@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 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 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);
}
}