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<title>Ace::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects</title>
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<ul>
<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#methods">METHODS</a></li>
<ul>
<li><a href="#constructors">CONSTRUCTORS</a></li>
<li><a href="#object_methods">OBJECT METHODS</a></li>
<li><a href="#accessors">ACCESSORS</a></li>
<li><a href="#internal_methods">INTERNAL METHODS</a></li>
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<p>
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<h1><a name="name">NAME</a></h1>
<p>Ace::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects</p>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
use Ace::Sequence;
use Ace::Graphics::Panel;</pre>
<pre>
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;</pre>
<pre>
my @transcripts = $cosmid->transcripts;</pre>
<pre>
my $panel = Ace::Graphics::Panel->new(
-segment => $cosmid,
-width => 800
);</pre>
<pre>
my $track = $panel->add_track('transcript'
-fillcolor => 'wheat',
-fgcolor => 'black',
-bump => +1,
-height => 10,
-label => 1);
foreach (@transcripts) {
$track->add_feature($_);
}</pre>
<pre>
my $boxes = $panel->boxes;
print $panel->png;</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<p>The Ace::Graphics::Track class is used by Ace::Graphics::Panel to lay
out a set of sequence features using a uniform glyph type. You will
ordinarily work with panels rather than directly with tracks.</p>
<p>
</p>
<hr />
<h1><a name="methods">METHODS</a></h1>
<p>This section describes the class and object methods for
Ace::Graphics::Panel.</p>
<p>
</p>
<h2><a name="constructors">CONSTRUCTORS</a></h2>
<p>There is only one constructor, the <a href="#new"><code>new()</code></a> method. It is ordinarily
called by Ace::Graphics::Panel, and not in end-developer code.</p>
<dl>
<dt><strong><a name="new" class="item">$track = Ace::Graphics::Track-><code>new($glyph_name,$features,@options)</code></a></strong>
<dd>
<p>The <a href="#new"><code>new()</code></a> method creates a new track object from the provided glyph
name and list of features. The arguments are similar to those in
Ace::Graphics::Panel-><a href="#new"><code>new()</code></a>.</p>
</dd>
<dd>
<p>If successful <a href="#new"><code>new()</code></a> will return a new Ace::Graphics::Track.
Otherwise, it will return undef.</p>
</dd>
<dd>
<p>If the specified glyph name is not a valid one, <a href="#new"><code>new()</code></a> will throw an
exception.</p>
</dd>
</li>
</dl>
<p>
</p>
<h2><a name="object_methods">OBJECT METHODS</a></h2>
<p>Once a track is created, the following methods can be invoked.</p>
<dl>
<dt><strong><a name="add_feature" class="item">$track-><code>add_feature($feature)</code></a></strong>
<dd>
<p>This adds a new feature to the track. The feature can either be a
single object that implements the Bio::SeqFeatureI interface (such as
an Ace::Sequence::Feature or Das::Segment::Feature), or can be an
anonymous array containing a set of related features. In the latter
case, the track will attempt to keep the features in the same
horizontal band and will not allow any other features to overlap.</p>
</dd>
</li>
<dt><strong><a name="add_group" class="item">$track-><code>add_group($group)</code></a></strong>
<dd>
<p>This behaves the same as <a href="#add_feature"><code>add_feature()</code></a>, but requires that its argument
be an array reference containing a list of grouped features.</p>
</dd>
</li>
<dt><strong><a name="draw" class="item">$track-><code>draw($gd,$left,$top)</code></a></strong>
<dd>
<p>Render the track on a previously-created GD::Image object. The $left
and $top arguments indicate the position at which to start rendering.</p>
</dd>
</li>
<dt><strong><a name="boxes" class="item">$boxes = $track-><code>boxes($left,$top)</code></a></strong>
<dt><strong>@boxes = $track-><code>boxes($left,$top)</code></strong>
<dd>
<p>Return an array of array references indicating glyph coordinates for
each of the render features. $left and $top indicate the offset for
the track on the image plane. In a scalar context, this method
returns an array reference of glyph coordinates. In a list context,
it returns the list itself.</p>
</dd>
<dd>
<p>See Ace::Graphics::Panel-><a href="#boxes"><code>boxes()</code></a> for the format of the result.</p>
</dd>
</li>
</dl>
<p>
</p>
<h2><a name="accessors">ACCESSORS</a></h2>
<p>The following accessor methods provide access to various attributes of
the track object. Called with no arguments, they each return the
current value of the attribute. Called with a single argument, they
set the attribute and return its previous value.</p>
<p>Note that in most cases you must change attributes before the track's
<a href="#layout"><code>layout()</code></a> method is called.</p>
<pre>
Accessor Name Description
------------- -----------</pre>
<pre>
scale() Get/set the track scale, measured in pixels/bp
lineheight() Get/set the height of each glyph, pixels
width() Get/set the width of the track
bump() Get/set the bump direction</pre>
<p>
</p>
<h2><a name="internal_methods">INTERNAL METHODS</a></h2>
<p>The following methods are used internally, but may be useful for those
implementing new glyph types.</p>
<dl>
<dt><strong><a name="layout" class="item">$glyphs = $track->layout</a></strong>
<dd>
<p>Layout the features, and return an anonymous array of
Ace::Graphics::Glyph objects that have been created and correctly
positioned.</p>
</dd>
<dd>
<p>Because layout is an expensive operation, calling this method several
times will return the previously-cached result, ignoring any changes
to track attributes.</p>
</dd>
</li>
<dt><strong><a name="height" class="item">$height = $track->height</a></strong>
<dd>
<p>Invokes <a href="#layout"><code>layout()</code></a> and returns the height of the track.</p>
</dd>
</li>
<dt><strong><a name="glyphs" class="item">$glyphs = $track->glyphs</a></strong>
<dd>
<p>Returns the glyph cache. Returns undef before <a href="#layout"><code>layout()</code></a> and a
reference to an array of glyphs after <a href="#layout"><code>layout()</code></a>.</p>
</dd>
</li>
<dt><strong><a name="make_factory" class="item">$factory = $track-><code>make_factory(@options)</code></a></strong>
<dd>
<p>Given a set of options (argument/value pairs), returns a
Ace::Graphics::GlyphFactory for use in creating the glyphs with the
desired settings.</p>
</dd>
</li>
</dl>
<p>
</p>
<hr />
<h1><a name="bugs">BUGS</a></h1>
<p>Please report them.</p>
<p>
</p>
<hr />
<h1><a name="see_also">SEE ALSO</a></h1>
<p><a href="/AcePerl/docs/./Ace/Sequence.html">the Ace::Sequence manpage</a>,<a href="/AcePerl/docs/./Ace/Sequence/Feature.html">the Ace::Sequence::Feature manpage</a>,<a href="/AcePerl/docs/./Ace/Graphics/Panel.html">the Ace::Graphics::Panel manpage</a>,
<a href="/AcePerl/docs/./Ace/Graphics/GlyphFactory.html">the Ace::Graphics::GlyphFactory manpage</a>,<a href="/AcePerl/docs/./Ace/Graphics/Glyph.html">the Ace::Graphics::Glyph manpage</a></p>
<p>
</p>
<hr />
<h1><a name="author">AUTHOR</a></h1>
<p>Lincoln Stein <<a href="mailto:lstein@cshl.org">lstein@cshl.org</a>>.</p>
<p>Copyright (c) 2001 Cold Spring Harbor Laboratory</p>
<p>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.</p>
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