On Wednesday 25 Jun 2003 9:24 am, Russell Smithies wrote: > Hi David, > Heres the output from a small -m7 blast. > Ignore the low-scoring hits as I've been toying with a blast db made of > only binding sites :-)
OK, I've had a look thru' but I don't know what Hsp_pattern-from and Hsp_pattern-to do, they seem to be always zero in your output ;-) As for the statistics at the end of the run, the current DTD has not got an element for them. The Summary element seems to have stuff for a HitSummary but not for a run summary. See dtd/BlastLikeDataSetCollection.dtd for details of what we have. We could define an additional element to pick up that stuff into but for that it'll be better to make a proposal to the mail-list and get some feedback on that. > > How do I create a listener to parse tags into the SAX output stream? I > think most of the useful ones are in the .dtd but can't find where to > implement them and haven't found the source file where the other > listeners are. > The blast xml parser stuff is in src/org/biojava/bio/program/sax/blastxml. All that stuff is written to the StAX API. Basically, each element handler delegates child elements to other handlers all of which call a listener written to an API for seq similarity searches. The BlastLikeDataSetCollection stuff is in src/org/biojava/bio/program/ssbind. Regards, David _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
