - if the CrossOverFunction is not allowed to be changed
- setFitnessFunction
  
  public final void setFitnessFunction(FitnessFunction func) throws ChangeVetoException
  
  Description copied from interface: GeneticAlgorithm
  
  The fitness function that will be used to compute the fitness of each organism.
  
  Specified by:
  
  setFitnessFunction in interface GeneticAlgorithm
  
  Parameters:
  
  func - the FitnessFunction to be used
  
  Throws:
  
  ChangeVetoException - if the change is vetoed.
- setMutationFunction
  
  public final void setMutationFunction(MutationFunction function) throws ChangeVetoException
  
  Description copied from interface: GeneticAlgorithm
  
  Sets the current MutationFunction
  
  Specified by:
  
  setMutationFunction in interface GeneticAlgorithm
  
  Parameters:
  
  function - a MutationFunction
  
  Throws:
  
  ChangeVetoException - if the MutationFunction change is Vetoed by a listener.
- setPopulation
  
  public final void setPopulation(Population pop) throws ChangeVetoException
  
  Description copied from interface: GeneticAlgorithm
  
  Sets the Population of Organisms to the Algorithm.
  
  Specified by:
  
  setPopulation in interface GeneticAlgorithm
  
  Parameters:
  
  pop - the population to add.
  
  Throws:
  
  ChangeVetoException - if new populations are not allowed.
- setSelectionFunction
  
  public final void setSelectionFunction(SelectionFunction function) throws ChangeVetoException
  
  Description copied from interface: GeneticAlgorithm
  
  Changes the SelectionFunction used to select candidates for the next generation
  
  Specified by:
  
  setSelectionFunction in interface GeneticAlgorithm
  
  Parameters:
  
  function - a SelectionFunction
  
  Throws:
  
  ChangeVetoException - if the SelectionFunction is not allowed to be changed

Class AbstractGeneticAlgorithm

Field Summary

Fields inherited from interface org.biojavax.ga.GeneticAlgorithm

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.GeneticAlgorithm

Field Details

population

Constructor Details

AbstractGeneticAlgorithm

Method Details

getCrossOverFunction

getFitnessFunction

getMutationFunction

getPopulation

getSelectionFunction

initPopulation

setCrossOverFunction

setFitnessFunction

setMutationFunction

setPopulation

setSelectionFunction