[Biojava-l] blast xml parser

[David Huen]

On Mon, 11 Jun 2001, Ewan Birney wrote:

> On Mon, 11 Jun 2001, Wiepert, Mathieu wrote:
> 
> > You know, you are more than welcome to add any functionality you desire.
> > You have made a good point (as supported by Ewan), and besides that, no one
> > is going to stop you from adding functionality to the code base.  This is
> > open source code, so be open and code...
> 
> Hear hear.
> 
Though do try to maintain a separation between the xml parsing and the
backend object generation.  I have found this separation VERY useful
recently when writing an XML parser.  My GAME frontend feeds straight into
existing SeqIOListener backends allowing me to immediately instantiate
biojava objects.  I was pleasantly surprised how fast and easy that
was. 300 KB of sequence plus annotations in a blink. Later, I can always
switch to direct entry to an SQL database without instantiating any
biojava objects in the process merely with a new backend.

But as for coding, I'd make a go of a blast object-making backend except
I've got plenty of windmills of my own to tilt at just now [large bribes
in brown paper bags can sway the priority... ;-) e.g., some hardware
to biojava org to run an experimental DAS server would do nicely...]. Do
look at the StAX framework of Thomas Down's. It's ever so nice for what
you propose.

Facetiously yours,
David Huen, Dept. of Genetics, Univ. of Cambridge, U.K.
P.S. Apologies for the commercial plug... I tend to be on the lookout for
innovative and possibly ridiculous opportunities to fund open source
developments.