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

[Lincoln Stein]

Hi Malay,

Since Bio::Graphics already works very nicely hand-in-hand with
BioPerl annotation objects and there is a web-based browser and other
application software based on it, could I suggest that you have a look
at creating a format-independent graphics layer that can be used by
Bio::Graphics and your code to draw on top of either GD or SVG at the
switch of a software toggle?

Lincoln

Malay writes:
 > 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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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
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