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 <[EMAIL PROTECTED]>: > 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
