Dear All, We've finally got around to adding pretty full support for parsing HMMER output in the BlastLikeSAXParser. Specifically, HmmerSearch and HmmerPfam. It should just work out of the box - i.e. you throw HMMER output at the BlastLikeSAXParser, and it should deal with it. As a consequence, we've made some minor changes to the DTD relating to dealing properly with hmmer output. Whilst we were doing this, we also incorporated: o Keith's suggestions on the list (with one minor difference discussed off-line). o Added a bitScore attribute (from a request at the last biojava bootcamp) (the blast parsers don't report this yet, but they will...) We don't think the changes to the DTD break anything that has gone before - shout if they do. Simon -- Simon M. Brocklehurst, Ph.D. Head of Bioinformatics & Advanced IS Cambridge Antibody Technology The Science Park, Melbourn, Cambridgeshire, UK http://www.CambridgeAntibody.com/ mailto:[EMAIL PROTECTED] _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
