Ace::Graphics::Track

NAME

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

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;

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.

METHODS

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

CONSTRUCTORS

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

$track = Ace::Graphics::Track->new($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.

OBJECT METHODS

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

$track->add_feature($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.

$track->add_group($group): This behaves the same as add_feature(), but requires that its argument be an array reference containing a list of grouped features.

$track->draw($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.

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

@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.

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

INTERNAL METHODS

The following methods are used internally, but may be useful for those implementing new glyph types.

$glyphs = $track->layout: Layout the features, and return an anonymous array of Ace::Graphics::Glyph objects that have been created and correctly positioned. Because layout is an expensive operation, calling this method several times will return the previously-cached result, ignoring any changes to track attributes.

$height = $track->height: Invokes layout() and returns the height of the track.

$glyphs = $track->glyphs: Returns the glyph cache. Returns undef before layout() and a reference to an array of glyphs after layout().

$factory = $track->make_factory(@options): Given a set of options (argument/value pairs), returns a Ace::Graphics::GlyphFactory for use in creating the glyphs with the desired settings.

BUGS

Please report them.

AUTHOR

Lincoln Stein <[email protected]>.

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.

2022-10-19

perl v5.36.0