Package 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

  • Constructor Details

  • Method Details

    • 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.