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

Lincoln Stein lincoln.stein at gmail.com
Fri Sep 15 18:12:33 EDT 2006


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
>
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>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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