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. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
