Made some changes to allow xyplot subtracks to be drawn on a single p…

…lot.

lib/Bio/Graphics/Glyph.pm

@@ -700,7 +700,7 @@ sub fillcolor {
 # we also look for the "fillcolor" option for Ace::Graphics compatibility
 sub bgcolor {
   my $self = shift;
-  my $bgcolor = $self->option('bgcolor');
+  my $bgcolor = $self->feature->attributes('bgcolor') || $self->option('bgcolor'); # Let feature attribute override color
   my $index = defined $bgcolor ? $bgcolor : $self->option('fillcolor');
   $index = 'white' unless defined $index;
 

lib/Bio/Graphics/Glyph/scale.pm

@@ -0,0 +1,109 @@
+package Bio::Graphics::Glyph::scale;
+
+use strict;
+use base qw(Bio::Graphics::Glyph::segmented_keyglyph Bio::Graphics::Glyph::xyplot);
+
+sub my_description {
+    return <<END;
+This glyph is used internally by GBrowse to draw a scale bar.
+It should not be used explicitly.
+END
+}
+
+sub my_options {
+    return;
+}
+
+sub draw {
+    my $self = shift;
+
+    my ($gd,$dx,$dy) = @_;
+    my ($left,$top,$right,$bottom) = $self->calculate_boundaries($dx,$dy);
+
+    $self->panel->startGroup($gd);
+
+    my $max_score = $self->max_score || 100;
+    my $min_score = $self->min_score || 0;
+
+    $max_score = Bio::Graphics::Glyph::xyplot::max10($max_score);
+    $min_score = Bio::Graphics::Glyph::xyplot::min10($min_score);
+
+    my $height = $bottom - $top;
+    my $scale  = $max_score > $min_score ? $height/($max_score-$min_score)
+                                       : 1;
+    my $x = $left;
+    my $y = $top + $self->pad_top;
+
+    # position of "0" on the scale
+    my $y_origin = $min_score <= 0 ? $bottom - (0 - $min_score) * $scale : $bottom;
+    $y_origin    = $top if $max_score < 0;
+
+    $self->panel->startGroup($gd);
+    $self->_draw_scale($gd,$scale,$min_score,$max_score,$dx,$dy,$y_origin);
+
+    $self->panel->endGroup($gd);
+}
+
+sub _determine_side {
+    my $self = shift;
+    return 'three';
+}
+
+# Added pad_top subroutine (pad_top of Glyph.pm, which is called when executing $self->pad_top
+# returns 0, so we need to override it here)
+sub pad_top {
+  my $self = shift;
+  my $pad = $self->Bio::Graphics::Glyph::generic::pad_top(@_);
+  if ($pad < ($self->font('gdTinyFont')->height)) {
+    $pad = $self->font('gdTinyFont')->height;  # extra room for the scale
+  }
+  $pad;
+}
+
+sub pad_left {
+    my $self = shift;
+    my $pad  = $self->SUPER::pad_left(@_);
+    return $pad unless $self->option('variance_band');
+    $pad    += length('+1sd')/2 * $self->font('gdTinyFont')->width+3;
+    return $pad;
+}
+
+sub new {
+  my $self = shift;
+  return $self->SUPER::new(@_,-level=>-1);
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+Bio::Graphics::Glyph::scale - The "scale" glyph
+
+=head1 SYNOPSIS
+
+  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
+
+=head1 DESCRIPTION
+
+This glyph is used internally by GBrowse to draw a scale bar.
+It should not be used explicitly.
+
+=head1 BUGS
+
+Please report them.
+
+=head1 SEE ALSO
+
+L<Bio::Graphics::Glyph::xyplot>,
+
+=head1 AUTHOR
+
+Copyright (c) 2010 Ontario Institute for Cancer Research
+
+This library is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.  See DISCLAIMER.txt for
+disclaimers of warranty.
+
+=cut

lib/Bio/Graphics/Glyph/xyplot.pm

@@ -542,6 +542,13 @@ sub minor_ticks {
 
 }
 
+# Let the feature attributes override the labelcolor
+sub labelcolor {
+  my $self = shift;
+  return $self->feature->attributes('labelcolor') ? $self->translate_color($self->feature->attributes('labelcolor'))
+    : $self->SUPER::labelcolor;
+}
+
 # we are unbumpable!
 sub bump {
   return 0;

lib/Bio/Graphics/Panel.pm

@@ -355,18 +355,21 @@ sub _do_add_track {
       my $feature = shift;
       return 'track' if eval { defined $feature->primary_tag && $feature->primary_tag  eq 'track' };
       return 'group' if eval { defined $feature->primary_tag && $feature->primary_tag  eq 'group' };
+      return 'scale' if eval { defined $feature->primary_tag && $feature->primary_tag  eq 'scale' };
       return $map->($feature,'glyph',$self);
     }
    : ref($map) eq 'HASH' ? sub {
      my $feature = shift;
      return 'track' if eval { defined $feature->primary_tag && $feature->primary_tag  eq 'track' };
      return 'group' if eval { defined $feature->primary_tag && $feature->primary_tag  eq 'group' };
+     return 'scale' if eval { defined $feature->primary_tag && $feature->primary_tag  eq 'scale' };
      return eval {$map->{$feature->primary_tag}} || 'generic';
    }
    : sub {
      my $feature = shift;
      return 'track' if eval { defined $feature->primary_tag && $feature->primary_tag  eq 'track' };
      return 'group' if eval { defined $feature->primary_tag && $feature->primary_tag  eq 'group' };
+     return 'scale' if eval { defined $feature->primary_tag && $feature->primary_tag  eq 'scale' };
      return $glyph_name;
    };
   $self->_add_track($position,$features,-map=>$panel_map,-stylesheet=>$ss,-options=>\%options);