Hi,I have done some work on the top of current biojava blast parser. The implementation of the BlastContentHandler class allows to use the eventbased parser in biojava to instantiate blast/hit/hsp/hspsummary/blastlikealignment objects.It is a very quick implementation following the bioperl ideas such that the parsing details like xml parser part is hiden from the user such that the user only needs to deal with the blast/hit/hsp APIs. Because biojava xml parser has also implemented the parsing of hmmer etc, the extention of the code to accomodate those should be easy.Further, extension of the code to parse NCBI blast result should be quick based upon current code and any xml parser implementing SAX. I should have a DOM based parser for ncbi xml result very soon as well.If you want the source code and jar file, just contact me and I will send you over.
Thanks.
Bruce Ling, Ph.D.
Director, Bioinformatics
Tularik, Inc -- http://www.tularik.com
Email: [EMAIL PROTECTED]
Phone: 650-825-7143
fax: 1-435-804-4009
