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<title>Ace::Sequence::GappedAlignment - Gapped alignment object</title>
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<li><a href="#name">NAME</a></li>
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<li><a href="#description">DESCRIPTION</a></li>
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<li><a href="#object_methods">OBJECT METHODS</a></li>
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<h1><a name="name">NAME</a></h1>
<p>Ace::Sequence::GappedAlignment - Gapped alignment object</p>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
# open database connection and get an Ace::Sequence object
use Ace::Sequence;</pre>
<pre>
# get a megabase from the middle of chromosome I
$seq = Ace::Sequence->new(-name => 'CHROMOSOME_I,
-db => $db,
-offset => 3_000_000,
-length => 1_000_000);</pre>
<pre>
# get all the gapped alignments
@alignments = $seq->alignments('EST_GENOME');</pre>
<pre>
# get the aligned segments from the first one
@segs = $alignments[0]->segments;</pre>
<pre>
# get the position of the first aligned segment on the
# source sequence:
($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);</pre>
<pre>
# get the target position for the first aligned segment
($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<p>Ace::Sequence::GappedAlignment is a subclass of
Ace::Sequence::Feature. It inherits all the methods of
Ace::Sequence::Feature, but adds the ability to retrieve the positions
of the aligned segments. Each segment is an Ace::Sequence::Feature,
from which you can retrieve the source and target coordinates.</p>
<p>
</p>
<hr />
<h1><a name="object_creation">OBJECT CREATION</a></h1>
<p>You will not ordinarily create an <em>Ace::Sequence::GappedAlignment</em>
object directly. Instead, objects will be created in response to a
<code>alignments()</code> call to an <em>Ace::Sequence</em> object.</p>
<p>
</p>
<hr />
<h1><a name="object_methods">OBJECT METHODS</a></h1>
<p>Most methods are inherited from <em>Ace::Sequence::Feature</em>. The
following methods are also supported:</p>
<dl>
<dt><strong><a name="segments" class="item"><code>segments()</code></a></strong>
<dd>
<pre>
@segments = $gene->segments;</pre>
</dd>
<dd>
<p>Return a list of Ace::Sequence::Feature objects corresponding to
similar segments.</p>
</dd>
<dt><strong><a name="relative" class="item"><code>relative()</code></a></strong>
<dd>
<pre>
$relative = $gene->relative;
$gene->relative(1);</pre>
</dd>
<dd>
<p>This turns on and off relative coordinates. By default, the exons and
intron features will be returned in the coordinate system used by the
gene. If <a href="#relative"><code>relative()</code></a> is set to a true value, then coordinates will be
expressed as relative to the start of the gene. The first exon will
(usually) be 1.</p>
</dd>
</dl>
<p>
</p>
<hr />
<h1><a name="see_also">SEE ALSO</a></h1>
<p><a href="/AcePerl/docs/./Ace.html">the Ace manpage</a>, <a href="/AcePerl/docs/./Ace/Object.html">the Ace::Object manpage</a>, <a href="/AcePerl/docs/./Ace/Sequence.html">the Ace::Sequence manpage</a>,<a href="/AcePerl/docs/./Ace/Sequence/Homol.html">the Ace::Sequence::Homol manpage</a>,
<a href="/AcePerl/docs/./Ace/Sequence/Feature.html">the Ace::Sequence::Feature manpage</a>, <a href="/AcePerl/docs/./Ace/Sequence/FeatureList.html">the Ace::Sequence::FeatureList manpage</a>, <em>GFF</em></p>
<p>
</p>
<hr />
<h1><a name="author">AUTHOR</a></h1>
<p>Lincoln Stein <<a href="mailto:lstein@cshl.org">lstein@cshl.org</a>> with extensive help from Jean
Thierry-Mieg <<a href="mailto:mieg@kaa.crbm.cnrs-mop.fr">mieg@kaa.crbm.cnrs-mop.fr</a>></p>
<p>Copyright (c) 1999, Lincoln D. Stein</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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i586
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media
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contrib-release
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c0b2316b5320756fc35b43f35335d7ce
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