[Biojava-l] Is FullHmmerProfileHMM (or FlatModel) Broken?

[Todd Riley]

Hello again,

I have attempted to move up from the ProfileHMM class to the HMMER 
classes (FullHmmerProfileHMM and HmmerProfileHMM).  However, I 
immediately get an error when attempting to create the DP matrix passing 
in the FullHmmerProfileHMM object.

java.lang.ClassCastException: org.biojava.bio.dp.SimpleDotState
   at org.biojava.bio.dp.FlatModel.<init>(FlatModel.java:185)
   at org.biojava.bio.dp.DP.flatView(DP.java:169)
   at 
org.biojava.bio.dp.DPFactory$DefaultFactory.createDP(DPFactory.java:52)
   at BioJavaHMM.trainHmm(BioJavaHMM.java:840)

Here is the code from FlatModel.java in the ModelInState section:

         if(t instanceof DotState) {
           DotStateWrapper dsw = new DotStateWrapper(t);
           addAState(dsw);
           inModel.put(t, flatM);
           toM.put(t, dsw);
           toM.put(((Wrapper) t).getWrapped(), dsw);   
<-------------line 185!!!!!!!!!
           //System.out.println("Added wrapped dot state " + 
dsw.getName());
         } else if(t instanceof EmissionState) {

This code is a bit confusing, but t appears to be of type 
SimpleDotState, which I do not believe can be cast to type Wrapper.  
Also, should both lines 184 and 185 be executed?

Also, I found this in the source code as well:

     //
     // FIXME -- Matthew broked this...          <--------line 243!!!!!!!!!
     //

Does this mean that some functionality of FlatModel.java is broken?  
Should the ModelInState (and thus the Hmmer classes) be avoided?

Any help would be greatly appreciated,
Todd