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

package Ace::Graphics::Panel;
# This embodies the logic for drawing multiple tracks.

use Ace::Graphics::Track;
use GD;
use Carp 'croak';
use strict;
use constant KEYLABELFONT => gdSmallFont;
use constant KEYSPACING   => 10; # extra space between key columns
use constant KEYPADTOP    => 5;  # extra padding before the key starts
use constant KEYCOLOR     => 'cornsilk';

*push_track = \&add_track;

# package global
my %COLORS;

# Create a new panel of a given width and height, and add lists of features
# one by one
sub new {
  my $class = shift;
  my %options = @_;

  $class->read_colors() unless %COLORS;

  my $length = $options{-length} || 0;
  my $offset = $options{-offset} || 0;
  my $spacing = $options{-spacing} || 5;
  my $keycolor = $options{-keycolor} || KEYCOLOR;
  my $keyspacing = $options{-keyspacing} || KEYSPACING;

  $length   ||= $options{-segment}->length  if $options{-segment};
  $offset   ||= $options{-segment}->start-1 if $options{-segment};

  return bless {
		tracks => [],
		width  => $options{-width} || 600,
		pad_top    => $options{-pad_top}||0,
		pad_bottom => $options{-pad_bottom}||0,
		pad_left   => $options{-pad_left}||0,
		pad_right  => $options{-pad_right}||0,
		length => $length,
		offset => $offset,
		height => 0, # AUTO
		spacing => $spacing,
		keycolor => $keycolor,
		keyspacing => $keyspacing,
	       },$class;
}

sub width {
  my $self = shift;
  my $d = $self->{width};
  $self->{width} = shift if @_;
  $d + $self->pad_left + $self->pad_right;
}

sub spacing {
  my $self = shift;
  my $d = $self->{spacing};
  $self->{spacing} = shift if @_;
  $d;

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

  -label      Whether to draw a label	false

  -bump	      Bump direction		0

  -connect_groups                       false
              Connect groups by a
	      dashed line (see below)

  -key        Show this track in the    undef
              key

Colors can be expressed in either of two ways: as symbolic names such
as "cyan" and as HTML-style #RRGGBB triples.  The symbolic names are
the 140 colors defined in the Netscape/Internet Explorer color cube,
and can be retrieved using the Ace::Graphics::Panel->color_names()
method.

The background color is used for the background color of the track
itself.  The foreground color controls the color of lines and strings.
The interior color is used for filled objects such as boxes.

The -label argument controls whether or not the ID of the feature
should be printed next to the feature.  It is accepted by most, but
not all of the glyphs.

The -bump argument controls what happens when glyphs collide.  By
default, they will simply overlap (value 0).  A -bump value of +1 will
cause overlapping glyphs to bump downwards until there is room for
them.  A -bump value of -1 will cause overlapping glyphs to bump
upwards.

The -key argument declares that the track is to be shown in a key
appended to the bottom of the image.  The key contains a picture of a
glyph and a label describing what the glyph means.  The label is
specified in the argument to -key.

If present, the -glyph argument overrides the glyph given in the first
or second argument.

add_track() returns an Ace::Graphics::Track object.  You can use this
object to add additional features or to control the appearance of the
track with greater detail, or just ignore it.  Tracks are added in
order from the top of the image to the bottom.  To add tracks to the
top of the image, use unshift_track().

Typical usage is:

 $panel->add_track( thistle    => \@genes,
 		    -fillcolor =>  'green',
 		    -fgcolor   =>  'black',
 		    -bump      =>  +1,
 		    -height    => 10,
 		    -label     => 1);

=item $track = unshift_track($glyph,$features,@options)

unshift_track() works like add_track(), except that the new track is
added to the top of the image rather than the bottom.

B<Adding groups of features:> It is not uncommon to add a group of
features which are logically connected, such as the 5' and 3' ends of
EST reads.  To group features into sets that remain on the same
horizontal position and bump together, pass the sets as an anonymous
array.  To connect the groups by a dashed line, pass the
-connect_groups argument with a true value.  For example:

  $panel->add_track(segments => [[$abc_5,$abc_3],
				 [$xxx_5,$xxx_3],
				 [$yyy_5,$yyy_3]],
		    -connect_groups => 1);

=item $gd = $panel->gd

The gd() method lays out the image and returns a GD::Image object
containing it.  You may then call the GD::Image object's png() or
jpeg() methods to get the image data.

=item $png = $panel->png

The png() method returns the image as a PNG-format drawing, without
the intermediate step of returning a GD::Image object.

=item $boxes = $panel->boxes

=item @boxes = $panel->boxes

The boxes() method returns the coordinates of each glyph, useful for
constructing an image map.  In a scalar context, boxes() returns an
array ref.  In an list context, the method returns the array directly.

Each member of the list is an anonymous array of the following format:

  [ $feature, $x1, $y1, $x2, $y2 ]

The first element is the feature object; either an
Ace::Sequence::Feature, a Das::Segment::Feature, or another Bioperl
Bio::SeqFeatureI object.  The coordinates are the topleft and
bottomright corners of the glyph, including any space allocated for
labels.

=back

=head2 ACCESSORS

The following accessor methods provide access to various attributes of
the panel 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 prior to invoking
gd(), png() or boxes().  These three methods all invoke an internal
layout() method which places the tracks and the glyphs within them,
and then caches the result.

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

   width()	      Get/set width of panel
   spacing()	      Get/set spacing between tracks
   length()	      Get/set length of segment (bp)
   pad_top()	      Get/set top padding