|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojavax.ga.functions.AbstractMutationFunction
org.biojavax.ga.functions.SwapMutationFunction
public class SwapMutationFunction
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
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 |
---|
public SwapMutationFunction(double[] probabilities)
probabilities
- An array, which contains the mutation probabilities.Method Detail |
---|
public SymbolList mutate(SymbolList seq) throws IllegalAlphabetException, ChangeVetoException, IllegalSymbolException
MutationFunction
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.
seq
- the sequence to mutate
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
.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |