[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


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




------- Comment #4 from holland at ebi.ac.uk  2006-12-13 15:08 -------

ON BEHALF OF ORIGINAL POSTER:

i couldn't add a comment in bugzilla. i click commit and wait and wait, 
but nothing happens. what i wanted to add:

I've downloaded and compiled. it still doesn't work. what happens:

1- on my single-core machine, it stops working after 4925. sequence 
every time. It quits from main, but it still runs. probably one or more 
threads are still alive. I've surrounded the code with try/catch in 
main. But it catches no exception and no exception is thrown. At least i 
don't see anything on the monitor.

2- on dual-core machine, this exception is thrown. it doesn't quit too.
Exception in thread "Thread-1" org.biojava.bio.BioRuntimeException: 
Failed to complete search for NarI GGCGCC (2/4)
        at 
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:140)
        at 
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.NullPointerException
        at 
org.biojava.bio.seq.io.SymbolListCharSequence.charAt(SymbolListCharSequence.java:114)
        at java.lang.Character.codePointAt(Unknown Source)
        at java.util.regex.Pattern$Single.match(Unknown Source)
        at java.util.regex.Pattern$Curly.match(Unknown Source)
        at java.util.regex.Pattern$Start.match(Unknown Source)
        at java.util.regex.Matcher.search(Unknown Source)
        at java.util.regex.Matcher.find(Unknown Source)
        at 
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:103)
        ... 1 more


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