[Biojava-l] SAX parser demo

[David Huen]

Hi,
OK, I have uploaded a demo to CVS.  It is at biojava-live/demos/blastxml.  
It's just a plain ripoff of Mark Schreiber's demo in Biojava In Anger 
ported to use the BlastXML parser.  You will need to do a "cvs update -d" 
to create the new directories for the demos and for the DTD directory.

I have added a facade to the BlastXML parsing framework.  The facade is 
called BlastXMLParserFacade and is used identically to the way the existing 
BlastLikeSAXParser is used with blast text output.  I think this will make 
it easier for users all round: that both have the same interface.  You can 
look in that class to see how the BJ parsing framework is actually set up.

I won't have more time available to work on this for a bit but bug reports 
are welcome for eventual fixes.  As previously mentioned, running multiple 
sequence queries on a database with NCBI blast results in the concatenation 
of all the Blast XML outputs resulting in an almighty completely non-XML 
compliant file (multiple <xml> and <DOCTYPE> elements for example).  
Parsing those requires a hack I have previously described but it is ugly, 
ugly, ugly.  Maybe the latest NCBI version might have fixed this problem 
but I haven't looked.

Best wishes,
David Huen
P.S. It is really really bedtime, guys.....
P.P.S There is an ugly entity resolver hack I will need to clean up later 
too.