<?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.Mindy.SimpleSeqRecord.FixDocumentBuilder</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.Mindy-module.html">Package Mindy</a> :: <a href="Bio.Mindy.SimpleSeqRecord-module.html">Module SimpleSeqRecord</a> :: Class FixDocumentBuilder </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.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class FixDocumentBuilder</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Mindy.SimpleSeqRecord-pysrc.html#FixDocumentBuilder">source code</a></span></p> <pre class="base-tree"> xml.sax.handler.ContentHandler --+ | <a href="Martel.Dispatch.DispatchHandler-class.html">Martel.Dispatch.DispatchHandler</a> --+ | <a href="Martel.Dispatch.Dispatcher-class.html">Martel.Dispatch.Dispatcher</a> --+ | <a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html">builders.SeqRecord.sequence.BuildSeqRecord</a> --+ | <strong class="uidshort">FixDocumentBuilder</strong> </pre> <hr /> <p>A SAX builder-style class to make a parsed SeqRecord available.</p> <p>This class does a lot of trickery to make things fit in the SAX framework and still have the flexibility to use a built SeqRecord object.</p> <p>You shouldn't really need to use this class unless you are doing something really fancy-pants; otherwise, just use the BaseSeqRecordIndexer interfaces.</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.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">get_ids_callback</span>)</span><br /> Intialize with a callback function to gets id info from a SeqRecord.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Mindy.SimpleSeqRecord-pysrc.html#FixDocumentBuilder.__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 href="Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html#end_record" class="summary-sig-name">end_record</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">tag</span>)</span><br /> Overrride the builder function to muck with the document attribute.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Mindy.SimpleSeqRecord-pysrc.html#FixDocumentBuilder.end_record">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.builders.SeqRecord.sequence.BuildSeqRecord-class.html">builders.SeqRecord.sequence.BuildSeqRecord</a></code></b>: <code><a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_dbid">add_dbid</a></code>, <code><a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_dbxref">add_dbxref</a></code>, <code><a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_dbxref_dbids">add_dbxref_dbids</a></code>, <code><a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_description">add_description</a></code>, <code><a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_features">add_features</a></code>, <code><a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_sequence">add_sequence</a></code>, <code><a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#start_record">start_record</a></code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Martel.Dispatch.Dispatcher-class.html">Martel.Dispatch.Dispatcher</a></code></b>: <code><a href="Martel.Dispatch.Dispatcher-class.html#acquire">acquire</a></code>, <code><a href="Martel.Dispatch.Dispatcher-class.html#characters">characters</a></code>, <code><a href="Martel.Dispatch.Dispatcher-class.html#endDocument">endDocument</a></code>, <code><a href="Martel.Dispatch.Dispatcher-class.html#endElement">endElement</a></code>, <code><a href="Martel.Dispatch.Dispatcher-class.html#get_characters">get_characters</a></code>, <code><a href="Martel.Dispatch.Dispatcher-class.html#save_characters">save_characters</a></code>, <code><a href="Martel.Dispatch.Dispatcher-class.html#startDocument">startDocument</a></code>, <code><a href="Martel.Dispatch.Dispatcher-class.html#startElement">startElement</a></code>, <code><a href="Martel.Dispatch.Dispatcher-class.html#uses_tags">uses_tags</a></code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code>xml.sax.handler.ContentHandler</code></b>: <code>endElementNS</code>, <code>endPrefixMapping</code>, <code>ignorableWhitespace</code>, <code>processingInstruction</code>, <code>setDocumentLocator</code>, <code>skippedEntity</code>, <code>startElementNS</code>, <code>startPrefixMapping</code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Martel.Dispatch.DispatchHandler-class.html">Martel.Dispatch.DispatchHandler</a></code></b>: <code><a href="Martel.Dispatch.DispatchHandler-class.html#get_supported_features">get_supported_features</a></code>, <code><a href="Martel.Dispatch.DispatchHandler-class.html#setCharacterSaver">setCharacterSaver</a></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">get_ids_callback</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Mindy.SimpleSeqRecord-pysrc.html#FixDocumentBuilder.__init__">source code</a></span> </td> </tr></table> <p>Intialize with a callback function to gets id info from a SeqRecord.</p> <p>get_ids_callback should be a callable function that will take a SeqRecord object and return a dictionary mapping id names to the valid ids for these names.</p> <dl class="fields"> <dt>Overrides: <a href="Martel.Dispatch.DispatchHandler-class.html#__init__">Martel.Dispatch.DispatchHandler.__init__</a> </dt> </dl> </td></tr></table> </div> <a name="end_record"></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">end_record</span>(<span class="sig-arg">self</span>, <span class="sig-arg">tag</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Mindy.SimpleSeqRecord-pysrc.html#FixDocumentBuilder.end_record">source code</a></span> </td> </tr></table> <p>Overrride the builder function to muck with the document attribute.</p> <dl class="fields"> <dt>Overrides: <a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#end_record">builders.SeqRecord.sequence.BuildSeqRecord.end_record</a> </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 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