Panel documentation.

 # This script parses a GenBank or EMBL file named on the command
 # line and produces a PNG rendering of it.  Call it like this:
 # render.pl my_file.embl | display -

 use strict;
 use Bio::Graphics;
 use Bio::SeqIO;

 my $file = shift                       or die "provide a sequence file as the argument";
 my $io = Bio::SeqIO->new(-file=>$file) or die "could not create Bio::SeqIO";
 my $seq = $io->next_seq                or die "could not find a sequence in the file";

 my @features = $seq->all_SeqFeatures;

 # sort features by their primary tags
 my %sorted_features;
 for my $f (@features) {
   my $tag = $f->primary_tag;
   push @{$sorted_features{$tag}},$f;
 }

 my $panel = Bio::Graphics::Panel->new(
                                      -length    => $seq->length,
 				      -key_style => 'between',
 				      -width     => 800,
 				      -pad_left  => 10,
 				      -pad_right => 10,
 				      );
 $panel->add_track( arrow => Bio::SeqFeature::Generic->new(-start=>1,
                                                           -end=>$seq->length),
 		  -bump => 0,
 		  -double=>1,
 		  -tick => 2);
 $panel->add_track(generic => Bio::SeqFeature::Generic->new(-start=>1,
							  -end=>$seq->length),
 		  -glyph  => 'generic',
 		  -bgcolor => 'blue',
 		  -label  => 1,
 		 );

 # general case
 my @colors = qw(cyan orange blue purple green chartreuse magenta yellow aqua);
 my $idx    = 0;
 for my $tag (sort keys %sorted_features) {
   my $features = $sorted_features{$tag};
   $panel->add_track($features,
 		    -glyph    =>  'generic',
 		    -bgcolor  =>  $colors[$idx++ % @colors],
 		    -fgcolor  => 'black',
 		    -font2color => 'red',
 		    -key      => "${tag}s",
 		    -bump     => +1,
 		    -height   => 8,
 		    -label    => 1,
 		    -description => 1,
 		   );
 }

 print $panel->png;
 exit 0;

Description

The Bio::Graphics::Panel class provides drawing and formatting
services for any object that implements the Bio::SeqFeatureI
interface, including Ace::Sequence::Feature and Das::Segment::Feature
objects. It can be used to draw sequence annotations, physical
(contig) maps, or any other type of map in which a set of discrete
ranges need to be laid out on the number line.
The module supports a drawing style in which each type of feature
occupies a discrete "track" that spans the width of the display. Each
track will have its own distinctive "glyph", a configurable graphical
representation of the feature.
The module also supports a more flexible style in which several
different feature types and their associated glyphs can occupy the
same track. The choice of glyph is under run-time control.
Semantic zooming (for instance, changing the type of glyph depending
on the density of features) is supported by a callback system for
configuration variables. The module has built-in support for Bio::Das
stylesheets, and stylesheet-driven configuration can be intermixed
with semantic zooming, if desired.
You can add a key to the generated image using either of two key
styles. One style places the key captions at the top of each track.
The other style generates a graphical key at the bottom of the image.
Note that this modules depends on GD.

Methods

_add_track	No description	Code
_do_add_track	No description	Code
add_track	No description	Code
all_callbacks	No description	Code
bgcolor	No description	Code
boxes	No description	Code
colorClosest	No description	Code
color_name_to_rgb	No description	Code
color_names	No description	Code
draw_between_key	No description	Code
draw_bottom_key	No description	Code
draw_empty	No description	Code
draw_grid	No description	Code
draw_side_key	No description	Code
empty_track_style	No description	Code
end	No description	Code
flip	No description	Code
format_key	No description	Code
gd	No description	Code
height	No description	Code
insert_track	No description	Code
key_spacing	No description	Code
key_style	No description	Code
left	No description	Code
length	No description	Code
location2pixel	No description	Code
map_no_trunc	No description	Code
map_pt	No description	Code
new	No description	Code
offset	No description	Code
pad_bottom	No description	Code
pad_left	No description	Code
pad_right	No description	Code
pad_top	No description	Code
png	No description	Code
read_colors	No description	Code
rgb	No description	Code
right	No description	Code
scale	No description	Code
set_pen	No description	Code
spacing	No description	Code
ticks	No description	Code
track_position	No description	Code
translate_color	No description	Code
unshift_track	No description	Code
width	No description	Code

Methods description

None available.

Methods code

_add_track

description