SimpleMutationFunction (biojava-legacy 1.9.5 API)

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 Description
  
  SimpleMutationFunction()
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method 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.