Beispiel #1
0
  @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);
    }
  }
Beispiel #2
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);
  }
Beispiel #3
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());
  }
Beispiel #4
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;
 }
Beispiel #5
0
 public void preTick() {
   for (AbstractWaveletGene gene : this.sequencedGenes) gene.preTick();
 }
Beispiel #6
0
 public Set<AbstractKey> getKeys() {
   final HashSet<AbstractKey> allKeys = new HashSet<AbstractKey>();
   for (AbstractWaveletGene gene : this.sequencedGenes) allKeys.addAll(gene.getKeys());
   return Collections.unmodifiableSet(allKeys);
 }