[Biojava-dev] Blast SAX parser update

[Simon Brocklehurst]

Keith James wrote:
> 
> Hi folks,
> 
> I've added NCBI Blast 2.2.2 and 2.2.3 to the versions supported in
> strict mode. It turned out that this didn't require changes to the
> parser.
> 
> I generated new test data for all NCBI Blast versions using the same
> queries and databases and made a few diffs. The format differences are
> essentially minor whitespace variations between 2.0.11 and
> 2.2.2/2.2.3. Nevertheless, I've added tests specifically for version
> 2.2.3.
> 

Hi Keith,

I'd just like to echo Matthew's comments - really good stuff!

Also, I'm sure that you've captured all the changes between formats, but
just in case... I have a dim and distant memory that NCBI made a minor
change to the summary ouput lines for one or more versions of Blast
between versions 2.0.* and 2.2.*.  Something like adding a frame number
for translations maybe, or number of HSPs? Kind of like some of the
difference in summary line output between Wu-Blast and NCBI-Blast?  Did
you get that one?

I could easily be wrong of course...  memorizing the precise formats of
different versions of Blast really isn't one of my major hobbies ;-)

Simon
--
Simon M. Brocklehurst, Ph.D.
Director of Informatics & Robotics
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com