<?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.Blast.NCBIXML._XMLparser</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.Blast-module.html">Package Blast</a> :: <a href="Bio.Blast.NCBIXML-module.html">Module NCBIXML</a> :: Class _XMLparser </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.Blast.NCBIXML._XMLparser-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class _XMLparser</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser">source code</a></span></p> <pre class="base-tree"> xml.sax.handler.ContentHandler --+ | <strong class="uidshort">_XMLparser</strong> </pre> <dl><dt>Known Subclasses:</dt> <dd> <ul class="subclass-list"> <li><a href="Bio.Blast.NCBIXML.BlastParser-class.html">BlastParser</a></li> </ul> </dd></dl> <hr /> <p>Generic SAX Parser</p> <p>Just a very basic SAX parser.</p> <p>Redefine the methods startElement, characters and endElement.</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.Blast.NCBIXML._XMLparser-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">debug</span>=<span class="summary-sig-default">0</span>)</span><br /> Constructor</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser.__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.Blast.NCBIXML._XMLparser-class.html#_secure_name" class="summary-sig-name" onclick="show_private();">_secure_name</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">name</span>)</span><br /> Removes 'dangerous' from tag names</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser._secure_name">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.Blast.NCBIXML._XMLparser-class.html#startElement" class="summary-sig-name">startElement</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">name</span>, <span class="summary-sig-arg">attr</span>)</span><br /> Found XML start tag</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser.startElement">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.Blast.NCBIXML._XMLparser-class.html#characters" class="summary-sig-name">characters</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">ch</span>)</span><br /> Found some text</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser.characters">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.Blast.NCBIXML._XMLparser-class.html#endElement" class="summary-sig-name">endElement</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">name</span>)</span><br /> Found XML end tag</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser.endElement">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code>xml.sax.handler.ContentHandler</code></b>: <code>endDocument</code>, <code>endElementNS</code>, <code>endPrefixMapping</code>, <code>ignorableWhitespace</code>, <code>processingInstruction</code>, <code>setDocumentLocator</code>, <code>skippedEntity</code>, <code>startDocument</code>, <code>startElementNS</code>, <code>startPrefixMapping</code> </p> </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">debug</span>=<span class="sig-default">0</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser.__init__">source code</a></span> </td> </tr></table> <p>Constructor</p> <p>debug - integer, amount of debug information to print</p> <dl class="fields"> <dt>Overrides: xml.sax.handler.ContentHandler.__init__ </dt> </dl> </td></tr></table> </div> <a name="_secure_name"></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">_secure_name</span>(<span class="sig-arg">self</span>, <span class="sig-arg">name</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser._secure_name">source code</a></span> </td> </tr></table> <p>Removes 'dangerous' from tag names</p> <p>name -- name to be 'secured'</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="startElement"></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">startElement</span>(<span class="sig-arg">self</span>, <span class="sig-arg">name</span>, <span class="sig-arg">attr</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser.startElement">source code</a></span> </td> </tr></table> <p>Found XML start tag</p> <p>No real need of attr, BLAST DTD doesn't use them</p> <p>name -- name of the tag</p> <p>attr -- tag attributes</p> <dl class="fields"> <dt>Overrides: xml.sax.handler.ContentHandler.startElement </dt> </dl> </td></tr></table> </div> <a name="characters"></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">characters</span>(<span class="sig-arg">self</span>, <span class="sig-arg">ch</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser.characters">source code</a></span> </td> </tr></table> <p>Found some text</p> <p>ch -- characters read</p> <dl class="fields"> <dt>Overrides: xml.sax.handler.ContentHandler.characters </dt> </dl> </td></tr></table> </div> <a name="endElement"></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">endElement</span>(<span class="sig-arg">self</span>, <span class="sig-arg">name</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#_XMLparser.endElement">source code</a></span> </td> </tr></table> <p>Found XML end tag</p> <p>name -- tag name</p> <dl class="fields"> <dt>Overrides: xml.sax.handler.ContentHandler.endElement </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 09:26:30 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"> <!-- // 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