[Biojava-l] SAX parser demo

[jinchen at ufl.edu]

I am a little confused. I got your BlastParser.java from WebCVS but didn't find
any about BlastXMLParserFacade class in that directory. Where should I get that
file to make BlastParser compiled?

I have written a simple SAX parser for my simple use. But I am really interested
in how to those handler in your blastxml package.
Thanks,
Jin
 
Quoting David Huen <david.huen at ntlworld.com>:

> 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.
> 
>