[Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core cpu) problem

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #12 from gwaldon at geneinfinity.org  2008-01-21 14:15 EST -------
I have seen a similar problem (at least producing similar log) and it was
solved by adding pool.stopThreads() at the end of your code:

SequenceIterator iter = SeqIOTools.readFastaDNA(br);
SimpleThreadPool pool = new SimpleThreadPool();
RestrictionMapper mapper = new RestrictionMapper(pool);

 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("MseI"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("HpaII"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("AluI"));
 Sequence seq;
 while(iter.hasNext()){
     seq = iter.nextSequence();
     mapper.annotate(seq);
 }
pool.stopThreads();

Hope it helps. 
- George


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