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<title>Ace::Sequence::FeatureList - Lightweight Access to Features</title>
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<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
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<li><a href="#object_methods">OBJECT METHODS</a></li>
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<p>
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<h1><a name="name">NAME</a></h1>
<p>Ace::Sequence::FeatureList - Lightweight Access to Features</p>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
<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>
# find out what's there
$list = $seq->feature_list;</pre>
<pre>
# Scalar context: count all the features
$feature_count = $list->types;</pre>
<pre>
# Array context: list all the feature types
@feature_types = $list->types;</pre>
<pre>
# Scalar context, 1 argument. Count this type
$gene_cnt = $list->types('Predicted_gene');
print "There are $gene_cnt genes here.\n";</pre>
<pre>
# Array context, 1 argument. Get list of subtypes
@subtypes = $list->types('Predicted_gene');</pre>
<pre>
# Two arguments. Count type & subtype
$genefinder_cnt = $list->types('Predicted_gene','genefinder');</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<p><em>Ace::Sequence::FeatureList</em> is a small class that provides
statistical information about sequence features. From it you can
obtain summary counts of the features and their types within a
selected region.</p>
<p>
</p>
<hr />
<h1><a name="object_creation">OBJECT CREATION</a></h1>
<p>You will not ordinarily create an <em>Ace::Sequence::FeatureList</em> object
directly. Instead, objects will be created by calling a
<em>Ace::Sequence</em> object's <code>feature_list()</code> method. If you wish to
create an <em>Ace::Sequence::FeatureList</em> object directly, please consult
the source code for the <em>new()</em> method.</p>
<p>
</p>
<hr />
<h1><a name="object_methods">OBJECT METHODS</a></h1>
<p>There are only two methods in <em>Ace::Sequence::FeatureList</em>.</p>
<dl>
<dt><strong><a name="type" class="item"><code>type()</code></a></strong>
<dd>
<p>This method has five distinct behaviors, depending on its context and
the number of parameters. Usage should be intuitive</p>
</dd>
<dd>
<pre>
Context Arguments Behavior
------- --------- --------</pre>
</dd>
<dd>
<pre>
scalar -none- total count of features in list
array -none- list feature types (e.g. "exon")
scalar type count features of this type
array type list subtypes of this type
-any- type,subtype count features of this type & subtype</pre>
</dd>
<dd>
<p>For example, this code fragment will count the number of exons present
on the list:</p>
</dd>
<dd>
<pre>
$exon_count = $list->type('exon');</pre>
</dd>
<dd>
<p>This code fragment will count the number of exons found by "genefinder":</p>
</dd>
<dd>
<pre>
$predicted_exon_count = $list->type('exon','genefinder');</pre>
</dd>
<dd>
<p>This code fragment will print out all subtypes of "exon" and their
counts:</p>
</dd>
<dd>
<pre>
for my $subtype ($list->type('exon')) {
print $subtype,"\t",$list->type('exon',$subtype),"\n";
}</pre>
</dd>
</li>
<dt><strong><a name="asstring" class="item"><code>asString()</code></a></strong>
<dd>
<pre>
print $list->asString;</pre>
</dd>
<dd>
<p>This dumps the list out in tab-delimited format. The order of columns
is type, subtype, count.</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/Feature.html">the Ace::Sequence::Feature manpage</a>, <em>GFF</em></p>
<p>
</p>
<hr />
<h1><a name="author">AUTHOR</a></h1>
<p>Lincoln Stein <<a href="mailto:lstein@w3.org">lstein@w3.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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Mandriva
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2010.0
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i586
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media
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contrib-release
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by-pkgid
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c0b2316b5320756fc35b43f35335d7ce
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files
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153
