public String tokenizeSymbolList(SymbolList sl) throws IllegalAlphabetException {
    if (sl.getAlphabet() != getAlphabet()) {
      throw new IllegalAlphabetException(
          "Alphabet " + sl.getAlphabet().getName() + " does not match " + getAlphabet().getName());
    }
    StringBuffer sb = new StringBuffer();
    for (Iterator i = sl.iterator(); i.hasNext(); ) {
      Symbol sym = (Symbol) i.next();
      try {
        Character c = _tokenizeSymbol(sym);
        sb.append(c.charValue());
      } catch (IllegalSymbolException ex) {
        throw new IllegalAlphabetException(ex, "Couldn't tokenize");
      }
    }

    return sb.substring(0);
  }
Пример #2
0
  public SymbolList mutate(SymbolList seq)
      throws ChangeVetoException, IllegalAlphabetException, IllegalSymbolException {

    int maxIndex = getMutationProbs().length - 1;
    OrderNDistribution d = getMutationSpectrum();
    Random r = new Random();

    for (int i = 1; i < seq.length(); i++) {
      int index = Math.min(i - 1, maxIndex);
      double mutProb = getMutationProbs()[index];

      if (r.nextDouble() < mutProb) {

        Edit e = new Edit(i, seq.getAlphabet(), d.getDistribution(seq.symbolAt(i)).sampleSymbol());
        seq.edit(e);
      }
    }

    return seq;
  }