Re: [Biojava-l] seqString() produces stacktrace

Mon, 12 Jan 2004 10:50:12 -0800

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

[EMAIL PROTECTED] 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" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
01/11/2004 12:38 AM


To: <[EMAIL PROTECTED]>
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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