[Bioperl-guts-l] bioperl-live/Bio/Graphics FeatureBase.pm, 1.7, 1.8 Glyph.pm, 1.106, 1.107 Panel.pm, 1.116, 1.117

Lincoln Stein lstein at dev.open-bio.org
Thu Jun 15 14:28:26 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Graphics
In directory dev.open-bio.org:/tmp/cvs-serv29188/Bio/Graphics

Modified Files:
	FeatureBase.pm Glyph.pm Panel.pm 
Log Message:
added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list

Index: Panel.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Panel.pm,v
retrieving revision 1.116
retrieving revision 1.117
diff -C2 -d -r1.116 -r1.117
*** Panel.pm	15 Jun 2006 02:03:35 -0000	1.116
--- Panel.pm	15 Jun 2006 18:28:24 -0000	1.117
***************
*** 1140,1143 ****
--- 1140,1144 ----
  goldenrod            DA           A5            20
  gray                 80           80            80
+ grey                 80           80            80
  green                00           80            00
  greenyellow          AD           FF            2F

Index: FeatureBase.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/FeatureBase.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** FeatureBase.pm	9 Jun 2006 19:45:33 -0000	1.7
--- FeatureBase.pm	15 Jun 2006 18:28:24 -0000	1.8
***************
*** 77,81 ****
    my $method = $self->primary_tag;
    my $source = $self->source_tag;
!   return defined $source ? "$method:$source" : $method;
  }
  
--- 77,81 ----
    my $method = $self->primary_tag;
    my $source = $self->source_tag;
!   return $source ne '' ? "$method:$source" : $method;
  }
  

Index: Glyph.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph.pm,v
retrieving revision 1.106
retrieving revision 1.107
diff -C2 -d -r1.106 -r1.107
*** Glyph.pm	15 Jun 2006 02:03:35 -0000	1.106
--- Glyph.pm	15 Jun 2006 18:28:24 -0000	1.107
***************
*** 1025,1029 ****
  sub filled_arrow {
    my $self = shift;
!   my ($gd,$orientation,$x1,$y1,$x2,$y2,$fg,$bg)  = @_;
  
    $orientation *= -1 if $self->{flip};
--- 1025,1031 ----
  sub filled_arrow {
    my $self = shift;
!   my $gd   = shift;
!   my $orientation = shift;
!   my ($x1,$y1,$x2,$y2,$fg,$bg)  = @_;
  
    $orientation *= -1 if $self->{flip};



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