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Generate GD images of biological sequences and annotations

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Bio::Graphics::Panel - Generate GD images of Bio::Seq objects


  use Ace::Sequence;  # or any Bio::Seq factory
  use Bio::Graphics::Panel;

  my $db     = Ace->connect(-host=>'',-port=>2005) or die;
  my $cosmid = Ace::Sequence->new(-seq=>'Y16B4A',
				  -db=>$db,-start=>-15000,-end=>15000) or die;

  my @transcripts = $cosmid->transcripts;

  my $panel = Ace::Graphics::Panel->new(
				      -segment => $cosmid,
				      -width  => 800

  $panel->add_track(arrow => $cosmid,
 		  -bump => 0,

  $panel->add_track(transcript => \@transcripts,
 		    -bgcolor   =>  'wheat',
 		    -fgcolor   =>  'black',
                    -key       => 'Curated Genes',
 		    -bump      =>  +1,
 		    -height    =>  10,
 		    -label     =>  1);

  my $boxes = $panel->boxes;
  print $panel->png;


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.
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