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);
}
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;
}