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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.AlignIO-module.html">Package AlignIO</a> ::
<a href="Bio.AlignIO.PhylipIO-module.html">Module PhylipIO</a> ::
Class PhylipIterator
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class PhylipIterator</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.AlignIO.PhylipIO-pysrc.html#PhylipIterator">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.AlignIO.Interfaces.AlignmentIterator-class.html">Interfaces.AlignmentIterator</a> --+
|
<strong class="uidshort">PhylipIterator</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.AlignIO.PhylipIO.RelaxedPhylipIterator-class.html">RelaxedPhylipIterator</a></li> </ul>
</dd></dl>
<hr />
<p>Reads a Phylip alignment file returning a MultipleSeqAlignment
iterator.</p>
<p>Record identifiers are limited to at most 10 characters.</p>
<p>It only copes with interlaced phylip files! Sequential files won't
work where the sequences are split over multiple lines.</p>
<p>For more information on the file format, please see:
http://evolution.genetics.washington.edu/phylip/doc/sequence.html
http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles</p>
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<span class="summary-sig-arg">line</span>)</span></td>
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<td><span class="summary-sig"><a href="Bio.AlignIO.PhylipIO.PhylipIterator-class.html#_split_id" class="summary-sig-name" onclick="show_private();">_split_id</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">line</span>)</span><br />
Extracts the sequence ID from a Phylip line, returning a tuple
containing:</td>
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<span class="codelink"><a href="Bio.AlignIO.PhylipIO-pysrc.html#PhylipIterator._split_id">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next" class="summary-sig-name">next</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the next alignment in the file.</td>
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<span class="codelink"><a href="Bio.AlignIO.PhylipIO-pysrc.html#PhylipIterator.next">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.AlignIO.Interfaces.AlignmentIterator-class.html">Interfaces.AlignmentIterator</a></code></b>:
<code><a href="Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__">__init__</a></code>,
<code><a href="Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__iter__">__iter__</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<span class="summary-type"> </span>
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<a name="id_width"></a><span class="summary-name">id_width</span> = <code title="10">10</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<a name="_split_id"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_split_id</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">line</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.AlignIO.PhylipIO-pysrc.html#PhylipIterator._split_id">source code</a></span>
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<pre class="literalblock">
Extracts the sequence ID from a Phylip line, returning a tuple
containing:
(sequence_id, sequence_residues)
The first 10 characters in the line are are the sequence id, the
remainder are sequence data.
</pre>
<dl class="fields">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">next</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.AlignIO.PhylipIO-pysrc.html#PhylipIterator.next">source code</a></span>
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<p>Return the next alignment in the file.</p>
<p>This method should be replaced by any derived class to do something
useful.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next">Interfaces.AlignmentIterator.next</a>
<dd><em class="note">(inherited documentation)</em></dd>
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