<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.AlignIO.StockholmIO.StockholmWriter</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.AlignIO-module.html">Package AlignIO</a> :: <a href="Bio.AlignIO.StockholmIO-module.html">Module StockholmIO</a> :: Class StockholmWriter </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class StockholmWriter</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.AlignIO.StockholmIO-pysrc.html#StockholmWriter">source code</a></span></p> <pre class="base-tree"> <a href="Bio.AlignIO.Interfaces.AlignmentWriter-class.html">Interfaces.AlignmentWriter</a> --+ | <a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html">Interfaces.SequentialAlignmentWriter</a> --+ | <strong class="uidshort">StockholmWriter</strong> </pre> <hr /> <p>Stockholm/PFAM alignment writer.</p> <!-- ==================== INSTANCE METHODS ==================== --> <a name="section-InstanceMethods"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Instance Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-InstanceMethods" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html#write_alignment" class="summary-sig-name">write_alignment</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">alignment</span>)</span><br /> Use this to write (another) single alignment to an open file.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.AlignIO.StockholmIO-pysrc.html#StockholmWriter.write_alignment">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_write_record"></a><span class="summary-sig-name">_write_record</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">record</span>)</span><br /> Write a single SeqRecord to the file</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.AlignIO.StockholmIO-pysrc.html#StockholmWriter._write_record">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html">Interfaces.SequentialAlignmentWriter</a></code></b>: <code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__">__init__</a></code>, <code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_file">write_file</a></code>, <code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_footer">write_footer</a></code>, <code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_header">write_header</a></code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.AlignIO.Interfaces.AlignmentWriter-class.html">Interfaces.AlignmentWriter</a></code></b>: <code><a href="Bio.AlignIO.Interfaces.AlignmentWriter-class.html#clean">clean</a></code> </p> </td> </tr> </table> <!-- ==================== CLASS VARIABLES ==================== --> <a name="section-ClassVariables"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Class Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-ClassVariables" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html#pfam_gr_mapping" class="summary-name">pfam_gr_mapping</a> = <code title="{'active_site': 'AS', 'intron': 'IN', 'ligand_binding': 'LI', 'posterior_probability': 'PP', 'secondary_structure': 'SS', 'surface_accessibility': 'SA', 'transmembrane': 'TM'}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">active_site</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">AS</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">intron</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">IN</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ligan</code><code class="variable-ellipsis">...</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html#pfam_gs_mapping" class="summary-name">pfam_gs_mapping</a> = <code title="{'look': 'LO', 'organism': 'OS', 'organism_classification': 'OC'}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">look</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">LO</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">organism</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">OS</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">organism_c</code><code class="variable-ellipsis">...</code></code> </td> </tr> </table> <!-- ==================== METHOD DETAILS ==================== --> <a name="section-MethodDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Method Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-MethodDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="write_alignment"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">write_alignment</span>(<span class="sig-arg">self</span>, <span class="sig-arg">alignment</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.AlignIO.StockholmIO-pysrc.html#StockholmWriter.write_alignment">source code</a></span> </td> </tr></table> <p>Use this to write (another) single alignment to an open file.</p> <p>Note that sequences and their annotation are recorded together (rather than having a block of annotation followed by a block of aligned sequences).</p> <dl class="fields"> <dt>Overrides: <a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_alignment">Interfaces.SequentialAlignmentWriter.write_alignment</a> </dt> </dl> </td></tr></table> </div> <br /> <!-- ==================== CLASS VARIABLE DETAILS ==================== --> <a name="section-ClassVariableDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Class Variable Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-ClassVariableDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="pfam_gr_mapping"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">pfam_gr_mapping</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">active_site</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">AS</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">intron</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">IN</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">ligand_binding</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">LI</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">posterior_probability</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">PP</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">secondary_structure</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">SS</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">surface_accessibility</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">SA</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">transmembrane</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">TM</code><code class="variable-quote">'</code><code class="variable-group">}</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="pfam_gs_mapping"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">pfam_gs_mapping</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">look</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">LO</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">organism</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">OS</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">organism_classification</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">OC</code><code class="variable-quote">'</code><code class="variable-group">}</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" 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