[Bioperl-l] identifying objects in Bio::Graphics SVG

[Lincoln Stein]

Following up on this old email message, I've placed this on the TODO 
list.

Lincoln

On Friday 06 August 2004 02:20 pm, Crabtree, Jonathan wrote:
> Hi Steve-
>
> I looked into this briefly and I'm pretty sure that the answer is
> "no". The way that the Bio::Graphics module generates SVG output is
> by using GD::SVG, which is more or less a drop-in replacement for
> GD.  Since the GD API doesn't require (or permit, AFAIK) the
> association of logical identifiers with graphics primitives (e.g.,
> these four lines are part of exon #1234), this information isn't
> included in the GD API calls and therefore isn't available to
> GD::SVG.  So even if GD::SVG wanted to group the various elements
> within an SVG <g>roup, it doesn't have any way of gleaning the
> necessary information without going beyond the GD API.
>
> Now of course this isn't to say that it wouldn't be possible to
> implement this type of functionality, but it would require making
> Bio::Graphics somewhat more SVG-aware than it is now, and would
> probably entail delving into the workings of GD::SVG a little bit. 
> I can also imagine taking a somewhat heavyweight approach that
> would be relatively inefficient but might be easier to implement. 
> One could conceivably make a fresh GD::SVG object for each glyph to
> be rendered, and then add some code to Bio::Graphics to strip out
> the essential SVG rendered by each glyph, wrap it in a <g> element,
> and place it into a dummy top-level GD::SVG object that serves only
> to collect the text of the SVG document.  I don't know...at some
> point it's going to be easier to just go ahead and add direct SVG
> support into Bio::Graphics.
>
> Jonathan
>
> p.s. Re-reading your original message, it might be possible to do
> something using the bounding box of the feature of interest (which
> can be obtained from the Bio::Graphics panel) to search through the
> SVG text for the relevant section.  It would be messy, though, and
> rather indirect.
>
> > -----Original Message-----
> > From: bioperl-l-bounces at portal.open-bio.org
> > [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of
> > Roels, Steven
> > Sent: Friday, August 06, 2004 1:49 PM
> > To: bioperl-l at bioperl.org
> > Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG
> >
> >
> >
> > Hello,
> >
> > I'd like to take the nice SVG output I can generate with the
> > Bio::Graphics modules, and add javascript to (for example)
> > alter/hide elements based on a slider or other user-controlled
> > input.
> >
> > Is there a way to map various panel items to the resulting
> > svg components?
> >
> > e.g transcript3, exon4 == <rect id="3633-9-510">
> >
> > Given that the "<g>" grouping element doesn't seem to be used
> > (which would facilitate this for non-simple elements), I'm
> > guessing not, but thought I would ask.
> >
> > Thanks,
> >
> > -Steve
> >
> > *****************************************************************
> > Steve Roels, Ph.D.
> > Senior Scientist I
> > Computational Biology
> > Millennium Pharmaceuticals, Inc.   Phone: 617.761.6820
> > 640 Memorial Drive                 FAX:   617.577.3555
> > Cambridge, MA 02139-4815           Email: steven.roels at mpi.com
> > *****************************************************************
> >
> >
> >
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724