private WaveletChromatid() {
this.sequencedGenes = new ArrayList<AbstractWaveletGene>();
this.promoters = new ArrayList<PromoterGene>();
this.localSignalGenes = new ArrayList<SignalGene>();
this.externalSignalGenes = new ArrayList<ExternalSignalGene>();
mutability = Mutations.getRandom().nextDouble() * 10;
this.centromerePosition = 0;
}
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 class WaveletChromatid implements Chromatid<AbstractWaveletGene>, Cloneable {
private final int max = 50;
// contains all the genes as their sequenced in the chromatid
private List<AbstractWaveletGene> sequencedGenes;
// contains all the promoter genes in an arbitrary order
private List<PromoterGene> promoters;
// contains just the local (non-external) signal genes in an arbitrary order.
private List<SignalGene> localSignalGenes;
// contains al the external signal genes in an arbitrary order.
private List<ExternalSignalGene> externalSignalGenes;
// Logger used to log debugging information.
private static final Logger LOGGER = Logger.getLogger(WaveletChromatid.class);
// Random used for all random values.
private static final Random RANDOM = Mutations.getRandom();
// Position of the gene's centromere. This is the origin where chromatid
// pairs are joined.
private int centromerePosition;
// This chomatids chance of mutating. This value itself will mutate.
private double mutability;
private WaveletChromatid() {
this.sequencedGenes = new ArrayList<AbstractWaveletGene>();
this.promoters = new ArrayList<PromoterGene>();
this.localSignalGenes = new ArrayList<SignalGene>();
this.externalSignalGenes = new ArrayList<ExternalSignalGene>();
mutability = Mutations.getRandom().nextDouble() * 10;
this.centromerePosition = 0;
}
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 static WaveletChromatid newRandomWaveletChromatid() {
final WaveletChromatid newChromatid = new WaveletChromatid();
while (newChromatid.sequencedGenes.size() <= 0) newChromatid.mutate(null);
while (Mutations.mutationEvent(newChromatid.mutability)) newChromatid.mutate(null);
return newChromatid;
}
Set<SignalKey> getExpressedSignals(final boolean external) {
// calculate the signal concentrations
final HashSet<SignalKey> allSignals = new HashSet<SignalKey>();
for (AbstractWaveletGene waveletGene : this.sequencedGenes) {
// if the current gene doesnt express a signal then skip it.
if (!(waveletGene instanceof SignalGene)) continue;
// convert the gene's type
final SignalGene gene = (SignalGene) waveletGene;
// check if the gene's signal is internal or external. continue if
// it doesnt match
if (external) {
// if its not an outward pointing external gene then just skip it
if (!(gene instanceof ExternalSignalGene)) continue;
else if (!((ExternalSignalGene) gene).isOutward()) continue;
} else {
// if its an outward pointing external than just skip it.
if ((gene instanceof ExternalSignalGene) && (((ExternalSignalGene) gene).isOutward()))
continue;
}
allSignals.add(gene.getOutputSignal());
}
return Collections.unmodifiableSet(allSignals);
}
public Set<AbstractKey> getKeys() {
final HashSet<AbstractKey> allKeys = new HashSet<AbstractKey>();
for (AbstractWaveletGene gene : this.sequencedGenes) allKeys.addAll(gene.getKeys());
return Collections.unmodifiableSet(allKeys);
}
public void preTick() {
for (AbstractWaveletGene gene : this.sequencedGenes) gene.preTick();
}
public void tick() {
// first we need to calculate the promotion of each site
final Hashtable<Integer, Double> promotions = new Hashtable<Integer, Double>();
for (PromoterGene promoter : this.promoters) {
final int promoterIndex = this.sequencedGenes.indexOf(promoter);
final int promotedIndex = promoter.getTargetDistance() + promoterIndex;
if (promotedIndex < this.sequencedGenes.size()) {
double promotion = 0.0;
if (promotions.contains(promotedIndex)) promotion = promotions.get(promotedIndex);
final double newPromotion = promotion + promoter.expressionActivity();
if (newPromotion != 0.0) promotions.put(promotedIndex, newPromotion);
}
}
for (int sequenceIndex = 0; sequenceIndex < this.sequencedGenes.size(); sequenceIndex++) {
this.sequencedGenes
.get(sequenceIndex)
.tick(promotions.containsKey(sequenceIndex) ? promotions.get(sequenceIndex) : 0);
}
}
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 int getCentromerePosition() {
return this.centromerePosition;
}
public List<AbstractWaveletGene> getGenes() {
return Collections.unmodifiableList(this.sequencedGenes);
}
public List<PromoterGene> getPromoterGenes() {
return Collections.unmodifiableList(this.promoters);
}
public List<SignalGene> getLocalSignalGenes() {
return Collections.unmodifiableList(this.localSignalGenes);
}
public List<ExternalSignalGene> getExternalSignalGenes() {
return Collections.unmodifiableList(this.externalSignalGenes);
}
public List<AbstractWaveletGene> crossover(final int point) {
final int index = point + this.centromerePosition;
if ((index < 0) || (index > this.sequencedGenes.size())) return null;
if ((index == 0) || (index == this.sequencedGenes.size()))
return Collections.unmodifiableList(new ArrayList<AbstractWaveletGene>());
if (point < 0) return Collections.unmodifiableList(this.sequencedGenes.subList(0, index));
else
return Collections.unmodifiableList(
this.sequencedGenes.subList(index, this.sequencedGenes.size()));
}
public void crossover(final List<AbstractWaveletGene> geneticSegment, final int point) {
final int index = point + this.centromerePosition;
if (geneticSegment == null) return;
if ((index < 0) || (index > this.sequencedGenes.size()))
throw new IllegalArgumentException("point " + index + "is out of range for crossover");
// calculate new centromere position
final int newCentromerePostion = this.centromerePosition - (index - geneticSegment.size());
// create new sequence of genes after crossover
ArrayList<AbstractWaveletGene> newGenes;
List<AbstractWaveletGene> oldGenes;
if (point < 0) {
newGenes = new ArrayList<AbstractWaveletGene>(geneticSegment);
newGenes.addAll(this.sequencedGenes.subList(index, this.sequencedGenes.size()));
oldGenes = this.sequencedGenes.subList(0, index);
} else {
newGenes = new ArrayList<AbstractWaveletGene>(this.sequencedGenes.subList(0, index));
newGenes.addAll(geneticSegment);
oldGenes = this.sequencedGenes.subList(index, this.sequencedGenes.size());
}
// remove displaced genes from specific gene type lists
for (AbstractWaveletGene oldGene : oldGenes) {
if (oldGene instanceof PromoterGene) this.promoters.remove(oldGene);
else if (oldGene instanceof ExternalSignalGene) this.externalSignalGenes.remove(oldGene);
else if (oldGene instanceof SignalGene) this.localSignalGenes.remove(oldGene);
}
// add new genes to the specific gene type list
for (AbstractWaveletGene newGene : geneticSegment) {
if (newGene instanceof PromoterGene) this.promoters.add((PromoterGene) newGene);
else if (newGene instanceof ExternalSignalGene)
this.externalSignalGenes.add((ExternalSignalGene) newGene);
else if (newGene instanceof SignalGene) this.localSignalGenes.add((SignalGene) newGene);
}
// update sequence genes to use the new genes
this.sequencedGenes = newGenes;
this.centromerePosition = newCentromerePostion;
}
@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);
}
}
private static AbstractKey randomKey(final Set<AbstractKey> keyPool) {
if ((keyPool != null) && (!keyPool.isEmpty())) {
// select a random key from the pool
AbstractKey randomKey = null;
int keyIndex = RANDOM.nextInt(keyPool.size());
for (AbstractKey key : keyPool) {
if (keyIndex <= 0) {
randomKey = key;
break;
} else keyIndex--;
}
if (randomKey == null) {
LOGGER.error("randomKey was null which shouldnt be possible");
throw new UnexpectedDannError("randomKey was unexpectidly null");
}
return new ReceptorKey(randomKey);
}
return new ReceptorKey();
}
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);
}
}