[Bioperl-l] Bio::Graphics::Glyph->parts differences between 1.636 and 1.654

Lincoln Stein lincoln.stein at gmail.com
Fri Sep 15 18:28:54 EDT 2006


Hi Oliver,

Sorry the answer didn't occur to me earlier. There is a new maxdepth method
that returns the number of levels of descent that the glyph can draw.
Bio::Graphics::Glyph returns undef from this method, meaning that it can
draw an unlimited number of levels of subparts, but
Bio::Graphics::Glyph::generic returns 0, meaning that it only cares about
the top level feature. This is a major performance boost.

For your glyph, you can do one of three things:

 1) override maxdepth() so that it returns the number of levels to descend
into.
 2) inherit from Bio::Graphics::Glyph, not generic
 3) pass the -maxdepth option to the track when you create it.

I will fix the documentation now.

Lincoln

On 9/15/06, Lincoln Stein <lincoln.stein at gmail.com> wrote:
>
> I will test this. The parts() API is not supposed to have changed. If you
> could send me your script, that would be very helpful.
>
> Best,
>
> Lincoln
>
>
> On 9/15/06, Oliver Burren <oliver.burren at cimr.cam.ac.uk> wrote:
> >
> > Hi Bioperlers,
> >
> > I'm having some problems with the CVS version of Bio::Graphics::Glyph
> > especially the 'parts' method. I have written a script and module to
> > demonstrate behaviour which I am happy to supply on request.
> >
> > Script is called test_parts.pl. It creates a 100 random features and
> > adds them to a holding feature. A Bio::Graphics::Panel is created that
> > this is then passed to for rendering. The glyph used to render is
> > test_parts with following 'draw' sub
> >
> > sub draw{
> >   my $self=shift;
> >   warn "Bio::Graphics::Panel API is ".Bio::Graphics::Panel::api_version
> > ()."\n";
> >   warn "Bio::Graphics::Glyph:: testparts.pm can find ".(($self->parts
> > =~ /ARRAY/?@{$self->parts}:$self->parts)|'no')." parts\n";
> > }
> >
> >
> > #With 'old' version of Bio::Graphics.
> >
> > perl test_parts.pl
> > Top level feature contains 100 features
> > Bio::Graphics::Panel API is 1.636
> > Bio::Graphics::Glyph::testparts.pm can find 100 parts
> >
> > #with 'new' (CVS co) version.
> >
> > perl test_parts.pl
> > Top level feature contains 100 features
> > Bio::Graphics::Panel API is 1.654
> > Bio::Graphics::Glyph::testparts.pm can find 0 parts
> >
> > Looks as if I'm loosing parts between the two apis ?
> >
> > I saw a thread on gmod mailing list
> >
> > http://sourceforge.net/mailarchive/forum.php?
> > forum_id=31947&max_rows=25&style=flat&viewmonth=200607&viewday=26 which
> > may be relevant but I wasn't able to find any follow up.
> >
> > Would somone be able to advise/document the changes that have occured
> > between the 2 api versions that might be relevant so that I can patch
> > some of my custom glyphs so they are compatible.
> >
> > Many thanks,
> >
> >
> > Olly Burren
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT michelse at cshl.edu
>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu


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