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'
24 -fillcolor => 'wheat',
25 -fgcolor => 'black',
26 -bump => +1,
27 -height => 10,
28 -label => 1);
29 foreach (@transcripts) {
30 $track->add_feature($_);
31 }
32 my $boxes = $panel->boxes;
34 print $panel->png;
35
37 The Ace::Graphics::Track class is used by Ace::Graphics::Panel to lay
38 out a set of sequence features using a uniform glyph type. You will
39 ordinarily work with panels rather than directly with tracks.
40
42 This section describes the class and object methods for Ace::Graph‐
43 ics::Panel.
44 CONSTRUCTORS
46 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. Other‐
56 wise, 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.
64 $track->add_feature($feature)
66 This adds a new feature to the track. The feature can either be a
67 single object that implements the Bio::SeqFeatureI interface (such
68 as an Ace::Sequence::Feature or Das::Segment::Feature), or can be
69 an anonymous array containing a set of related features. In the
70 latter case, the track will attempt to keep the features in the
71 same horizontal band and will not allow any other features to over‐
72 lap.
73 $track->add_group($group)
75 This behaves the same as add_feature(), but requires that its argu‐
76 ment be an array reference containing a list of grouped 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 off‐
87 set 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
96 the track object. Called with no arguments, they each return the cur‐
97 rent value of the attribute. Called with a single argument, they set
98 the attribute and return its previous value.
99 Note that in most cases you must change attributes before the track's
101 layout() method is called.
102 Accessor Name Description
104 ------------- -----------
105 scale() Get/set the track scale, measured in pixels/bp
107 lineheight() Get/set the height of each glyph, pixels
108 width() Get/set the width of the track
109 bump() Get/set the bump direction
110 INTERNAL METHODS
112 The following methods are used internally, but may be useful for those
114 implementing new glyph types.
115 $glyphs = $track->layout
117 Layout the features, and return an anonymous array of Ace::Graph‐
118 ics::Glyph objects that have been created and correctly positioned.
119 Because layout is an expensive operation, calling this method sev‐
121 eral times will return the previously-cached result, ignoring any
122 changes to track attributes.
123 $height = $track->height
125 Invokes layout() and returns the height of the track.
126 $glyphs = $track->glyphs
128 Returns the glyph cache. Returns undef before layout() and a ref‐
129 erence to an array of glyphs after layout().
130 $factory = $track->make_factory(@options)
132 Given a set of options (argument/value pairs), returns a
133 Ace::Graphics::GlyphFactory for use in creating the glyphs with the
134 desired settings.
135
137 Please report them.
138
140 Ace::Sequence,Ace::Sequence::Feature,Ace::Graphics::Panel, Ace::Graph‐
141 ics::GlyphFactory,Ace::Graphics::Glyph
142
144 Lincoln Stein <lstein@cshl.org>.
145 Copyright (c) 2001 Cold Spring Harbor Laboratory
147 This library is free software; you can redistribute it and/or modify it
149 under the same terms as Perl itself. See DISCLAIMER.txt for dis‐
150 claimers of warranty.
151perl v5.8.8 2001-02-20 Ace::Graphics::Track(3)