support get_tag_values() and get_SeqFeatures() calls rather than nons…

…tandard Bio::Graphics::Feature API

lib/Bio/Graphics/Glyph/ideogram.pm

@@ -1,6 +1,6 @@
 package Bio::Graphics::Glyph::ideogram;
 
-# $Id: ideogram.pm,v 1.3 2009-03-10 16:02:58 scottcain Exp $
+# $Id: ideogram.pm,v 1.4 2009-03-17 12:45:07 lstein Exp $
 # Glyph to draw chromosome ideograms
 
 use strict qw/vars refs/;
@@ -74,8 +74,8 @@ sub draw_component {
   # force odd width so telomere arcs are centered
   $y2 ++ if ($y2 - $y1) % 2;
 
-  my ($stain) = $feat->attributes('stain');
-  ($stain)    = $feat->attributes('Stain') unless $stain;
+  my ($stain) = $feat->get_tag_values('stain');
+  ($stain)    = $feat->get_tag_values('Stain') unless $stain;
 
   # Some genome sequences don't contain substantial telomere sequence (i.e. Arabidopsis)
   # We can suggest their presence at the tips of the chromosomes by setting fake_telomeres = 1
@@ -316,7 +316,7 @@ sub parts {
   my $self  = shift;
   my $f     = $self->feature;
   my $level = $self->level + 1;
-  my @subf  = sort {$a->start <=> $b->start} $f->segments;
+  my @subf  = sort {$a->start <=> $b->start} $f->get_SeqFeatures;
   return  $self->factory->make_glyph($level,@subf);
 }
 

lib/Bio/Graphics/Glyph/wiggle_xyplot.pm

@@ -182,8 +182,8 @@ sub draw_plot {
 	my $y1             = $bottom - ($mean+$variance - $min_score) * $y_scale;
 	my $y2             = $bottom - ($mean-$variance - $min_score) * $y_scale;
 	my $y              = $bottom - ($mean - $min_score) * $y_scale;
-	my $mean_color     = $self->panel->translate_color('red:0.25');
-	my $variance_color = $self->panel->translate_color('grey:0.05');
+	my $mean_color     = $self->panel->translate_color('yellow:0.80');
+	my $variance_color = $self->panel->translate_color('grey:0.25');
 	$gd->filledRectangle($left,$y1,$right,$y2,$variance_color);
 	$gd->line($left,$y,$right,$y,$mean_color);
 
@@ -194,7 +194,7 @@ sub draw_plot {
 	$gd->string($font,$x1,$y1-$font->height/2,'+1sd',$fcolor);
 	$gd->string($font,$x1,$y2-$font->height/2,'-1sd',$fcolor);
 	$gd->string($font,$x1,$y2-$font->height/2,'-1sd',$fcolor);
-	$gd->string($font,$x2,$y -$font->height/2,'mn',  $fcolor);
+	$gd->string($font,$x2,$y -$font->height/2,'mn',  $variance_color);
     }
 }