1Ace::Graphics::Track(3)User Contributed Perl DocumentatioAnce::Graphics::Track(3)
2
6 Ace::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects
7
9 use Ace::Sequence;
10 use Ace::Graphics::Panel;
11 my $db = Ace->connect(-host=>'brie2.cshl.org',-port=>2005) or die;
13 my $cosmid = Ace::Sequence->new(-seq=>'Y16B4A',
14 -db=>$db,-start=>-15000,-end=>15000) or die;
15 my @transcripts = $cosmid->transcripts;
17 my $panel = Ace::Graphics::Panel->new(
19 -segment => $cosmid,
20 -width => 800
21 );
22 my $track = $panel->add_track('transcript'
25 -fillcolor => 'wheat',
26 -fgcolor => 'black',
27 -bump => +1,
28 -height => 10,
29 -label => 1);
30 foreach (@transcripts) {
31 $track->add_feature($_);
32 }
33 my $boxes = $panel->boxes;
35 print $panel->png;
36
38 The Ace::Graphics::Track class is used by Ace::Graphics::Panel to lay
39 out a set of sequence features using a uniform glyph type. You will
40 ordinarily work with panels rather than directly with tracks.
41
43 This section describes the class and object methods for
44 Ace::Graphics::Panel.
45 CONSTRUCTORS
47 There is only one constructor, the new() method. It is ordinarily
48 called by Ace::Graphics::Panel, and not in end-developer code.
49 $track = Ace::Graphics::Track->new($glyph_name,$features,@options)
51 The new() method creates a new track object from the provided glyph
52 name and list of features. The arguments are similar to those in
53 Ace::Graphics::Panel->new().
54 If successful new() will return a new Ace::Graphics::Track.
56 Otherwise, it will return undef.
57 If the specified glyph name is not a valid one, new() will throw an
59 exception.
60 OBJECT METHODS
62 Once a track is created, the following methods can be invoked.
63 $track->add_feature($feature)
65 This adds a new feature to the track. The feature can either be a
66 single object that implements the Bio::SeqFeatureI interface (such
67 as an Ace::Sequence::Feature or Das::Segment::Feature), or can be
68 an anonymous array containing a set of related features. In the
69 latter case, the track will attempt to keep the features in the
70 same horizontal band and will not allow any other features to
71 overlap.
72 $track->add_group($group)
74 This behaves the same as add_feature(), but requires that its
75 argument be an array reference containing a list of grouped
76 features.
77 $track->draw($gd,$left,$top)
79 Render the track on a previously-created GD::Image object. The
80 $left and $top arguments indicate the position at which to start
81 rendering.
82 $boxes = $track->boxes($left,$top)
84 @boxes = $track->boxes($left,$top)
85 Return an array of array references indicating glyph coordinates
86 for each of the render features. $left and $top indicate the
87 offset for the track on the image plane. In a scalar context, this
88 method returns an array reference of glyph coordinates. In a list
89 context, it returns the list itself.
90 See Ace::Graphics::Panel->boxes() for the format of the result.
92 ACCESSORS
94 The following accessor methods provide access to various attributes of
95 the track object. Called with no arguments, they each return the
96 current value of the attribute. Called with a single argument, they
97 set the attribute and return its previous value.
98 Note that in most cases you must change attributes before the track's
100 layout() method is called.
101 Accessor Name Description
103 ------------- -----------
104 scale() Get/set the track scale, measured in pixels/bp
106 lineheight() Get/set the height of each glyph, pixels
107 width() Get/set the width of the track
108 bump() Get/set the bump direction
109 INTERNAL METHODS
111 The following methods are used internally, but may be useful for those
112 implementing new glyph types.
113 $glyphs = $track->layout
115 Layout the features, and return an anonymous array of
116 Ace::Graphics::Glyph objects that have been created and correctly
117 positioned.
118 Because layout is an expensive operation, calling this method
120 several times will return the previously-cached result, ignoring
121 any changes to track attributes.
122 $height = $track->height
124 Invokes layout() and returns the height of the track.
125 $glyphs = $track->glyphs
127 Returns the glyph cache. Returns undef before layout() and a
128 reference to an array of glyphs after layout().
129 $factory = $track->make_factory(@options)
131 Given a set of options (argument/value pairs), returns a
132 Ace::Graphics::GlyphFactory for use in creating the glyphs with the
133 desired settings.
134
136 Please report them.
137
139 Ace::Sequence,Ace::Sequence::Feature,Ace::Graphics::Panel,
140 Ace::Graphics::GlyphFactory,Ace::Graphics::Glyph
141
143 Lincoln Stein <lstein@cshl.org>.
144 Copyright (c) 2001 Cold Spring Harbor Laboratory
146 This library is free software; you can redistribute it and/or modify it
148 under the same terms as Perl itself. See DISCLAIMER.txt for
149 disclaimers of warranty.
150perl v5.32.0 2020-07-28 Ace::Graphics::Track(3)