[Biojava-l] Creating a dp object for a profile HMM (2)

[hlr02 at doc.ic.ac.uk]

Hi,

I have narrowed down the problem in creating a dp object for a profile HMM to a 
possible bug in the code below from the DP class. I could really use some help 
here..

Thanks,

Henry Romijn

  public static State[] stateList(MarkovModel mm) 
  throws IllegalSymbolException, IllegalTransitionException,
  BioException {

      // .....code here works ok

        for (Iterator addStates = alpha.iterator(); addStates.hasNext(); ) {
        Object state = addStates.next();
        if (state instanceof MagicalState) {
          emissionStates.add(0, state);
        }
        else if (state instanceof EmissionState) {
          emissionStates.add(state);
        }
        else {
          ListIterator checkOld = dotStates.listIterator();
          int insertPos = -1;
          while (checkOld.hasNext() && insertPos == -1) {
            Object oldState = checkOld.next();
            if (comp.compare(state, oldState) == comp.LESS_THAN) {
              insertPos = checkOld.nextIndex() - 1;
            }
          }
          if (insertPos >= 0) {
            dotStates.add(insertPos, state);
          }
          else {
            dotStates.add(state);
          }
        }
      }

      //......
  }


Quoting hlr02 at doc.ic.ac.uk:

> Hi,
> 
> After I have successfully created and initialized a profile HMM, I try to 
> register the model with a new DP object as follows:
> 
>    DP dp = DPFactory.DEFAULT.createDP(profile);
> 
> This causes the program to hang. Any ideas why this may not work?
> 
> Thanks,
> 
> Henry Romijn
> 
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