[Biojava-l] Visualisation??

[Thomas Down]

On Mon, Nov 26, 2001 at 01:30:08PM -0000, Warren, Jonathan wrote:
> Hello BioJava people.
> 
> I'm developing a visualisation tool for presenting biological
> sequences/features as graphics blocks (not showing the bases) on a backbone
> (according to their start-stop positions), rather like the Ensembl viewer
> does.
> 
> As the Ensembl project is going to move to Java I assume there are
> objects/interfaces and methods that I could use??? Could someone point me in
> the right direction or give me examples related to this type of biological
> display?? How far has the Ensembl java got??

I don't think the `official' Ensembl-Java project has written
any graphical code yet.  (Craig: is this right?) However, I believe 
Omnigene's viewer code started out life as more-or-less a straight
port of ensembl-draw, so you might find that interesting:

   http://omnigene.sourceforge.net/

Getting back to the BioJava side of things...

We've actually got a certain amount of GUI code in the
package org.biojava.bio.gui.sequence.  This is a framework
which is designed to work both at small `symbol' scale and
large `overview' scales.  The BioJava das-client.jar application
was built using this toolkit.

If you're interested in talking with Ensembl, there is a
biojava-ensembl library which allows you to view the Ensembl
data using BioJava interfaces [note: this is separate from the
official Ensembl-Java port].  We usually use this as a backend
for DAS servers, but in principle it would also be possible to
glue a viewer on directly.


Anyway, that's the code I know of -- hope you find some
of it interesting, anyway.

Good luck with your project,

     Thomas.