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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