Hello,
I've just checked in a new package called
org.biojava.bio.program.blast2html. It's a companion to the
org.biojava.bio.program.sax package allowing you to go from blast-like
output to HTML, through a stream of SAX events. This means it should
scale to very large outputs indeed - though your browser may struggle!
There are faster ways of creating HTML from such an output, however it's
a nice example of how to write a content handler, plus I've added the
ability to markup the alignment in various ways. It should also work for
all the programs that can be parsed by the Blast-Like parser, though I
haven't tested them all.
There is a new program in the demos/eventbasedparsing called Blast2HTML
and the <A
HREF="http://www.biojava.org/tutorials/blastlikeParsingCookBook/index.html";>tutorial</A>
has been updated, including some <A
HREF="http://www.biojava.org/tutorials/blastlikeParsingCookBook/blastp.html";>example<A>
output.
Colin
--
Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
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