Package org.biojavax.ga.functions

Class AbstractMutationFunction

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ga.functions.AbstractMutationFunction

All Implemented Interfaces:

Changeable, MutationFunction

Direct Known Subclasses:

SimpleMutationFunction, SwapMutationFunction

public abstract class AbstractMutationFunction
extends AbstractChangeable
implements MutationFunction

Abstract implementation of MutationFunction 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.MutationFunction

MutationFunction.NoMutation

Field Summary

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

DEFAULT_MUTATION_PROBS, MUTATION_PROBS, MUTATION_SPECTRUM, NO_MUTATION

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractMutationFunction()

Method Summary

Modifier and Type	Method	Description
double[]	getMutationProbs()
OrderNDistribution	getMutationSpectrum()
void	setMutationProbs(double[] mutationProbs)	Set the probability of a mutation occuring at a certain position Position 0 in the array corresponds to the probability of the first residue of seq mutating.
void	setMutationSpectrum(OrderNDistribution mutationSpectrum)	Sets the Distribution of Symbols that will be selected from when a mutation occurs.

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.functions.MutationFunction

mutate

Constructor Detail

AbstractMutationFunction

protected AbstractMutationFunction()

Method Detail

setMutationProbs

public final void setMutationProbs(double[] mutationProbs)
                            throws ChangeVetoException

Description copied from interface: MutationFunction

Set the probability of a mutation occuring at a certain position Position 0 in the array corresponds to the probability of the first residue of seq mutating. If the length of the array defined in getMutationProbs() is shorter than the length of the sequence the default behaivour of implementations will be to apply the last probability to each subsequence residue. A single member array will mutate all bases with equal probability.

Specified by:

setMutationProbs in interface MutationFunction

Parameters:

mutationProbs - an array of double values representing mutation probabilities

Throws:

ChangeVetoException - if a ChangeListener vetoes the change.

getMutationProbs

public final double[] getMutationProbs()

Specified by:

getMutationProbs in interface MutationFunction

setMutationSpectrum

public final void setMutationSpectrum(OrderNDistribution mutationSpectrum)
                               throws ChangeVetoException

Description copied from interface: MutationFunction

Sets the Distribution of Symbols that will be selected from when a mutation occurs. An OrderNDistribution is used so that you can model a situation where the identity of the 'mutant' Symbol is dependent on the original Symbol. The primary use is to prevent Symbols mutating to themselves. Another use would be to model transitions and transversions.

Specified by:

setMutationSpectrum in interface MutationFunction

Parameters:

mutationSpectrum - the Distribution of 'mutant' bases to choose from.

Throws:

ChangeVetoException - if a ChangeListener vetoes the change.

getMutationSpectrum

public final OrderNDistribution getMutationSpectrum()

Specified by:

getMutationSpectrum in interface MutationFunction

Returns:

null if the Distribution has not been set.