[Biojava-l] SAX parser demo

[Schreiber, Mark]

Hi -
 
Depends how much you want to bind it to biojava. If you don't need biojava objects just make a SAX parser to listen for the bits you want. If you do want to bind it to biojava objects I would suggest modifying the parser to put the info into an Annotation object.
 
- Mark
 

	-----Original Message----- 
	From: Russell Smithies [mailto:russell.smithies at xtra.co.nz] 
	Sent: Wed 25/06/2003 4:46 p.m. 
	To: smh1008 at cus.cam.ac.uk; Biojava-L at Biojava. Org 
	Cc: 
	Subject: Re: [Biojava-l] SAX parser demo
	
	

	Looks good but doesn't do what I need but I don't think it was ever going to
	:-(
	
	The blast XML data has loads of info in it (I guess thats the reason for the
	format) but I want to be able to get at individual tags, not just hits.  For
	example, some of the stats data (Statistics_entropy, Statistics_eff-space
	etc.) or other hit data (Hsp_align-len, Hsp_pattern-from etc.) instead of
	just hitID and e-value might be useful?
	I guess I'll have to implement some new bits (from
	SimpleSeqSimilaritySearchSubHit?) but not exactly sure where.
	
	any ideas?
	
	thanx
	Russell
	
	----- Original Message -----
	From: "David Huen" <david.huen at ntlworld.com>
	To: "Russell Smithies" <russell.smithies at xtra.co.nz>; "Biojava-L at Biojava.
	Org" <biojava-l at biojava.org>
	Cc: <jinchen at ufl.edu>
	Sent: Wednesday, June 25, 2003 2:28 PM
	Subject: Re: [Biojava-l] SAX parser demo
	
	
	> 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.
	>
	
	
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