[Biojava-l] biojava BLAST parser proposal

[Simon Brocklehurst]

Dear All,

Just to keep everyone up to date with where we are on this.  I have now
reviewed existing publically available Java frameworks for parsing
BLAST, and believe that what we will be proposing for biojava represents
one of the more elegant solutions that I've seen (although beauty is
obviously in the eye of the beholder!).

We're on track to have a fully working system and extensive
documentation available to everyone next week.  I think we're
incorporating just about everything that people said they wanted.

Potential users can expect to find:

o A facade layer that provides *really easy to use* classes for:
     o grabbing predefined BLAST-related biojava value objects
     o HTML-based visualization of BLAST results that allows extensive
configuration of:
                o look and feel
                o marked up links to other information sources

o A SAX layer that allows people to trivially:
      o Populate their own object models for BLAST output. For example,
grab only particular pieces of information from a large BLAST output.
      o Access the system in a language- and platform-neutral entry via
XSLT transforms if they are starting with existing XMLised BLAST output.

o A low-level parsing layer to allow for us to deal with the differences
between different versions of BLAST

o An even more low level code re-use layer will make it easier for
people to parse BLAST-like output from other programs e.g. HMMER

Further comments and ideas are still welcome. Whether there is now time
to incorporate much else before an initial release, I'm not sure (it's
gonna be a busy weekend's coding as it is!).

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