[Biojava-dev] ArrayIndexOutOfBoundsException in seqString() function

[Schreiber, Mark]

Hi -

Sounds like a possible bug. Can you send to the list an example of some
code that recreates this bug. Please also include the version of biojava
you are working with.

- Mark


> -----Original Message-----
> From: david de beule [mailto:daviddebeule at pandora.be] 
> Sent: Wednesday, 23 July 2003 6:10 a.m.
> To: biojava-dev at biojava.org
> Subject: [Biojava-dev] ArrayIndexOutOfBoundsException in 
> seqString() function
> 
> 
> Hi all,
> 
> I am getting an ArrayIndexOutOfBoundsException in the
> AbstractSymbolList.seqString() function.  This happens 
> typically after I first add and remove some gaps (with 
> AddGapsInSource()) and then after removing one more gap and 
> trying to display the new sequence, I suddenly get this 
> exception and it is impossible to ever retrieve the seqstring again.
> 
> Any thougths on this ?
> Thanks in advance,
> David
> 
> stacktrace:
> java.lang.ArrayIndexOutOfBoundsException: 17
> at
> org.biojava.bio.symbol.SimpleSymbolList.symbolAt(SimpleSymbolL
> ist.java:266)
> at 
> org.biojava.bio.seq.impl.SimpleSequence.symbolAt(SimpleSequenc
> e.java:101)
> at 
> org.biojava.bio.symbol.SimpleGappedSymbolList.symbolAt(SimpleG
> appedSymbolLis
> t.java:506)
> at 
> org.biojava.bio.symbol.AbstractSymbolList$SymbolIterator.next(
AbstractSymbol
> List.java:191)
> at 
> org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolLis
> t(CharacterTok
> enization.java:202)
> at 
> org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWr
> apper.tokenize
> SymbolList(AlphabetManager.java:1282)
> at
> org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSy
mbolList.java:
> 93)
> 
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> biojava-dev mailing list
> biojava-dev at biojava.org 
> http://biojava.org/mailman/listinfo/biojava-dev
> 
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