@Override
public WaveletChromatid clone() {
try {
final WaveletChromatid copy = (WaveletChromatid) super.clone();
copy.centromerePosition = this.centromerePosition;
copy.mutability = this.mutability;
copy.sequencedGenes = new ArrayList<AbstractWaveletGene>();
copy.promoters = new ArrayList<PromoterGene>();
copy.localSignalGenes = new ArrayList<SignalGene>();
copy.externalSignalGenes = new ArrayList<ExternalSignalGene>();
for (AbstractWaveletGene currentGene : this.sequencedGenes)
copy.sequencedGenes.add(currentGene.clone());
for (PromoterGene currentGene : this.promoters) copy.promoters.add(currentGene.clone());
for (SignalGene currentGene : this.localSignalGenes)
copy.localSignalGenes.add(currentGene.clone());
for (ExternalSignalGene currentGene : this.externalSignalGenes)
copy.externalSignalGenes.add(currentGene.clone());
return copy;
} catch (CloneNotSupportedException caught) {
LOGGER.error("CloneNotSupportedException caught but not expected!", caught);
throw new UnexpectedDannError("CloneNotSupportedException caught but not expected", caught);
}
}
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);
}
public WaveletChromatid(WaveletChromatid copy) {
this.centromerePosition = copy.centromerePosition;
this.mutability = copy.mutability;
this.sequencedGenes = new ArrayList<AbstractWaveletGene>();
this.promoters = new ArrayList<PromoterGene>();
this.localSignalGenes = new ArrayList<SignalGene>();
this.externalSignalGenes = new ArrayList<ExternalSignalGene>();
for (AbstractWaveletGene currentGene : copy.sequencedGenes)
this.sequencedGenes.add(currentGene.clone());
for (PromoterGene currentGene : copy.promoters) this.promoters.add(currentGene.clone());
for (SignalGene currentGene : copy.localSignalGenes)
this.localSignalGenes.add(currentGene.clone());
for (ExternalSignalGene currentGene : copy.externalSignalGenes)
this.externalSignalGenes.add(currentGene.clone());
}
public boolean bind(final SignalKeyConcentration concentration, final boolean isExternal) {
boolean bound = false;
for (AbstractWaveletGene gene : this.sequencedGenes)
if (gene.bind(concentration, isExternal)) bound = true;
return bound;
}
public void preTick() {
for (AbstractWaveletGene gene : this.sequencedGenes) gene.preTick();
}
public Set<AbstractKey> getKeys() {
final HashSet<AbstractKey> allKeys = new HashSet<AbstractKey>();
for (AbstractWaveletGene gene : this.sequencedGenes) allKeys.addAll(gene.getKeys());
return Collections.unmodifiableSet(allKeys);
}