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Ace/Graphics/Track.pm  view on Meta::CPAN

Ace::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects

=head1 SYNOPSIS

  use Ace::Sequence;
  use Ace::Graphics::Panel;

  my $db     = Ace->connect(-host=>'brie2.cshl.org',-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
				     );


  my $track = $panel->add_track('transcript'
   		                -fillcolor =>  'wheat',
				-fgcolor   =>  'black',
				-bump      =>  +1,
				-height    =>  10,
				-label     =>  1);
  foreach (@transcripts) {
     $track->add_feature($_);
  }

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


=head1 DESCRIPTION

The Ace::Graphics::Track class is used by Ace::Graphics::Panel to lay
out a set of sequence features using a uniform glyph type. You will
ordinarily work with panels rather than directly with tracks.

=head1 METHODS

This section describes the class and object methods for
Ace::Graphics::Panel.

=head2 CONSTRUCTORS

There is only one constructor, the new() method.  It is ordinarily
called by Ace::Graphics::Panel, and not in end-developer code.

=over 4

=item $track = Ace::Graphics::Track->new($glyph_name,$features,@options)

The new() method creates a new track object from the provided glyph
name and list of features.  The arguments are similar to those in
Ace::Graphics::Panel->new().

If successful new() will return a new Ace::Graphics::Track.
Otherwise, it will return undef.

If the specified glyph name is not a valid one, new() will throw an
exception.

=back

=head2 OBJECT METHODS

Once a track is created, the following methods can be invoked.

=over 4

=item $track->add_feature($feature)

This adds a new feature to the track.  The feature can either be a
single object that implements the Bio::SeqFeatureI interface (such as
an Ace::Sequence::Feature or Das::Segment::Feature), or can be an
anonymous array containing a set of related features.  In the latter
case, the track will attempt to keep the features in the same
horizontal band and will not allow any other features to overlap.

=item $track->add_group($group)

This behaves the same as add_feature(), but requires that its argument
be an array reference containing a list of grouped features.

=item $track->draw($gd,$left,$top)

Render the track on a previously-created GD::Image object.  The $left
and $top arguments indicate the position at which to start rendering.

=item $boxes = $track->boxes($left,$top)

=item @boxes = $track->boxes($left,$top)

Return an array of array references indicating glyph coordinates for
each of the render features.  $left and $top indicate the offset for
the track on the image plane.  In a scalar context, this method
returns an array reference of glyph coordinates.  In a list context,
it returns the list itself.

See Ace::Graphics::Panel->boxes() for the format of the result.

=back

=head2 ACCESSORS

The following accessor methods provide access to various attributes of
the track object.  Called with no arguments, they each return the
current value of the attribute.  Called with a single argument, they
set the attribute and return its previous value.

Note that in most cases you must change attributes before the track's
layout() method is called.

   Accessor Name      Description
   -------------      -----------

   scale()	      Get/set the track scale, measured in pixels/bp
   lineheight()	      Get/set the height of each glyph, pixels
   width()	      Get/set the width of the track
   bump()	      Get/set the bump direction