<?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.config.FormatRegistry.FormatObject</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.config-module.html">Package config</a> :: <a href="Bio.config.FormatRegistry-module.html">Module FormatRegistry</a> :: Class FormatObject </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.config.FormatRegistry.FormatObject-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class FormatObject</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.config.FormatRegistry-pysrc.html#FormatObject">source code</a></span></p> <pre class="base-tree"> <a href="Bio.config.Registry.RegisterableObject-class.html">Registry.RegisterableObject</a> --+ | <strong class="uidshort">FormatObject</strong> </pre> <hr /> <p>This object stores Biopython file formats and provides methods to work on them.</p> <p>Methods: identify Identify the format at a URL. identifyFile Identify the format of a file. identifyString Identify the format of a string.</p> <p>make_parser Make a parser that can parse the format. make_iterator Make an iterator over files of this format.</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.config.FormatRegistry.FormatObject-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">name</span>, <span class="summary-sig-arg">expression</span>, <span class="summary-sig-arg">abbrev</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">doc</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">filter</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">multirecord</span>=<span class="summary-sig-default">1</span>)</span><br /> FormatObject(name, expression[, abbrev][, doc] [, filter][, multirecord])</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.FormatRegistry-pysrc.html#FormatObject.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">FormatObject or None</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="identifyFile"></a><span class="summary-sig-name">identifyFile</span>(<span class="summary-sig-arg">S</span>, <span class="summary-sig-arg">infile</span>, <span class="summary-sig-arg">debug_level</span>=<span class="summary-sig-default">...</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.FormatRegistry-pysrc.html#FormatObject.identifyFile">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">FormatObject or None</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="identifyString"></a><span class="summary-sig-name">identifyString</span>(<span class="summary-sig-arg">S</span>, <span class="summary-sig-arg">s</span>, <span class="summary-sig-arg">debug_level</span>=<span class="summary-sig-default">...</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.FormatRegistry-pysrc.html#FormatObject.identifyString">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">FormatObject or None</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="identify"></a><span class="summary-sig-name">identify</span>(<span class="summary-sig-arg">S</span>, <span class="summary-sig-arg">source</span>, <span class="summary-sig-arg">debug_level</span>=<span class="summary-sig-default">...</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.FormatRegistry-pysrc.html#FormatObject.identify">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="make_parser"></a><span class="summary-sig-name">make_parser</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">select_names</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">debug_level</span>=<span class="summary-sig-default">0</span>)</span><br /> S.make_parser([select_names][, debug_level]) -> parser</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.FormatRegistry-pysrc.html#FormatObject.make_parser">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="make_iterator"></a><span class="summary-sig-name">make_iterator</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">tag</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">record</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">select_names</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">debug_level</span>=<span class="summary-sig-default">0</span>)</span><br /> S.make_iterator([tag][, select_names][, debug_level]) -> iterator</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.config.FormatRegistry-pysrc.html#FormatObject.make_iterator">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="__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">name</span>, <span class="sig-arg">expression</span>, <span class="sig-arg">abbrev</span>=<span class="sig-default">None</span>, <span class="sig-arg">doc</span>=<span class="sig-default">None</span>, <span class="sig-arg">filter</span>=<span class="sig-default">None</span>, <span class="sig-arg">multirecord</span>=<span class="sig-default">1</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.config.FormatRegistry-pysrc.html#FormatObject.__init__">source code</a></span> </td> </tr></table> <p>FormatObject(name, expression[, abbrev][, doc] [, filter][, multirecord])</p> <p>name is the name of the object, abbrev is an abbreviation for the name, and doc is some documentation describing the object.</p> <p>expression is a Martel.Expression that can parse this format. filter is an optional Martel.Expression that can be used to quickly determine whether some input is parseable by this format.</p> <p>multirecord is either 0/1 indicating whether this format can be used to parse multiple records. By default, it is 1.</p> <dl class="fields"> <dt>Overrides: <a href="Bio.config.Registry.RegisterableObject-class.html#__init__">Registry.RegisterableObject.__init__</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 09:26:39 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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