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

Note that this modules depends on GD.

=head1 METHODS

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

=head2 CONSTRUCTORS

There is only one constructor, the new() method.

=over 4

=item $panel = Ace::Graphics::Panel->new(@options)

The new() method creates a new panel object.  The options are
a set of tag/value pairs as follows:

  Option      Value                                Default
  ------      -----                                -------

  -length     Length of sequence segment, in bp    0

  -segment    An Ace::Sequence or Das::Segment     none
              object, used to derive length if
	      not provided

  -offset     Base pair to place at extreme left   $segment->start
	      of image.

  -width      Desired width of image, in pixels    600

  -spacing    Spacing between tracks, in pixels    5

  -pad_top    Additional whitespace between top    0
	      of image and contents, in pixels

  -pad_bottom Additional whitespace between top    0
	      of image and bottom, in pixels

  -pad_left   Additional whitespace between left   0
	      of image and contents, in pixels

  -pad_right  Additional whitespace between right  0
	      of image and bottom, in pixels

  -keycolor   Background color for the key printed 'cornsilk'
              at bottom of panel (if any)

  -keyspacing Spacing between key glyphs in the    10
              key printed at bottom of panel
              (if any)

Typically you will pass new() an object that implements the
Bio::RangeI interface, providing a length() method, from which the
panel will derive its scale.

  $panel = Ace::Graphics::Panel->new(-segment => $sequence,
				     -width   => 800);

new() will return undef in case of an error. If the specified glyph
name is not a valid one, new() will throw an exception.

=back

=head2 OBJECT METHODS

=over 4

=item $track = $panel->add_track($glyph,$features,@options)

The add_track() method adds a new track to the image. 

Tracks are horizontal bands which span the entire width of the panel.
Each track contains a number of graphical elements called "glyphs",
each corresponding to a sequence feature. There are different glyph
types, but each track can only contain a single type of glyph.
Options passed to the track control the color and size of the glyphs,
whether they are allowed to overlap, and other formatting attributes.
The height of a track is determined from its contents and cannot be
directly influenced.

The first two arguments are the glyph name and an array reference
containing the list of features to display.  The order of the
arguments is irrelevant, allowing either of these idioms:

  $panel->add_track(arrow => \@features);
  $panel->add_track(\@features => 'arrow');

The glyph name indicates how each feature is to be rendered.  A
variety of glyphs are available, and the number is growing.
Currently, the following glyphs are available:

  Name        Description
  ----        -----------

  box	      A filled rectangle, nondirectional.

  ellipse     A filled ellipse, nondirectional.

  arrow	      An arrow; can be unidirectional or bidirectional.
	      It is also capable of displaying a scale with
	      major and minor tickmarks, and can be oriented
	      horizontally or vertically.

  segments    A set of filled rectangles connected by solid lines.
	      Used for interrupted features, such as gapped
	      alignments.

  transcript  Similar to segments, but the connecting line is
	      a "hat" shape, and the direction of transcription
	      is indicated by a small arrow.

  transcript2 Similar to transcript, but the arrow that indicates
              the direction of transcription is the last exon
              itself.

  primers     Two inward pointing arrows connected by a line.
	      Used for STSs.

  toomany     A "cloud", to indicate too many features to show