public void mutate(final Set<AbstractKey> keyPool) {
// there is a chance we will remove a signal gene from the chromatid
if (Mutations.mutationEvent(mutability))
if (this.localSignalGenes.size() > 0)
this.sequencedGenes.remove(
this.localSignalGenes.remove(
Mutations.getRandom().nextInt(this.localSignalGenes.size())));
// there is a chance we will add a new gene to the chromatid
if (Mutations.mutationEvent(mutability) && getGenes().size() < max) {
// generate the new receptorKey used in the new gene
ReceptorKey newReceptorKey = new ReceptorKey(randomKey(keyPool));
// mutate new receptorKey before using it
while (Mutations.mutationEvent(this.mutability))
newReceptorKey = newReceptorKey.mutate(mutability);
// create a new gene using the new receptor
AbstractWaveletGene newGene;
final SignalKey newSignalKey = new SignalKey(randomKey(keyPool));
switch (RANDOM.nextInt(3)) {
case 0:
final MutableInteger initialDistance = (new MutableInteger(0)).mutate(mutability);
newGene = new PromoterGene(newReceptorKey, initialDistance.intValue());
this.promoters.add((PromoterGene) newGene);
break;
case 1:
newGene = new SignalGene(newReceptorKey, newSignalKey);
this.localSignalGenes.add((SignalGene) newGene);
break;
default:
newGene = new ExternalSignalGene(newReceptorKey, newSignalKey, RANDOM.nextBoolean());
this.externalSignalGenes.add((ExternalSignalGene) newGene);
}
// add the new gene to the sequence. there is an equal chance the
// gene will be added to the head and tail
if (RANDOM.nextBoolean()) this.sequencedGenes.add(0, newGene);
else this.sequencedGenes.add(newGene);
}
// mutate each gene (the gene itself will handle if it actually mutates)
for (AbstractWaveletGene currentGene : this.sequencedGenes) currentGene.mutate(keyPool);
// mutate the mutability factor.
if (Mutations.mutationEvent(mutability))
this.mutability = Mutations.mutabilityMutation(this.mutability);
}
