/**
* Retrieve the weight for this distribution.
*
* <p>Performs the standard munge to handle ambiguity symbols. The actual weights for each atomic
* symbol should be calculated by the getWeightImpl functions.
*
* @param sym the Symbol to find the probability of
* @return the probability that one of the symbols matching amb was emitted
* @throws IllegalSymbolException if for any reason the symbols within amb are not recognized by
* this state
*/
public final double getWeight(Symbol sym) throws IllegalSymbolException {
if (sym instanceof AtomicSymbol) {
return getWeightImpl((AtomicSymbol) sym);
} else {
Alphabet ambA = sym.getMatches();
if (((FiniteAlphabet) ambA).size() == 0) { // a gap
getAlphabet().validate(sym);
double totalWeight = 0.0;
for (Iterator i = ((FiniteAlphabet) getAlphabet()).iterator(); i.hasNext(); ) {
Symbol s = (Symbol) i.next();
totalWeight += getWeight(s);
}
return 1.0 - totalWeight;
}
if (ambA instanceof FiniteAlphabet) {
FiniteAlphabet fa = (FiniteAlphabet) ambA;
double sum = 0.0;
for (Iterator i = fa.iterator(); i.hasNext(); ) {
Object obj = i.next();
if (!(obj instanceof AtomicSymbol)) {
throw new BioError("Assertion Failure: Not an instance of AtomicSymbol: " + obj);
}
AtomicSymbol as = (AtomicSymbol) obj;
sum += getWeightImpl(as);
}
return sum;
} else {
throw new IllegalSymbolException(
"Can't find weight for infinite set of symbols matched by " + sym.getName());
}
}
}
private void doSetWeight(Symbol sym, double weight)
throws IllegalSymbolException, ChangeVetoException {
if (sym instanceof AtomicSymbol) {
setWeightImpl((AtomicSymbol) sym, weight);
} else {
// need to divide the weight up amongst the atomic symbols according
// to the null model
FiniteAlphabet fa = (FiniteAlphabet) sym.getMatches();
double totalNullWeight = this.getNullModel().getWeight(sym);
for (Iterator si = fa.iterator(); si.hasNext(); ) {
AtomicSymbol as = (AtomicSymbol) si.next();
double symNullWeight = this.getNullModel().getWeight(as);
setWeightImpl(as, weight * symNullWeight / totalNullWeight);
}
}
}