[Biojava-l] Problem with blast file parser

Marcin Swiatek marcin.swiatek at mail.mcgill.ca
Thu Jan 29 21:56:29 UTC 2009

I personally would. Especially that I have just solved the problem
myself, unaware that someone did that already. 

BTW: the problem I picked up (which seems similar to the description
given) was that new set line (as evaluated by checkNewBlastLikeDataSet
in BlastSAXParser) wasn't picked up by HitSectionSAXParser and neither
it percolated up to BlastSAXParser, thus leaving the state machine of
the parser in a weird state. It would recover by skipping everything up
to the next data set (thus the result of having every other item

BTW2: XML parser in 1.6 doesn't deal with new BLAST files either (2.19,
was it?). Has this been fixed in the SVN repository?



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Marcel
Sent: Thursday, January 29, 2009 4:25 PM
To: Andreas Prlic
Cc: biojava-dev; biojava-l at biojava.org
Subject: Re: [Biojava-l] Problem with blast file parser

That sounds reasonable. I bet a lot of people would appreciate that!

Andreas Prlic wrote:
> Hi,
> We had a couple of bug reports recently regarding issues that already
> got fixed in the latest biojava builds from SVN. I think it is time to
> start preparing the next biojava release ( 1.7 )  to make sure
> everybody gets up to the latest status...
> Andreas
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