[Biojava-dev] ArrayIndexOutOfBoundsException in seqString() function

[david de beule]

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(SimpleSymbolList.java:266)
at org.biojava.bio.seq.impl.SimpleSequence.symbolAt(SimpleSequence.java:101)
at
org.biojava.bio.symbol.SimpleGappedSymbolList.symbolAt(SimpleGappedSymbolLis
t.java:506)
at
org.biojava.bio.symbol.AbstractSymbolList$SymbolIterator.next(AbstractSymbol
List.java:191)
at
org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTok
enization.java:202)
at
org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize
SymbolList(AlphabetManager.java:1282)
at
org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:
93)