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Automated update 69b466f0382fa5f407dcbd357e4e8c86fa819494
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18 changes: 14 additions & 4 deletions dev/api/Bio.SeqIO.SffIO.html
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<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.SffIO.</span></span><span class="sig-name descname"><span class="pre">SffIterator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.SffIO.SffIterator" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="Bio.SeqIO.Interfaces.html#Bio.SeqIO.Interfaces.SequenceIterator" title="Bio.SeqIO.Interfaces.SequenceIterator"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceIterator</span></code></a></p>
<p>Parser for Standard Flowgram Format (SFF) files.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="Bio.SeqIO.SffIO.SffIterator.read_header_fmt">
<span class="sig-name descname"><span class="pre">read_header_fmt</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'&gt;2HI4H'</span></em><a class="headerlink" href="#Bio.SeqIO.SffIO.SffIterator.read_header_fmt" title="Link to this definition"></a></dt>
<dd></dd></dl>

<dl class="py attribute">
<dt class="sig sig-object py" id="Bio.SeqIO.SffIO.SffIterator.read_header_size">
<span class="sig-name descname"><span class="pre">read_header_size</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">16</span></em><a class="headerlink" href="#Bio.SeqIO.SffIO.SffIterator.read_header_size" title="Link to this definition"></a></dt>
<dd></dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="Bio.SeqIO.SffIO.SffIterator.__init__">
<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.SffIO.SffIterator.__init__" title="Link to this definition"></a></dt>
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<dl class="py method">
<dt class="sig sig-object py" id="Bio.SeqIO.SffIO.SffIterator.parse">
<span class="sig-name descname"><span class="pre">parse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">handle</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.SffIO.SffIterator.parse" title="Link to this definition"></a></dt>
<dd><p>Start parsing the file, and return a SeqRecord generator.</p>
<dd><p>To be removed.</p>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="Bio.SeqIO.SffIO.SffIterator.iterate">
<span class="sig-name descname"><span class="pre">iterate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">handle</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.SffIO.SffIterator.iterate" title="Link to this definition"></a></dt>
<dd><p>Parse the file and generate SeqRecord objects.</p>
<dt class="sig sig-object py" id="Bio.SeqIO.SffIO.SffIterator.__next__">
<span class="sig-name descname"><span class="pre">__next__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.SffIO.SffIterator.__next__" title="Link to this definition"></a></dt>
<dd><p>Return the next entry.</p>
</dd></dl>

<dl class="py attribute">
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4 changes: 3 additions & 1 deletion dev/api/Bio.SeqIO.html
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Expand Up @@ -454,9 +454,11 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
<li class="toctree-l1"><a class="reference internal" href="Bio.SeqIO.SffIO.html">Bio.SeqIO.SffIO module</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.ReadRocheXmlManifest"><code class="docutils literal notranslate"><span class="pre">ReadRocheXmlManifest()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator"><code class="docutils literal notranslate"><span class="pre">SffIterator</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.read_header_fmt"><code class="docutils literal notranslate"><span class="pre">SffIterator.read_header_fmt</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.read_header_size"><code class="docutils literal notranslate"><span class="pre">SffIterator.read_header_size</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.__init__"><code class="docutils literal notranslate"><span class="pre">SffIterator.__init__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.parse"><code class="docutils literal notranslate"><span class="pre">SffIterator.parse()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.iterate"><code class="docutils literal notranslate"><span class="pre">SffIterator.iterate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.__next__"><code class="docutils literal notranslate"><span class="pre">SffIterator.__next__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.__abstractmethods__"><code class="docutils literal notranslate"><span class="pre">SffIterator.__abstractmethods__</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.__parameters__"><code class="docutils literal notranslate"><span class="pre">SffIterator.__parameters__</span></code></a></li>
</ul>
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8 changes: 6 additions & 2 deletions dev/genindex.html
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Expand Up @@ -1965,6 +1965,8 @@ <h2 id="_">_</h2>
<li><a href="api/Bio.SeqIO.QualityIO.html#Bio.SeqIO.QualityIO.QualPhredIterator.__next__">(Bio.SeqIO.QualityIO.QualPhredIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.SeqXmlIO.html#Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__next__">(Bio.SeqIO.SeqXmlIO.SeqXmlIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.__next__">(Bio.SeqIO.SffIO.SffIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.SnapGeneIO.html#Bio.SeqIO.SnapGeneIO.SnapGeneIterator.__next__">(Bio.SeqIO.SnapGeneIO.SnapGeneIterator method)</a>
</li>
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<ul>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.iterate">(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.iterate">(Bio.SeqIO.SffIO.SffIterator method)</a>
</li>
</ul></li>
<li><a href="api/Bio.Align.Applications.html#Bio.Align.Applications.ClustalwCommandline.iteration">iteration (Bio.Align.Applications.ClustalwCommandline property)</a>
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<li><a href="api/Bio.Sequencing.Applications.html#Bio.Sequencing.Applications.BwaSampeCommandline.read_file2">(Bio.Sequencing.Applications.BwaSampeCommandline property)</a>
</li>
</ul></li>
<li><a href="api/Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.read_header_fmt">read_header_fmt (Bio.SeqIO.SffIO.SffIterator attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.SffIO.html#Bio.SeqIO.SffIO.SffIterator.read_header_size">read_header_size (Bio.SeqIO.SffIO.SffIterator attribute)</a>
</li>
<li><a href="api/Bio.SearchIO.HmmerIO.hmmer2_text.html#Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser.read_next">read_next() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)</a>
</li>
<li><a href="api/Bio.PDB.PICIO.html#Bio.PDB.PICIO.read_PIC">read_PIC() (in module Bio.PDB.PICIO)</a>
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