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

[Oliver Burren]

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