org.biojavax.ga.functions
Class SwapMutationFunction

java.lang.Object
  org.biojava.utils.AbstractChangeable
      org.biojavax.ga.functions.AbstractMutationFunction
          org.biojavax.ga.functions.SwapMutationFunction

All Implemented Interfaces:

Changeable, MutationFunction

public class SwapMutationFunction
extends AbstractMutationFunction

This class does a sort of mutation by exchanging two positions on the chromosome. Thus it can be used for implementations where a change of the amount of one symbol is undesired, e.g. some TSP implementations

Author:

Susanne Merz

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

SwapMutationFunction(double[] probabilities)
Sets the mutation probabilities to the designated values.

Method Summary

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

SwapMutationFunction

public SwapMutationFunction(double[] probabilities)

Sets the mutation probabilities to the designated values.

Parameters:

probabilities - An array, which contains the mutation probabilities.

Method Detail

mutate

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

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

ChangeVetoException - if seq is unmodifiable

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