[Biojava-dev] Identifying EmissionStates

[Schreiber, Mark]

OK I'm a dumb ass,

I forgot that a StatePath is an Alignment and the correct way to do it
is to get the State part of the Alignment as follows

  if (sp.symbolAt(sp.STATES, i)  ==  es1)
    //do something

I hope someone else learnt something from my noise on the mailing list
:(

- Mark



> -----Original Message-----
> From: Schreiber, Mark 
> Sent: Wednesday, 9 July 2003 12:03 p.m.
> To: biojava-dev at biojava.org
> Subject: [Biojava-dev] Identifying EmissionStates
> 
> 
> 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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