AcePerl
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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;
}
sub length {
my $self = shift;
my $d = $self->{length};
if (@_) {
my $l = shift;
$l = $l->length if ref($l) && $l->can('length');
$self->{length} = $l;
}
$d;
}
sub pad_top {
my $self = shift;
my $d = $self->{pad_top};
$self->{pad_top} = shift if @_;
$d || 0;
}
sub pad_bottom {
my $self = shift;
my $d = $self->{pad_bottom};
$self->{pad_bottom} = shift if @_;
$d || 0;
}
sub pad_left {
my $self = shift;
my $d = $self->{pad_left};
$self->{pad_left} = shift if @_;
$d || 0;
}
sub pad_right {
my $self = shift;
my $d = $self->{pad_right};
$self->{pad_right} = shift if @_;
$d || 0;
}
sub add_track {
my $self = shift;
# due to indecision, we accept features
# and/or glyph types in the first two arguments
my ($features,$glyph_name) = ([],'generic');
while ( $_[0] !~ /^-/) {
my $arg = shift;
$features = $arg and next if ref($arg);
$glyph_name = $arg and next unless ref($arg);
}
$self->_add_track($glyph_name,$features,+1,@_);
}
sub unshift_track {
my $self = shift;
# due to indecision, we accept features
# and/or glyph types in the first two arguments
my ($features,$glyph_name) = ([],'generic');
while ( (my $arg = shift) !~ /^-/) {
$features = $arg and next if ref($arg);
$glyph_name = $arg and next unless ref($arg);
}
$self->_add_track($glyph_name,$features,-1,@_);
}
sub _add_track {
my $self = shift;
my ($glyph_type,$features,$direction,@options) = @_;
unshift @options,'-offset' => $self->{offset} if defined $self->{offset};
unshift @options,'-length' => $self->{length} if defined $self->{length};
$features = [$features] unless ref $features eq 'ARRAY';
my $track = Ace::Graphics::Track->new($glyph_type,$features,@options);
$track->set_scale(abs($self->length),$self->{width});
$track->panel($self);
if ($direction >= 0) {
push @{$self->{tracks}},$track;
} else {
unshift @{$self->{tracks}},$track;
}
return $track;
}
sub height {
my $self = shift;
my $spacing = $self->spacing;
my $key_height = $self->format_key;
my $height = 0;
$height += $_->height + $spacing foreach @{$self->{tracks}};
$height + $key_height + $self->pad_top + $self->pad_bottom;
}
sub gd {
my $self = shift;
return $self->{gd} if $self->{gd};
my $width = $self->width;
my $height = $self->height;
my $gd = GD::Image->new($width,$height);
my %translation_table;
for my $name ('white','black',keys %COLORS) {
my $idx = $gd->colorAllocate(@{$COLORS{$name}});
$translation_table{$name} = $idx;
}
$self->{translations} = \%translation_table;
$self->{gd} = $gd;
my $offset = 0;
my $pl = $self->pad_left;
my $pt = $self->pad_top;
for my $track (@{$self->{tracks}}) {
$track->draw($gd,$pl,$offset+$pt);
$offset += $track->height + $self->spacing;
}
$self->draw_key($gd,$pl,$offset);
return $self->{gd} = $gd;
}
sub draw_key {
my $self = shift;
my ($gd,$left,$top) = @_;
my $key_glyphs = $self->{key_glyphs} or return;
my $color = $self->translate($self->{keycolor});
$gd->filledRectangle($left,$top,$self->width,$self->height,$color);
$gd->string(KEYLABELFONT,$left,KEYPADTOP+$top,"KEY:",1);
$top += KEYLABELFONT->height + KEYPADTOP;
$_->draw($gd,$left,$top) foreach @$key_glyphs;
}
Ace/Graphics/Panel.pm view on Meta::CPAN
slateblue 6A 5A CD
slategray 70 80 90
snow FF FA FA
springgreen 00 FF 7F
steelblue 46 82 B4
tan D2 B4 8C
teal 00 80 80
thistle D8 BF D8
tomato FF 63 47
turquoise 40 E0 D0
violet EE 82 EE
wheat F5 DE B3
whitesmoke F5 F5 F5
yellow FF FF 00
yellowgreen 9A CD 32
__END__
=head1 NAME
Ace::Graphics::Panel - 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
);
$panel->add_track(arrow => $cosmid,
-bump => 0,
-tick=>2);
$panel->add_track(transcript => \@transcripts,
-fillcolor => 'wheat',
-fgcolor => 'black',
-key => 'Curated Genes',
-bump => +1,
-height => 10,
-label => 1);
my $boxes = $panel->boxes;
print $panel->png;
=head1 DESCRIPTION
The Ace::Graphics::Panel class provides drawing and formatting
services for Ace::Sequence::Feature objects or Das::Segment::Feature
objects.
Typically you will begin by creating a new Ace::Graphics::Panel
object, passing it the width of the visual display and the length of
the segment.
You will then call add_track() one or more times to add sets of
related features to the picture. When you have added all the features
you desire, you may call png() to convert the image into a PNG-format
image, or boxes() to return coordinate information that can be used to
create an imagemap.
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
Ace/Graphics/Panel.pm view on Meta::CPAN
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
pad_left() Get/set left padding
pad_bottom() Get/set bottom padding
pad_right() Get/set right padding
=head2 INTERNAL METHODS
The following methods are used internally, but may be useful for those
implementing new glyph types.
=over 4
=item @names = Ace::Graphics::Panel->color_names
Return the symbolic names of the colors recognized by the panel
object. In a scalar context, returns an array reference.
=item @rgb = $panel->rgb($index)
Given a GD color index (between 0 and 140), returns the RGB triplet
corresponding to this index. This method is only useful within a
glyph's draw() routine, after the panel has allocated a GD::Image and
is populating it.
=item $index = $panel->translate($color)
Given a color, returns the GD::Image index. The color may be
symbolic, such as "turquoise", or a #RRGGBB triple, as in #F0E0A8.
This method is only useful within a glyph's draw() routine, after the
panel has allocated a GD::Image and is populating it.
=item $panel->set_pen($width,$color)
Changes the width and color of the GD drawing pen to the values
indicated. This is called automatically by the GlyphFactory fgcolor()
method.
=back
=head1 BUGS
Please report them.
=head1 SEE ALSO
L<Ace::Sequence>,L<Ace::Sequence::Feature>,
L<Ace::Graphics::Track>,L<Ace::Graphics::Glyph>,
L<GD>
=head1 AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
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.
=cut
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