<?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.Ndb.NdbParser</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.Ndb-module.html">Package Ndb</a> :: Class NdbParser </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.Ndb.NdbParser-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class NdbParser</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser">source code</a></span></p> <pre class="base-tree"> markupbase.ParserBase --+ | sgmllib.SGMLParser --+ | <strong class="uidshort">NdbParser</strong> </pre> <hr /> <p>Parses Ndb sequence data into a Record object. data available at: http://ndbserver.rutgers.edu/NDB/NDBATLAS/index.html</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.Ndb.NdbParser-class.html#reset" class="summary-sig-name">reset</a>(<span class="summary-sig-arg">self</span>)</span><br /> Reset this instance.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.reset">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="parse"></a><span class="summary-sig-name">parse</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.parse">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="Bio.Ndb.NdbParser-class.html#feed" class="summary-sig-name">feed</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>)</span><br /> Feed in ndb data for scanning.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.feed">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="Bio.Ndb.NdbParser-class.html#handle_data" class="summary-sig-name">handle_data</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">newtext</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.handle_data">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="start_h1"></a><span class="summary-sig-name">start_h1</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">attrs</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.start_h1">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="end_h1"></a><span class="summary-sig-name">end_h1</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.end_h1">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="start_h2"></a><span class="summary-sig-name">start_h2</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">attrs</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.start_h2">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="end_h2"></a><span class="summary-sig-name">end_h2</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.end_h2">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="start_ul"></a><span class="summary-sig-name">start_ul</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">attrs</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.start_ul">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="end_ul"></a><span class="summary-sig-name">end_ul</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.end_ul">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="start_sub"></a><span class="summary-sig-name">start_sub</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">attrs</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.start_sub">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="end_sub"></a><span class="summary-sig-name">end_sub</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.end_sub">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="start_li"></a><span class="summary-sig-name">start_li</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">attrs</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.start_li">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="end_li"></a><span class="summary-sig-name">end_li</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.end_li">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="do_br"></a><span class="summary-sig-name">do_br</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">attrs</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.do_br">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="start_i"></a><span class="summary-sig-name">start_i</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">attrs</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.start_i">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="end_i"></a><span class="summary-sig-name">end_i</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.end_i">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="_parse_chain"></a><span class="summary-sig-name">_parse_chain</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser._parse_chain">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="_flush_text"></a><span class="summary-sig-name">_flush_text</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser._flush_text">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code>sgmllib.SGMLParser</code></b>: <code>__init__</code>, <code>close</code>, <code>convert_charref</code>, <code>convert_codepoint</code>, <code>convert_entityref</code>, <code>error</code>, <code>finish_endtag</code>, <code>finish_shorttag</code>, <code>finish_starttag</code>, <code>get_starttag_text</code>, <code>goahead</code>, <code>handle_charref</code>, <code>handle_comment</code>, <code>handle_decl</code>, <code>handle_endtag</code>, <code>handle_entityref</code>, <code>handle_pi</code>, <code>handle_starttag</code>, <code>parse_endtag</code>, <code>parse_pi</code>, <code>parse_starttag</code>, <code>report_unbalanced</code>, <code>setliteral</code>, <code>setnomoretags</code>, <code>unknown_charref</code>, <code>unknown_endtag</code>, <code>unknown_entityref</code>, <code>unknown_starttag</code> </p> <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>sgmllib.SGMLParser</code></b> (private): <code>_convert_ref</code> </p></div> <p class="indent-wrapped-lines"><b>Inherited from <code>markupbase.ParserBase</code></b>: <code>getpos</code>, <code>parse_comment</code>, <code>parse_declaration</code>, <code>parse_marked_section</code>, <code>unknown_decl</code>, <code>updatepos</code> </p> <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>markupbase.ParserBase</code></b> (private): <code>_parse_doctype_attlist</code>, <code>_parse_doctype_element</code>, <code>_parse_doctype_entity</code>, <code>_parse_doctype_notation</code>, <code>_parse_doctype_subset</code>, <code>_scan_name</code> </p></div> </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 colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code>sgmllib.SGMLParser</code></b>: <code>entity_or_charref</code>, <code>entitydefs</code> </p> <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>sgmllib.SGMLParser</code></b> (private): <code>_decl_otherchars</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="reset"></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">reset</span>(<span class="sig-arg">self</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.reset">source code</a></span> </td> </tr></table> <p>Reset this instance. Loses all unprocessed data.</p> <dl class="fields"> <dt>Overrides: markupbase.ParserBase.reset </dt> </dl> </td></tr></table> </div> <a name="feed"></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">feed</span>(<span class="sig-arg">self</span>, <span class="sig-arg">handle</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.feed">source code</a></span> </td> </tr></table> <p>Feed in ndb data for scanning. handle is a file-like object containing ndb data. consumer is a Consumer object that will receive events as the ndb data is scanned.</p> <dl class="fields"> <dt>Overrides: sgmllib.SGMLParser.feed </dt> </dl> </td></tr></table> </div> <a name="handle_data"></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">handle_data</span>(<span class="sig-arg">self</span>, <span class="sig-arg">newtext</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Ndb-pysrc.html#NdbParser.handle_data">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Overrides: sgmllib.SGMLParser.handle_data </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 09:26:36 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. So hide // them unless we have a cookie that says to show them. checkCookie(); // --> </script> </body> </html>