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. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
