<?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.StdHandler</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> :: Module StdHandler </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.StdHandler-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module StdHandler</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.StdHandler-pysrc.html">source code</a></span></p> <!-- ==================== CLASSES ==================== --> <a name="section-Classes"></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">Classes</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Classes" 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.StdHandler.ConvertHandler-class.html" class="summary-name">ConvertHandler</a><br /> Used to read records and produce output </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.ConvertDispatchHandler-class.html" class="summary-name">ConvertDispatchHandler</a><br /> Used to read records and produce output through a Dispatcher </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.RecognizeHandler-class.html" class="summary-name">RecognizeHandler</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_dbid-class.html" class="summary-name">Handle_dbid</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_description-class.html" class="summary-name">Handle_description</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_dbxref-class.html" class="summary-name">Handle_dbxref</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_sequence-class.html" class="summary-name">Handle_sequence</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Feature-class.html" class="summary-name">Feature</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_feature_location-class.html" class="summary-name">Handle_feature_location</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_feature_qualifier-class.html" class="summary-name">Handle_feature_qualifier</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_features-class.html" class="summary-name">Handle_features</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_hsp_seqalign-class.html" class="summary-name">Handle_hsp_seqalign</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_hsp-class.html" class="summary-name">Handle_hsp</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_search_table-class.html" class="summary-name">Handle_search_table</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_search_header-class.html" class="summary-name">Handle_search_header</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler.Handle_search_info-class.html" class="summary-name">Handle_search_info</a> </td> </tr> </table> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></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">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" 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="add_int_handler"></a><span class="summary-sig-name">add_int_handler</span>(<span class="summary-sig-arg">klass</span>, <span class="summary-sig-arg">tag</span>, <span class="summary-sig-arg">attrname</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#add_int_handler">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="add_text_handler"></a><span class="summary-sig-name">add_text_handler</span>(<span class="summary-sig-arg">klass</span>, <span class="summary-sig-arg">tag</span>, <span class="summary-sig-arg">attrname</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#add_text_handler">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="add_text_dict_handler"></a><span class="summary-sig-name">add_text_dict_handler</span>(<span class="summary-sig-arg">klass</span>, <span class="summary-sig-arg">tag</span>, <span class="summary-sig-arg">attrname</span>, <span class="summary-sig-arg">key</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#add_text_dict_handler">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="add_text_decode_handler"></a><span class="summary-sig-name">add_text_decode_handler</span>(<span class="summary-sig-arg">klass</span>, <span class="summary-sig-arg">tag</span>, <span class="summary-sig-arg">attrname</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#add_text_decode_handler">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="add_first_text_handler"></a><span class="summary-sig-name">add_first_text_handler</span>(<span class="summary-sig-arg">klass</span>, <span class="summary-sig-arg">tag</span>, <span class="summary-sig-arg">attrname</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#add_first_text_handler">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="add_text_block_handler"></a><span class="summary-sig-name">add_text_block_handler</span>(<span class="summary-sig-arg">klass</span>, <span class="summary-sig-arg">tag</span>, <span class="summary-sig-arg">joinattr</span>, <span class="summary-sig-arg">defaultjoin</span>, <span class="summary-sig-arg">attrname</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#add_text_block_handler">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="add_value_handler"></a><span class="summary-sig-name">add_value_handler</span>(<span class="summary-sig-arg">klass</span>, <span class="summary-sig-arg">tag</span>, <span class="summary-sig-arg">attrname</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#add_value_handler">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="_fixup_sp_pattern"></a><span class="summary-sig-name">_fixup_sp_pattern</span>(<span class="summary-sig-arg">exp</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#_fixup_sp_pattern">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="_fast_dbxref_sp_general"></a><span class="summary-sig-name">_fast_dbxref_sp_general</span>(<span class="summary-sig-arg">s</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#_fast_dbxref_sp_general">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="_fast_dbxref_sp_prosite"></a><span class="summary-sig-name">_fast_dbxref_sp_prosite</span>(<span class="summary-sig-arg">s</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#_fast_dbxref_sp_prosite">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="_fast_dbxref_sp_embl"></a><span class="summary-sig-name">_fast_dbxref_sp_embl</span>(<span class="summary-sig-arg">s</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.StdHandler-pysrc.html#_fast_dbxref_sp_embl">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== VARIABLES ==================== --> <a name="section-Variables"></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">Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Variables" class="privatelink" onclick="toggle_private();" >hide private</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"> <a name="_fast_dbxref_sp_general_data"></a><span class="summary-name">_fast_dbxref_sp_general_data</span> = <code title="None">None</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_fast_dbxref_sp_prosite_data"></a><span class="summary-name">_fast_dbxref_sp_prosite_data</span> = <code title="None">None</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_fast_dbxref_sp_embl_data"></a><span class="summary-name">_fast_dbxref_sp_embl_data</span> = <code title="None">None</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.StdHandler-module.html#_fast_dbxref_parser_table" class="summary-name" onclick="show_private();">_fast_dbxref_parser_table</a> = <code title="{"sp-general": _fast_dbxref_sp_general, "sp-prosite": _fast_dbxref_sp_\ prosite, "sp-embl": _fast_dbxref_sp_embl,}">{"sp-general": _fast_dbxref_sp_gen<code class="variable-ellipsis">...</code></code> </td> </tr> </table> <!-- ==================== VARIABLES DETAILS ==================== --> <a name="section-VariablesDetails"></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">Variables Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-VariablesDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="_fast_dbxref_parser_table"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">_fast_dbxref_parser_table</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> {"sp-general": _fast_dbxref_sp_general, "sp-prosite": _fast_dbxref_sp_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> prosite, "sp-embl": _fast_dbxref_sp_embl,} </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" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:25 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 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