[Bioperl-l] Fix to Bio::Graphics::Glyph

Sendu Bala bix at sendu.me.uk
Wed Nov 29 10:53:04 EST 2006


Lincoln Stein wrote:
> There were two branch-1-5-2 commits last night. Both are needed to back 
> out the changes.

I'm not seeing the changes as a true revert.

cvs diff -r 1.113.4.6 Bio/Graphics/Glyph.pm
Index: Bio/Graphics/Glyph.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph.pm,v
retrieving revision 1.113.4.6
retrieving revision 1.113.4.9
diff -r1.113.4.6 -r1.113.4.9
3c3
< # $Id: Glyph.pm,v 1.113.4.6 2006/11/19 17:18:45 lstein Exp $
---
 > # $Id: Glyph.pm,v 1.113.4.9 2006/11/29 02:38:33 lstein Exp $
126a127,128
 >   my $feature = $self->feature;
 >   return 1 if $feature->can('compound') && $feature->compound;
1636a1639
 >

cvs diff -r 1.40.2.2 Bio/Graphics/Glyph/generic.pm
Index: Bio/Graphics/Glyph/generic.pm
===================================================================
RCS file: 
/home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/generic.pm,v
retrieving revision 1.40.2.2
retrieving revision 1.40.2.4
diff -r1.40.2.2 -r1.40.2.4
113,115c113,115
<   my $md   = $self->SUPER::maxdepth;
<   return $md if defined $md;
<   return 0;
---
 >   my $maxdepth =  $self->option('maxdepth');
 >   return $maxdepth if defined $maxdepth;
 >   return 1;

cvs diff -r 1.6.8.1 Bio/Graphics/Glyph/box.pm
Index: Bio/Graphics/Glyph/box.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/box.pm,v
retrieving revision 1.6.8.1
retrieving revision 1.6.8.2
diff -r1.6.8.1 -r1.6.8.2
14a15,21
 > sub maxdepth {
 >   my $self = shift;
 >   my $maxdepth =  $self->option('maxdepth');
 >   return $maxdepth if defined $maxdepth;
 >   return 0;
 > }
 >

Is this intended? Are you sure this is safe to go into final release for 
1.5.2?


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