[Biojava-l] seqString() produces stacktrace

[Matthew Pocock]

I've fixed the symptom - aprox line 285 of SimpleGappedSymbolList we 
where renumbering the ungapped blocks before measuring the number of 
gaps in the block of gaps being edited. I've added lots more error 
checking code to this class. Code in CVS.

Does this now give the result you expected, or have I introduced a bug 
in removing the error?

Matthew

mark.schreiber at group.novartis.com wrote:

>I've done some investigations and the offending line is:
>
>
>gappedSequence.removeGaps(11, 6);
>
>This seems to be a real bug (at least in BJ1.3.1). Confusingly if you 
>change the 6 to any other legal value everything works as expected. 
>Matthew do you know whats going on here??
>
>- Mark
>
>
>Mark Schreiber
>Principal Scientist (Bioinformatics)
>
>Novartis Institute for Tropical Diseases (NITD)
>1 Science Park Road
>#04-14 The Capricorn
>Singapore 117528
>
>phone +65 6722 2973
>fax  +65 6722 2910
>
>
>
>
>
>"david de beule" <daviddebeule at pandora.be>
>Sent by: biojava-l-bounces at portal.open-bio.org
>01/11/2004 12:38 AM
>
> 
>        To:     <biojava-l at biojava.org>
>        cc: 
>        Subject:        [Biojava-l] seqString() produces stacktrace
>
>
>Hi all,
>
>This piece of code:
>
>Alphabet dna1 = DNATools.getDNA();
>   SymbolTokenization dnaToke1 = dna1.getTokenization("token");
>   SymbolList symbolList = new SimpleSymbolList(dnaToke1, 
>"ACTGGACCTAAGG");
>   Sequence sequence = new SimpleSequence(symbolList, "test", "test", 
>null);
>   SimpleGappedSequence gappedSequence = new 
>SimpleGappedSequence(sequence);
>
>   gappedSequence.addGapsInView(4, 4);
>   gappedSequence.removeGap(7);
>   gappedSequence.removeGaps(4, 3);
>   gappedSequence.addGapsInView(7, 2);
>   gappedSequence.addGapsInView(9, 3);
>   gappedSequence.addGapsInView(12, 2);
>   gappedSequence.addGapsInView(14, 3);
>   gappedSequence.addGapsInView(17, 2);
>   gappedSequence.removeGap(18);
>   gappedSequence.removeGaps(11, 6);
>
>   System.out.println(gappedSequence.seqString());
>
>breaks on the seqString() call and gives produces the following 
>stacktrace:
>
>java.lang.ArrayIndexOutOfBoundsException: 13
> at
>org.biojava.bio.symbol.SimpleSymbolList.symbolAt(SimpleSymbolList.java:271)
> at
>org.biojava.bio.seq.impl.SimpleSequence.symbolAt(SimpleSequence.java:120)
> at
>org.biojava.bio.symbol.SimpleGappedSymbolList.symbolAt(SimpleGappedSymbolLis
>t.java:508)
> at
>org.biojava.bio.symbol.AbstractSymbolList$SymbolIterator.next(AbstractSymbol
>List.java:201)
> at
>org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTok
>enization.java:211)
> at
>org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize
>SymbolList(AlphabetManager.java:1383)
> at
>org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:
>102)
>
>Can this be a bug ?
>Any help would be appreciated,
>
>David De Beule
>
>
>
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