[Biojava-l] Programming hang while trying to do Profile HMM

[Matthew Pocock]

Hi @llan,

There was a bug in the 1.3 release that made this code infinite-loop. 
It's fixed in the nightly builds.

Has anybody ported the fixes to DP back to the 1.3 branch? Is it time to 
make a maintainance release?

Matthew

allanlee wrote:

>Hi, Good day!
> 
>I am trying to follow the exmaple given in http://www.biojava.org/docs/bj_in_anger/profileHMM.htm
> 
>but when I tried to run it, it just hang there. It hang there when I call:
> 
>DP dp = DPFactory.DEFAULT.createDP(hmm);
> 
>-------------------------------------------------------------------------------------------------------------------------------
>import org.biojava.bio.seq.*;
>import org.biojava.bio.seq.db.*;
>import org.biojava.bio.dist.*;
>import org.biojava.bio.dp.*;
>import org.biojava.bio.symbol.*;
>import org.biojava.bio.seq.Sequence;
>public class PHMM 
>{
>  public PHMM()
>  {
>    try
>    {
>      /*
>       * Make a profile HMM over the DNA Alphabet with 12 'columns' and default
>       * DistributionFactories to construct the transition and emmission
>       * Distributions
>       */
>      ProfileHMM hmm = new ProfileHMM(DNATools.getDNA(),
>                                      12,
>                                      DistributionFactory.DEFAULT,
>                                      DistributionFactory.DEFAULT,
>                                      "my profilehmm");
>      //create the Dynamic Programming matrix for the model.
>      DP dp = DPFactory.DEFAULT.createDP(hmm);
>      //Database to hold the training set
>      //SequenceDB db = new HashSequenceDB();
>      //Load the training set
>      //System.out.println("name=["+db.getName()+"]");
>    }catch (Exception e)
>    {
>      e.printStackTrace();
>    }
>  }
>  public static void main(String[] args)
>  {
>    PHMM phmm = new PHMM();
>    System.out.println("exit");
>  }
>}
>-------------------------------------------------------------------------------------------------------------------------------
>FYI, I am using the follow libraries:
> 
>a)biojava-1.30-jdk14.jar 
>b)bytecode-0.92.jar
>c)xerces
> 
>Btw, as I am new to profileHMM, do you have more complete sample that I can work around??
> 
>I appreciate your help very very much!! Thanks!
> 
> 
>best regards,
>@llan
> 
>
>
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