org.biojavax.ga.functions

Class SimpleMutationFunction

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ga.functions.AbstractMutationFunction

org.biojavax.ga.functions.SimpleMutationFunction

All Implemented Interfaces:

Changeable, MutationFunction

public final class SimpleMutationFunction
extends AbstractMutationFunction

Simple no frills Implementation of the MutationFunction interface

This class is final, custom implementations should extend AbstractMutationFunction

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

Constructor and Description
SimpleMutationFunction()

Method Summary

Modifier and Type	Method and Description
SymbolList	mutate(SymbolList seq) Produces a new SymbolList by mutation.

Methods inherited from class org.biojavax.ga.functions.AbstractMutationFunction

getMutationProbs, getMutationSpectrum, setMutationProbs, setMutationSpectrum

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

Constructor Detail

SimpleMutationFunction

public SimpleMutationFunction()

Method Detail

mutate

public SymbolList mutate(SymbolList seq)
                  throws ChangeVetoException,
                         IllegalAlphabetException,
                         IllegalSymbolException

Description copied from interface: MutationFunction

Produces a new SymbolList by mutation. Each position i in the SymbolList seq is mutated with probability getMutationProbs[i]. The new residue is selected at random from the Distribution mutation. The use of an array of probabilities allows the modelling of mutational hotspots. 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.

Parameters:

seq - the sequence to mutate

Returns:

The mutated sequence.

Throws:

ChangeVetoException - if seq is unmodifiable

IllegalAlphabetException - If the mutationSpectrum Distribution is not emitting Symbols from the same Alphabet as seq.

IllegalSymbolException - if the mutationSpectrum Distribution is not conditioned with the same Alphabet as the seq Alphabet.