[Bioperl-l] BioSVG [ Was ABI file parsing]

[Malay]

Hi Heikki:

> Malay,
> 
> I tried to have a look at the your modules at CPAN,
> but could not find them
> there yet.  

Yep. It's not there yet. I hate writing documentation
and I don't want to upload it till there is enough doc
to make it usable.

>Could  you consider submitting your code
> into BioPerl instead? 
> If you have generic SGV code ready I am sure we can
> come up with other uses
> of it.

I'd be happy but there is only one problem. All the
BioSVG code depends on "Pastel" a graphics framework
in Perl to generate SVG data.

> 
> In more general terms:
> 
> We have a separate bioperl-gui CVS repository which
> gives you a cmplete TK
> based user interface. Lincold has already committed
> code using GD to draw
> genome pictures. Jason has written Pedigree modules,
> again using GD, to draw
> family pedigrees.
> SGV is getting more and attractive choice of
> graphics and now you have
> written code to draw the cromatograms.
> 
> In my opinion we should have a namespace for
> generating Bio related
> graphics, e.g.:
> 
> Bio::Graphics
> Bio::Graphics::GD
> Bio::Graphics::SGV

Pastel has a API exactly like Java2D graphics API.
Pastel is more or less in usable state except
animation and stuff like that which anyway are not
very important for biological data. Incorporating
BioSVG code along with Pastel in BioPerl will be too
much of work and if internally SVG code uses Pastel
then that will increase dependencies which may not be
acceptable to majority of the BioPerl users. 

Ofcourse, I am working on BioSVG to make it compatible
with BioPerl Annotation object. So simply passing a
BioPerl Annotation object to BioSVG will make it draw
the features.

> ...
> 
> If these different graphics formats objects end up
> using same objects, the
> interfaces would be e.g Bio::Graphics::ChromosomeI
> 
> There should be standards for calling these drawing
> modules and so on...
> 

Regards,

Malay

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