<?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>BioSQL.BioSeqDatabase.Adaptor</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="BioSQL-module.html">Package BioSQL</a> :: <a href="BioSQL.BioSeqDatabase-module.html">Module BioSeqDatabase</a> :: Class Adaptor </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="BioSQL.BioSeqDatabase.Adaptor-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Adaptor</h1><p class="nomargin-top"><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor">source code</a></span></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 name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">conn</span>, <span class="summary-sig-arg">dbutils</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.__init__">source code</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 name="last_id"></a><span class="summary-sig-name">last_id</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">table</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.last_id">source code</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 name="autocommit"></a><span class="summary-sig-name">autocommit</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">y</span>=<span class="summary-sig-default">True</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.autocommit">source code</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 name="commit"></a><span class="summary-sig-name">commit</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.commit">source code</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 name="rollback"></a><span class="summary-sig-name">rollback</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.rollback">source code</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 name="close"></a><span class="summary-sig-name">close</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.close">source code</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 name="fetch_dbid_by_dbname"></a><span class="summary-sig-name">fetch_dbid_by_dbname</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dbname</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_dbid_by_dbname">source code</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 name="fetch_seqid_by_display_id"></a><span class="summary-sig-name">fetch_seqid_by_display_id</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dbid</span>, <span class="summary-sig-arg">name</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqid_by_display_id">source code</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 name="fetch_seqid_by_accession"></a><span class="summary-sig-name">fetch_seqid_by_accession</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dbid</span>, <span class="summary-sig-arg">name</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqid_by_accession">source code</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 name="fetch_seqids_by_accession"></a><span class="summary-sig-name">fetch_seqids_by_accession</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dbid</span>, <span class="summary-sig-arg">name</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqids_by_accession">source code</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 name="fetch_seqid_by_version"></a><span class="summary-sig-name">fetch_seqid_by_version</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dbid</span>, <span class="summary-sig-arg">name</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqid_by_version">source code</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 name="fetch_seqid_by_identifier"></a><span class="summary-sig-name">fetch_seqid_by_identifier</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dbid</span>, <span class="summary-sig-arg">identifier</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqid_by_identifier">source code</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 name="list_biodatabase_names"></a><span class="summary-sig-name">list_biodatabase_names</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_biodatabase_names">source code</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 name="list_bioentry_ids"></a><span class="summary-sig-name">list_bioentry_ids</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dbid</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_bioentry_ids">source code</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 name="list_bioentry_display_ids"></a><span class="summary-sig-name">list_bioentry_display_ids</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dbid</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_bioentry_display_ids">source code</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="BioSQL.BioSeqDatabase.Adaptor-class.html#list_any_ids" class="summary-sig-name">list_any_ids</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">sql</span>, <span class="summary-sig-arg">args</span>)</span><br /> Return ids given a SQL statement to select for them.</td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_any_ids">source code</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 name="execute_one"></a><span class="summary-sig-name">execute_one</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">sql</span>, <span class="summary-sig-arg">args</span>=<span class="summary-sig-default">None</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.execute_one">source code</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 name="execute"></a><span class="summary-sig-name">execute</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">sql</span>, <span class="summary-sig-arg">args</span>=<span class="summary-sig-default">None</span>)</span><br /> Just execute an sql command.</td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.execute">source code</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 name="get_subseq_as_string"></a><span class="summary-sig-name">get_subseq_as_string</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">seqid</span>, <span class="summary-sig-arg">start</span>, <span class="summary-sig-arg">end</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.get_subseq_as_string">source code</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 name="execute_and_fetch_col0"></a><span class="summary-sig-name">execute_and_fetch_col0</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">sql</span>, <span class="summary-sig-arg">args</span>=<span class="summary-sig-default">None</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.execute_and_fetch_col0">source code</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 name="execute_and_fetchall"></a><span class="summary-sig-name">execute_and_fetchall</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">sql</span>, <span class="summary-sig-arg">args</span>=<span class="summary-sig-default">None</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.execute_and_fetchall">source code</a></span> </td> </tr> </table> </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="list_any_ids"></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">list_any_ids</span>(<span class="sig-arg">self</span>, <span class="sig-arg">sql</span>, <span class="sig-arg">args</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_any_ids">source code</a></span> </td> </tr></table> <p>Return ids given a SQL statement to select for them.</p> <p>This assumes that the given SQL does a SELECT statement that returns a list of items. This parses them out of the 2D list they come as and just returns them in a list.</p> <dl class="fields"> </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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