[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 #8 from ilhami.visne at gmail.com  2006-12-13 17:55 -------
Some good news. it has hanged on my single-core machine, because i forgot to
call pool.stopThreads(). i am sorry, if i made you do unnecessary efforts
because of it. It works now on my single machine. please roll back the "roll
back" :)

But still  it doesn't work on a dual-core machine. This time a different stack
trace from before. And it may help us to solve this problem

Exception in thread "Thread-0" org.biojava.bio.BioRuntimeException: Failed to
complete search for AluI AGCT (2/2)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:140)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 444
        at
org.biojava.bio.symbol.PackedSymbolList.symbolAt(PackedSymbolList.java:277)
        at
org.biojava.bio.symbol.ChunkedSymbolList.symbolAt(ChunkedSymbolList.java:91)
        at
org.biojavax.bio.seq.DummyRichSequenceHandler.symbolAt(DummyRichSequenceHandler.java:39)
        at
org.biojavax.bio.seq.ThinRichSequence.symbolAt(ThinRichSequence.java:163)
        at
org.biojava.bio.seq.impl.ViewSequence.symbolAt(ViewSequence.java:185)

        at
org.biojava.bio.seq.io.SymbolListCharSequence.charAt(SymbolListCharSequence.java:114)
        at java.util.regex.Pattern$BnM.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

As you see, it is an java.lang.ArrayIndexOutOfBoundsException: 444.
None of my sequences is smaller than 5000 bases. How can the index 444 cause
this exception???


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