[Biojava-dev] graphics code and more in biojava

[Scooter Willis]

Johan

You should organize your code by functional distinct modules which allows
Biojava to be a collection of libraries. We are following the apache
commons model. http://commons.apache.org/ The goal is to allow other
developers to have a minimal set of jars to add needed functionality. If
you need a way to view a sequence that should not force the inclusion of
15 different jars. We encourage the use of the biojava core module for
classes to represent "core" data objects that can then be passed around to
other modules. However, if you can accomplish what needs to be
accomplished with a String then even better. If you want to avoid code to
check for correctness of a protein string as an example then using
ProteinSequence will accomplish that.

Can you provide some GUI screen shots of what you currently have. This is
an area that needs work in BioJava. I ported over some of the Biojava 1.7
Sequence Viewer code over to BioJava 3 and was able to maintain the
ability to have custom feature renderers without making it overly
complicated. I need to put some cookbook examples up.

Thanks

Scooter

On 8/31/11 7:04 AM, "Johan Henriksson" <mahogny at areta.org> wrote:

>Hello!
>I'm doing bioinformatics in java and have gotten to the point where I have
>more in-house code than I find healthy; so my aim is to slowly move toward
>using biojava, and to push as much of my code into biojava itself. (I met
>Andreas recently to discuss biojava, but I bring it here instead; hello!)
>Obviously, it will need plenty of cleaning before it's good enough for
>everyone else to use. The first question that comes to mind is then: in
>what
>state does it have to be to be considered for inclusion? I see a
>temptation
>to include as much as possible but if the code finds too few users, it
>might
>just add a maintenance burden. So, where is the cut-off?
>
>More substantially, I recently wrote a piece of code to render chromosome
>maps and generate PDFs. I think this kind of code would be of common use;
>should I try and prepare a submission?
>
>/Johan
>
>-- 
>-----------------------------------------------------------
>Johan Henriksson
>PhD student, Karolinska Institutet
>http://mahogny.areta.org  http://www.endrov.net
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