[Biojava-dev] Biojava GUI

[Jim Johnson (CCGB)]

Kalle Näslund wrote:
> Christopher Mason wrote:
> 
>>
>> Hi.
>>
>> I wonder what development work is being pursued on the GUI code in 
>> biojava, particularly that in org.biojava.bio.gui?  I'm interested in 
>> working on GUI bits for biojava and have some ideas in this area, but 
>> I don't want to step on anyone's toes.  I'm hoping to coordinate with 
>> anyone already working in this area.
>>
>> Thanks very much,
>>
>> -c
>>
>> [ Christopher Mason    <cmason@cmason.com>   http://www.cmason.com/ ]
>>
> Hi, dunno if i am the person to answear to this, but as i dont see any 
> other replies so far, i will give it a try =).
> 
> Basicly, not that much have happened lately in the org.biojava.bio.gui 
> part of the source tree, a few small
> changes here and there but nothing big.
> 
> New code is always welcome, so my suggestion would be for you to drop 
> another mail here, outlining what it
> is you want to do. Most likely that will generate some comments, 
> suggestions and ideas for you to proceed with.
> 
> I have some basic understanding of the org.biojava.bio.gui.seq classes ( 
> i got the basic ideas sorted, but might not
> have all the small nitty gritty nasty details sorted ) So if needed, i 
> might be able to help you out in the begining
> aswell.
> 
> regards Kalle
> 
> 
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> 
> 

I've been interested in adding more features to the biojava GUI.
I would also like to see the development of applications that
can be launched through JavaWebStart.


I like Jalview as a model of what we could add in GUI package:

   Mutliple views of the datamodel.
   Coordinated selection that would be represented in all views.
   Properties such as various color models that could be coordinated 
across views.

Article: 
http://acer.gen.tcd.ie/embnet.news/vol5_4/embnet/body_jalview.html/
Availability:   http://circinus.ebi.ac.uk:6543/jalview/ and 
http://www2.ebi.ac.uk/clustalw
JavaWebStart:   http://mgd.ahc.umn.edu/java/apps/Jalview.jnlp


I started prototyping some color schemes into a biojava demo last spring:
JavaWebStart:   http://mgd.ahc.umn.edu/java/apps/BiojavaDemo.jnlp
Snaps:          http://mgd.ahc.umn.edu/java/apps/BioJavaDemo_expanded.jpg
                 http://mgd.ahc.umn.edu/java/apps/BioJavaDemo_scaled.jpg

I thought it might make sense to have a StyleManager that would be the 
repository for color mapping schemes available for particular alphabets. 
  Default color schemes could be loaded from resources in a similar 
fashion to the AlphabetManager.

NCBI has started work on a Genome WorkBench.  It looks similar in 
concept to the Sequence Feature viewer.


I've employed the datamodel with muliple view and common selection
in another project:
http://ccgb.umn.edu/software/java/apps/TableView/

JJ


-- 
James E. Johnson <jj@ccgb.umn.edu>
Center for Computational Genomics and Bioinformatics
Mayo Mail Code 43, AHC, University of Minnesota
420 Delaware St SE
Minneapolis, MN 55455
612-626-6937