<?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.config.DBRegistry.BioSQLDB</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.config-module.html">Package config</a> :: <a href="Bio.config.DBRegistry-module.html">Module DBRegistry</a> :: Class BioSQLDB </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.config.DBRegistry.BioSQLDB-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class BioSQLDB</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB">source code</a></span></p> <pre class="base-tree"> <a href="Bio.config.Registry.RegisterableObject-class.html">Registry.RegisterableObject</a> --+ | <a href="Bio.config.DBRegistry.DBObject-class.html">DBObject</a> --+ | <strong class="uidshort">BioSQLDB</strong> </pre> <hr /> <p>Represent a BioSQL-style database to retrieve SeqRecord objects.</p> <p>This returns a SeqRecord-like object from _get() instead of a handle (since BioSQL is not going to give you a handle).</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.config.DBRegistry.BioSQLDB-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">name</span>, <span class="summary-sig-arg">doc</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">db_host</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">localhost</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">db_port</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">db_user</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">root</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">db_passwd</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">sql_db</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">namespace_db</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">db_type</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">mysql</code><code class="variable-quote">'</code></span>)</span><br /> Intialize with information for connecting to the BioSQL db.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB.__init__">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 href="Bio.config.DBRegistry.BioSQLDB-class.html#_get_db_module" class="summary-sig-name" onclick="show_private();">_get_db_module</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">db_type</span>)</span><br /> Retrieve the appropriate module to use for connecting to a database</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._get_db_module">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">data</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.config.DBRegistry.BioSQLDB-class.html#_get" class="summary-sig-name" onclick="show_private();">_get</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">key</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._get">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">another data type</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.config.DBRegistry.BioSQLDB-class.html#_convert_to" class="summary-sig-name" onclick="show_private();">_convert_to</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">data</span>, <span class="summary-sig-arg">to_io</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._convert_to">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">pickleable_obj</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.config.DBRegistry.BioSQLDB-class.html#_make_pickleable" class="summary-sig-name" onclick="show_private();">_make_pickleable</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">item</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._make_pickleable">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">data</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.config.DBRegistry.BioSQLDB-class.html#_unmake_pickleable" class="summary-sig-name" onclick="show_private();">_unmake_pickleable</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">item</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._unmake_pickleable">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.config.DBRegistry.DBObject-class.html">DBObject</a></code></b>: <code><a href="Bio.config.DBRegistry.DBObject-class.html#__getitem__">__getitem__</a></code>, <code><a href="Bio.config.DBRegistry.DBObject-class.html#get">get</a></code>, <code><a href="Bio.config.DBRegistry.DBObject-class.html#get_as">get_as</a></code>, <code><a href="Bio.config.DBRegistry.DBObject-class.html#set">set</a></code> </p> <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.config.DBRegistry.DBObject-class.html">DBObject</a></code></b> (private): <code><a href="Bio.config.DBRegistry.DBObject-class.html#_set" onclick="show_private();">_set</a></code> </p></div> </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="__init__"></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">__init__</span>(<span class="sig-arg">self</span>, <span class="sig-arg">name</span>, <span class="sig-arg">doc</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="sig-arg">db_host</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">localhost</code><code class="variable-quote">'</code></span>, <span class="sig-arg">db_port</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="sig-arg">db_user</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">root</code><code class="variable-quote">'</code></span>, <span class="sig-arg">db_passwd</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="sig-arg">sql_db</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="sig-arg">namespace_db</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="sig-arg">db_type</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">mysql</code><code class="variable-quote">'</code></span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB.__init__">source code</a></span> </td> </tr></table> <p>Intialize with information for connecting to the BioSQL db.</p> <dl class="fields"> <dt>Overrides: <a href="Bio.config.Registry.RegisterableObject-class.html#__init__">Registry.RegisterableObject.__init__</a> </dt> </dl> </td></tr></table> </div> <a name="_get_db_module"></a> <div class="private"> <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">_get_db_module</span>(<span class="sig-arg">self</span>, <span class="sig-arg">db_type</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._get_db_module">source code</a></span> </td> </tr></table> <p>Retrieve the appropriate module to use for connecting to a database</p> <p>This parses a description of the database and tries to determine which module is appropriate for that database type.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_get"></a> <div class="private"> <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">_get</span>(<span class="sig-arg">self</span>, <span class="sig-arg">key</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._get">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Returns: data</dt> <dt>Overrides: <a href="Bio.config.DBRegistry.DBObject-class.html#_get" onclick="show_private();">DBObject._get</a> <dd><em class="note">(inherited documentation)</em></dd> </dt> </dl> </td></tr></table> </div> <a name="_convert_to"></a> <div class="private"> <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">_convert_to</span>(<span class="sig-arg">self</span>, <span class="sig-arg">data</span>, <span class="sig-arg">to_io</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._convert_to">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Returns: another data type</dt> <dt>Overrides: <a href="Bio.config.DBRegistry.DBObject-class.html#_convert_to" onclick="show_private();">DBObject._convert_to</a> <dd><em class="note">(inherited documentation)</em></dd> </dt> </dl> </td></tr></table> </div> <a name="_make_pickleable"></a> <div class="private"> <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">_make_pickleable</span>(<span class="sig-arg">self</span>, <span class="sig-arg">item</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._make_pickleable">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Returns: pickleable_obj</dt> <dt>Overrides: <a href="Bio.config.DBRegistry.DBObject-class.html#_make_pickleable" onclick="show_private();">DBObject._make_pickleable</a> <dd><em class="note">(inherited documentation)</em></dd> </dt> </dl> </td></tr></table> </div> <a name="_unmake_pickleable"></a> <div class="private"> <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">_unmake_pickleable</span>(<span class="sig-arg">self</span>, <span class="sig-arg">item</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.config.DBRegistry-pysrc.html#BioSQLDB._unmake_pickleable">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Returns: data</dt> <dt>Overrides: <a href="Bio.config.DBRegistry.DBObject-class.html#_unmake_pickleable" onclick="show_private();">DBObject._unmake_pickleable</a> <dd><em class="note">(inherited documentation)</em></dd> </dt> </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" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:39 2008 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide them. 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