org.biojavax.ga.functions

Class AbstractCrossOverFunction

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ga.functions.AbstractCrossOverFunction

All Implemented Interfaces:

Changeable, CrossOverFunction

Direct Known Subclasses:

OrderCrossover, SimpleCrossOverFunction

public abstract class AbstractCrossOverFunction
extends AbstractChangeable
implements CrossOverFunction

Abstract implementation of CrossOverFunction. All custom implementations should inherit from here.

Since:

1.5

Version:

1.0

Author:

Mark Schreiber

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.ga.functions.CrossOverFunction

CrossOverFunction.NoCross

Field Summary

Fields inherited from interface org.biojavax.ga.functions.CrossOverFunction

CROSS_PROB, DEFAULT_CROSS_PROB, DEFAULT_MAX_CROSS, MAX_CROSSES, NO_CROSS

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractCrossOverFunction()

Method Summary

Modifier and Type	Method and Description
double[]	getCrossOverProbs()
int	getMaxCrossOvers()
void	setCrossOverProbs(double[] crossOverProbs) Sets the probability of crossing at each base.
void	setMaxCrossOvers(int maxCrossOvers) Sets an upper limit on the number of crosses.

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.functions.CrossOverFunction

performCrossOver

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

AbstractCrossOverFunction

protected AbstractCrossOverFunction()

Method Detail

setMaxCrossOvers

public final void setMaxCrossOvers(int maxCrossOvers)
                            throws ChangeVetoException

Description copied from interface: CrossOverFunction

Sets an upper limit on the number of crosses. Its up to the implementation to decide what to do when the limit is reached although a good convention would be to keep only the first N crosses from the left end (5' end) of the sequence. By convention the default upper limit is DEFAULT_MAX_CROSS (eg infinite). This value should be used as the default by all implementations.

Specified by:

setMaxCrossOvers in interface CrossOverFunction

Parameters:

maxCrossOvers - the limit on crosses

Throws:

ChangeVetoException - if a ChangeListener vetoes this change

getMaxCrossOvers

public final int getMaxCrossOvers()

Specified by:

getMaxCrossOvers in interface CrossOverFunction

Returns:

the limit on crosses.

setCrossOverProbs

public final void setCrossOverProbs(double[] crossOverProbs)
                             throws ChangeVetoException

Description copied from interface: CrossOverFunction

Sets the probability of crossing at each base. Each position in the array corresponds to a position in the sequences to be crossed. The probability of a cross occuring after position 1 in the SymbolList is given by crossOverProbs[1]. CrossOverProbs[0] is effectively redundant as the cross would occur before the 1st position in the SymbolList. By convention if the array is shorter than the SymbolList it is being applied to then the last value in the array will be applied to every subsequent residue. The default value in all implementations should be DEFAULT_CROSS_PROB

Specified by:

setCrossOverProbs in interface CrossOverFunction

Parameters:

crossOverProbs - an array of doubles giving the probability of a cross occuring at any place.

Throws:

ChangeVetoException

getCrossOverProbs

public final double[] getCrossOverProbs()

Specified by:

getCrossOverProbs in interface CrossOverFunction