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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqIO-module.html">Package SeqIO</a> ::
<a href="Bio.SeqIO.Interfaces-module.html">Module Interfaces</a> ::
Class InterlacedSequenceIterator
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class InterlacedSequenceIterator</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator">source code</a></span></p>
<pre class="base-tree">
<a href="Bio.SeqIO.Interfaces.SequenceIterator-class.html">SequenceIterator</a> --+
|
<strong class="uidshort">InterlacedSequenceIterator</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.SeqIO.StockholmIO.StockholmIterator-class.html">StockholmIO.StockholmIterator</a></li> </ul>
</dd></dl>
<hr />
<p>Base class for any iterator of a non-sequential file type.</p>
<p>This object is not intended for use directly.</p>
<p>When writing a parser for any interlaced sequence file where the whole
file must be read in order to extract any single record, then you should
subclass this object.</p>
<p>All you need to do is to define your own: (1) __init__ method to parse
the file and call self.move_start() (2) __len__ method to return the
number of records (3) __getitem__ to return any requested record.</p>
<p>This class will then provide the iterator methods including next(),
but relies on knowing the total number of records and tracking the
pending record index in as self._n</p>
<p>It is up to the subclassed object to decide if it wants to generate a
cache of SeqRecords when initialised, or simply use its own lists and
dicts and create SeqRecords on request.</p>
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<td><span class="summary-sig"><a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">i</span>)</span><br />
Return the requested record.</td>
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<span class="codelink"><a href="Bio.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator.__getitem__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Create the object.</td>
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<span class="codelink"><a href="Bio.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator.__init__">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.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__iter__" class="summary-sig-name">__iter__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over the entries as a SeqRecord objects.</td>
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<span class="codelink"><a href="Bio.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator.__iter__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the number of records.</td>
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<span class="codelink"><a href="Bio.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator.__len__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="move_start"></a><span class="summary-sig-name">move_start</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator.move_start">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next" class="summary-sig-name">next</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the next record in the file.</td>
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<span class="codelink"><a href="Bio.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator.next">source code</a></span>
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<a name="__getitem__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">i</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
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<p>Return the requested record.</p>
<p>This method should be replaced by any derived class to do something
useful.</p>
<p>It should NOT touch the value of self._n</p>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
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><span class="codelink"><a href="Bio.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator.__init__">source code</a></span>
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<p>Create the object.</p>
<p>This method should be replaced by any derived class to do something
useful.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.SequenceIterator-class.html#__init__">SequenceIterator.__init__</a>
</dt>
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<a name="__iter__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__iter__</span>(<span class="sig-arg">self</span>)</span>
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<pre class="literalblock">
Iterate over the entries as a SeqRecord objects.
Example usage for Fasta files:
myFile = open("example.fasta","r")
myFastaReader = FastaIterator(myFile)
for record in myFastaReader :
print record.id
print record.seq
myFile.close()
</pre>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.SequenceIterator-class.html#__iter__">SequenceIterator.__iter__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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<a name="__len__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__len__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Length operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator.__len__">source code</a></span>
</td>
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<p>Return the number of records.</p>
<p>This method should be replaced by any derived class to do something
useful.</p>
<dl class="fields">
</dl>
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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.SeqIO.Interfaces-pysrc.html#InterlacedSequenceIterator.next">source code</a></span>
</td>
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<p>Return the next record 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.SeqIO.Interfaces.SequenceIterator-class.html#next">SequenceIterator.next</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
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