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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