[Biojava-l] biojava GUI examples

[Keith James]

>>>>> "Tanya" == Tanya Vavouri <tvavouri@hotmail.com> writes:

[...]

    Tanya> Has biojava been used in any type of sequence
    Tanya> browser/viewer applications like that ? I would be
    Tanya> interested to have a look at what other people have done
    Tanya> using biojava before I start using it.

One example is a viewer for blast reports between pairs of sequences
on context with sequence features. It hasn't been released yet as it
has some rough edges, but you can get the (GPL) source from the Sanger
Institute CVS server, details of which are at http://cvs.sanger.ac.uk/

Checkout

 [Pathogen] / psu / gemini

and the library it needs under

 [Pathogen] / psu / genlib / java

If you don't have cvs and Ant (the build tool) installed, then I can
tar up the source and the compiled jar files and mail them to you.

>From the README

Gemini is a tool for viewing pairwise sequence comparison results
generated by programs such as Blast and Fasta. It presents a "dotplot"
style view where individual Blast HSPs or Fasta hits are represented
as diagonal lines. In addition, any annotation available on the
sequences may be viewed in context on the axes of the plot.

...

Once the viewer is displayed, the view maybe panned using the
scrollbars or by using the middle mouse button to drag the dotplot
panel (the mouse icon will change when this is active). The view may
be zoomed and hits may be filtered by score using the control panel,
which is available under the Options menu.

It uses the classes from org.biojava.bio.gui.sequence extensively.
Unfortunately I don't have screenshots to hand. As for clicking on
features and getting data - yes this is possible.

Also see the demo programs in the seqviewer package which is part of
the biojava distribution.

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK