[Biojava-l] SAX parser demo

[David Huen]

On Wednesday 25 Jun 2003 9:24 am, Russell Smithies wrote:
> Hi David,
> Heres the output from a small -m7 blast.
> Ignore the low-scoring hits as I've been toying with a blast db made of
> only binding sites  :-)

OK, I've had a look thru' but I don't know what Hsp_pattern-from and 
Hsp_pattern-to do, they seem to be always zero in your output ;-)

As for the statistics at the end of the run, the current DTD has not got an 
element for them.  The Summary element seems to have stuff for a HitSummary 
but not for a run summary.  See dtd/BlastLikeDataSetCollection.dtd for 
details of what we have.  We could define an additional element to pick up 
that stuff into but for that it'll be better to make a proposal to the 
mail-list and get some feedback on that.

>
> How do I create a listener to parse tags into the SAX output stream? I
> think most of the useful ones are in the .dtd but can't find where to
> implement them and haven't found the source file where the other
> listeners are.
>

The blast xml parser stuff is in src/org/biojava/bio/program/sax/blastxml.  
All that stuff is written to the StAX API.  Basically, each element handler 
delegates child elements to other handlers all of which call a listener 
written to an API for seq similarity searches.  The 
BlastLikeDataSetCollection stuff is in src/org/biojava/bio/program/ssbind.

Regards,
David