[Biojava-dev] Identifying EmissionStates

[Schreiber, Mark]

Hi -

I was wondering what the recommended proceedure for identifying and
emission state in a StatePath is.

If I create two states:

    int[] adv = {1};
    Distribution biased =
OrderNDistributionFactory.DEFAULT.createDistribution(a);
    Distribution unbiased  = new UniformDistribution((FiniteAlphabet)a);

    SimpleEmissionState es1 = new
SimpleEmissionState("1",Annotation.EMPTY_ANNOTATION,
                                    adv, biased);
    SimpleEmissionState es2 = new
SimpleEmissionState("2",Annotation.EMPTY_ANNOTATION,
                                    adv, unbiased);

And then get the StatePath:

  StatePath sp = dp.viterbi(sla,ScoreType.PROBABILITY);

I seem to have no easy way to do either of the following:

    for(int i = 1; i <= sp.length(); i++){
      if(sp.symbolAt() == es1)
        //do something
    }

Or this:

    for(int i = 1; i <= sp.length(); i++){
      if(sp.symbolAt().equalrs(es1))
        //do something
    }

I can identify them using the name of the state but this is pretty
painful, there must be a better way??

- Mark
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