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

[Schreiber, Mark]

Hi Henry -

It's difficult to know without knowing how you made the model. The code
example in BioJava in Anger
http://www.biojava.org/docs/bj_in_anger/profileHMM.htm worked last time
I tried. It could be that the ProfileHMM has not been properly
initialized. It could also be a real bug :)

If the above example doesn't help can you send the code where you set up
the HMM?

- Mark


> -----Original Message-----
> From: hlr02 at doc.ic.ac.uk [mailto:hlr02 at doc.ic.ac.uk] 
> Sent: Friday, 11 July 2003 3:56 a.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] Creating a dp object for a profile HMM (2)
> 
> 
> 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
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
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