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32 changes: 16 additions & 16 deletions dev/api/Bio.SeqIO.FastaIO.html
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<dl class="py method">
<dt class="sig sig-object py" id="Bio.SeqIO.FastaIO.FastaIterator.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.FastaIO.FastaIterator.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.FastaIO.FastaIterator.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.FastaIO.FastaIterator.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.FastaIO.FastaIterator.__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.FastaIO.FastaIterator.__next__" title="Link to this definition"></a></dt>
<dd><p>Return the next entry.</p>
</dd></dl>

<dl class="py attribute">
Expand Down Expand Up @@ -300,13 +300,13 @@
<dl class="py method">
<dt class="sig sig-object py" id="Bio.SeqIO.FastaIO.FastaTwoLineIterator.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.FastaIO.FastaTwoLineIterator.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.FastaIO.FastaTwoLineIterator.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.FastaIO.FastaTwoLineIterator.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.FastaIO.FastaTwoLineIterator.__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.FastaIO.FastaTwoLineIterator.__next__" title="Link to this definition"></a></dt>
<dd><p>Return the next entry.</p>
</dd></dl>

<dl class="py attribute">
Expand Down Expand Up @@ -375,13 +375,13 @@
<dl class="py method">
<dt class="sig sig-object py" id="Bio.SeqIO.FastaIO.FastaBlastIterator.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.FastaIO.FastaBlastIterator.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.FastaIO.FastaBlastIterator.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.FastaIO.FastaBlastIterator.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.FastaIO.FastaBlastIterator.__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.FastaIO.FastaBlastIterator.__next__" title="Link to this definition"></a></dt>
<dd><p>Return the next entry.</p>
</dd></dl>

<dl class="py attribute">
Expand Down Expand Up @@ -451,13 +451,13 @@
<dl class="py method">
<dt class="sig sig-object py" id="Bio.SeqIO.FastaIO.FastaPearsonIterator.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.FastaIO.FastaPearsonIterator.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.FastaIO.FastaPearsonIterator.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.FastaIO.FastaPearsonIterator.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.FastaIO.FastaPearsonIterator.__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.FastaIO.FastaPearsonIterator.__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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8 changes: 4 additions & 4 deletions dev/api/Bio.SeqIO.html
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Expand Up @@ -158,31 +158,31 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator"><code class="docutils literal notranslate"><span class="pre">FastaIterator</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.__init__"><code class="docutils literal notranslate"><span class="pre">FastaIterator.__init__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.parse"><code class="docutils literal notranslate"><span class="pre">FastaIterator.parse()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.iterate"><code class="docutils literal notranslate"><span class="pre">FastaIterator.iterate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.__next__"><code class="docutils literal notranslate"><span class="pre">FastaIterator.__next__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.__abstractmethods__"><code class="docutils literal notranslate"><span class="pre">FastaIterator.__abstractmethods__</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.__parameters__"><code class="docutils literal notranslate"><span class="pre">FastaIterator.__parameters__</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineIterator</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.__init__"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineIterator.__init__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.parse"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineIterator.parse()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.iterate"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineIterator.iterate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.__next__"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineIterator.__next__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.__abstractmethods__"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineIterator.__abstractmethods__</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.__parameters__"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineIterator.__parameters__</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__init__"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.__init__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.parse"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.parse()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.iterate"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.iterate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__next__"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.__next__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__abstractmethods__"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.__abstractmethods__</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__parameters__"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.__parameters__</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__init__"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.__init__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.parse"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.parse()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.iterate"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.iterate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__next__"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.__next__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__abstractmethods__"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.__abstractmethods__</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__parameters__"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.__parameters__</span></code></a></li>
</ul>
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22 changes: 10 additions & 12 deletions dev/genindex.html
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Expand Up @@ -1955,6 +1955,14 @@ <h2 id="_">_</h2>
<li><a href="api/Bio.Nexus.StandardData.html#Bio.Nexus.StandardData.StandardData.__next__">(Bio.Nexus.StandardData.StandardData method)</a>
</li>
<li><a href="api/Bio.SeqIO.AbiIO.html#Bio.SeqIO.AbiIO.AbiIterator.__next__">(Bio.SeqIO.AbiIO.AbiIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__next__">(Bio.SeqIO.FastaIO.FastaBlastIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.__next__">(Bio.SeqIO.FastaIO.FastaIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__next__">(Bio.SeqIO.FastaIO.FastaPearsonIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.__next__">(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.GckIO.html#Bio.SeqIO.GckIO.GckIterator.__next__">(Bio.SeqIO.GckIO.GckIterator method)</a>
</li>
Expand Down Expand Up @@ -8468,6 +8476,8 @@ <h2 id="I">I</h2>
<li><a href="api/Bio.Sequencing.Applications.html#Bio.Sequencing.Applications.SamtoolsIndexCommandline.input_bam">(Bio.Sequencing.Applications.SamtoolsIndexCommandline property)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/Bio.Blast.Applications.html#Bio.Blast.Applications.NcbimakeblastdbCommandline.input_file">input_file (Bio.Blast.Applications.NcbimakeblastdbCommandline property)</a>

<ul>
Expand All @@ -8480,8 +8490,6 @@ <h2 id="I">I</h2>
<li><a href="api/Bio.Sequencing.Applications.html#Bio.Sequencing.Applications.SamtoolsViewCommandline.input_file">(Bio.Sequencing.Applications.SamtoolsViewCommandline property)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/Bio.Phylo.Applications.html#Bio.Phylo.Applications.PhymlCommandline.input_tree">input_tree (Bio.Phylo.Applications.PhymlCommandline property)</a>
</li>
<li><a href="api/Bio.Blast.Applications.html#Bio.Blast.Applications.NcbimakeblastdbCommandline.input_type">input_type (Bio.Blast.Applications.NcbimakeblastdbCommandline property)</a>
Expand Down Expand Up @@ -8656,16 +8664,6 @@ <h2 id="I">I</h2>
<li><a href="api/BioSQL.BioSeqDatabase.html#BioSQL.BioSeqDatabase.BioSeqDatabase.items">(BioSQL.BioSeqDatabase.BioSeqDatabase method)</a>
</li>
<li><a href="api/BioSQL.BioSeqDatabase.html#BioSQL.BioSeqDatabase.DBServer.items">(BioSQL.BioSeqDatabase.DBServer method)</a>
</li>
</ul></li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.iterate">iterate() (Bio.SeqIO.FastaIO.FastaBlastIterator method)</a>

<ul>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.iterate">(Bio.SeqIO.FastaIO.FastaIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.iterate">(Bio.SeqIO.FastaIO.FastaPearsonIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.iterate">(Bio.SeqIO.FastaIO.FastaTwoLineIterator 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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