If you go to transitionsTo(), aprox line 666, you will see the text:
workingSet.add(i);
This should read
workingSet.add(i.next());
This removes your infinite loop.
There is an efficiency problem somewhere - stateList is being called
once per itteration, which is slow for complex models. I wil
Mmm. That's the topological sort of the states. It makes sure that when
the DP recursion does a foreach(state), it loops over them in an order
whereby all info is calculated that a state needs before it is reached.
I am fairly sure that the body of the stateList() method can't infinite
loop - a
f the above example doesn't help can you send the code where you set up
the HMM?
- Mark
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> Sent: Friday, 11 July 2003 3:56 a.m.
> To: [EMAIL PROTECTED]
> Subject: [Biojava-l] Creating a dp ob
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, IllegalTransitionE
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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