org.biojavax.ga.functions

Class CrossOverFunction.NoCross

java.lang.Object

org.biojavax.ga.functions.CrossOverFunction.NoCross

All Implemented Interfaces:

Changeable, CrossOverFunction

Enclosing interface:

CrossOverFunction

public static final class CrossOverFunction.NoCross
extends Object
implements CrossOverFunction

A place holder CrossOverFunction that doesn't perform cross overs

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

Constructor and Description
NoCross()

Method Summary

Modifier and Type	Method and Description
void	addChangeListener(ChangeListener cl) Add a listener that will be informed of all changes.
void	addChangeListener(ChangeListener cl, ChangeType ct) Add a listener that will be informed of changes of a given type.
double[]	getCrossOverProbs()
int	getMaxCrossOvers()
boolean	isUnchanging(ChangeType t) A particular ChangeType can never be raised by this Changeable.
GACrossResult	performCrossOver(SymbolList chromA, SymbolList chromB) Performs a cross between the pair of chromosomes
void	removeChangeListener(ChangeListener c) Remove a listener that was interested in all types of changes.
void	removeChangeListener(ChangeListener cl, ChangeType ct) Remove a listener that was interested in a specific types of changes.
void	setCrossOverProbs(double[] crossOverProb) Sets the probability of crossing at each base.
void	setMaxCrossOvers(int max) Sets an upper limit on the number of crosses.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NoCross

public NoCross()

Method Detail

getCrossOverProbs

public double[] getCrossOverProbs()

Specified by:

getCrossOverProbs in interface CrossOverFunction

Returns:

a single member array equal to {0.0}

getMaxCrossOvers

public int getMaxCrossOvers()

Specified by:

getMaxCrossOvers in interface CrossOverFunction

Returns:

0 (after all you can't cross over with this function)

performCrossOver

public GACrossResult performCrossOver(SymbolList chromA,
                                      SymbolList chromB)

Description copied from interface: CrossOverFunction

Performs a cross between the pair of chromosomes

Specified by:

performCrossOver in interface CrossOverFunction

Parameters:

chromA - The first chromosome in the cross

chromB - The second chromosome in the cross

Returns:

A GACross that holds the results of the cross

setCrossOverProbs

public void setCrossOverProbs(double[] crossOverProb)
                       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:

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

Throws:

ChangeVetoException

setMaxCrossOvers

public void setMaxCrossOvers(int max)
                      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:

max - the limit on crosses

Throws:

ChangeVetoException - if a ChangeListener vetoes this change

isUnchanging

public boolean isUnchanging(ChangeType t)

Description copied from interface: Changeable

A particular ChangeType can never be raised by this Changeable.

If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

Specified by:

isUnchanging in interface Changeable

Parameters:

t - the ChangeType to check

Returns:

true if ChangeEvents of this type are guaranteed to never be fired

removeChangeListener

public void removeChangeListener(ChangeListener c)

Description copied from interface: Changeable

Remove a listener that was interested in all types of changes.

Specified by:

removeChangeListener in interface Changeable

Parameters:

c - a ChangeListener to remove

addChangeListener

public void addChangeListener(ChangeListener cl)

Description copied from interface: Changeable

Add a listener that will be informed of all changes.

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - the ChangeListener to add

addChangeListener

public void addChangeListener(ChangeListener cl,
                              ChangeType ct)

Description copied from interface: Changeable

Add a listener that will be informed of changes of a given type.

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - the ChangeListener

ct - the ChangeType it is to be informed of

removeChangeListener

public void removeChangeListener(ChangeListener cl,
                                 ChangeType ct)

Description copied from interface: Changeable

Remove a listener that was interested in a specific types of changes.

Specified by:

removeChangeListener in interface Changeable

Parameters:

cl - a ChangeListener to remove

ct - the ChangeType that it was interested in