[Biojava-l] BioJava DAS client

[Thomas Down]

Hi...

After a couple of times when it's managed to get lost in my
TODO list, I've now merged the phase 1 BioJava DAS client into
the main CVS tree.  If you are interested, take a look at
the package

  org.biojava.bio.program.das

(remember, if you are doing a CVS update, use "update -dP"
to pick up newly created directories).

With this package, you can create a BioJava-style SequenceDB
which reflects the contents of a DAS reference datasource, then
layer feature sets from one or more `annotation' servers on top
of the reference sequence.  The code is currently missing a query-
optimizer module I'm working on at the moment, and it needs more
testing against different server implementations.  It should,
however, be fully functional -- if you can't access your favourite
DAS server, please report this as a bug. 

What I haven't done yet is build a graphical client application.
If anyone is interested in working on this, it shouldn't be too
hard to wire the client code up to the BioJava GUI packages to give
at least a first-pass attempt at a viewer.  Matthew demonstrated
something like this at ISMB over the summer, so we know it's
possible :).

For people who are interested in DAS, there is now a new web
site for the protocol specifications:

  http://biodas.org/

Happy hacking,

   Thomas
-- 
``If I was going to carry a large axe on my back to a diplomatic
function I think I'd want it glittery too.''
           -- Terry Pratchett