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);
}
@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());
}