Hi,
I have been getting IndexOutOfBoundsException errors when writing a
SequenceDB of large sequences to a fasta file. I added some diagnostics to
the IndexOutOfBoundsException call in the AbstractSymbolList$SubList.subStr
and I get the stack trace below.
for some unknown reason FastaFormat is calling a subList method using an end
value less than the start. It looks like it might be tied up with an error
in the SubList of the AbstractSymbolList. Is there a limit on the maximum
size for a sequence.
This error doesn't always occur, just on large sequences (sometimes)
java.lang.IndexOutOfBoundsException: Start = 67381 End = 67380 this.start =
10001 this.end = 77380 at
org.biojava.bio.symbol.AbstractSymbolList$SubList.subStr(AbstractSymbolList.
java:212) at
org.biojava.bio.seq.impl.SimpleSequence.subStr(SimpleSequence.java:82) at
org.biojava.bio.seq.io.FastaFormat.writeSequence(FastaFormat.java:187) at
org.biojava.bio.seq.io.StreamWriter.writeStream(StreamWriter.java:63)
Can anyone help??
Mark
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