[Bioperl-l] Bio::Graphics::Glyph::triangle

[Scott Cain]

Hi Hota,

You should always respond to the whole mailing list, especially since I
don't have a solution for you. :-)

>From your description, it seems to me like the best thing would be to
have a new glyph along the lines of the processed_transcript glyph,
where you would provide the ends and the components in a way that they
could be aggregated together and then the glyph magically renders all
the parts.  The trickiest thing about this would be that you really need
two levels of aggregation: the transposon as a whole and the individual
genes on the transposon.  I don't know how to do that or if is currently
possible.

If you think this accurately describes a solution to your problem,
perhaps we should put a feature request into bugzilla.

Scott


On Mon, 2005-04-18 at 17:57 +0200, Horvath Tamas wrote:
> Scott Cain wrote:
> 
> >Hota,
> >
> >I'm not sure what your ascii graphics are trying to represent.  To me,
> >it looks like you want a segments glyph and then specify the stranded
> >nest to point either E or W.  That would produce a rectangle with a
> >triangle on the end.
> >
> >Scott
> >  
> >
> Yes, you've got it right but the use of segments glyph is far less 
> straightforward then the triangle glyph. Here's my problem:
> 
> I want to display transposons. They have terminal inverted repeats 
> (TIRs) and 1 or 2 proteins coded. So the track should look like:
> TIR conector    encoded protein with 'hat' connectors        2nd 
> prot.                    TIR
> |||||>-------------||||||||***||||||||||||||||||||*****|||||||||||||||||||||||-----|||||||||||****|||||||||||----<|||||||
> 
> But I don't know how to do this using the segments glyph for the TIRs. I 
> also can't use 2 different connectors... actually I don't know why.
> 
> Hota
> 
> PS. thanks for the fast reply
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory