<?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.GenBank.LocationParser.LocationParser</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.GenBank-module.html">Package GenBank</a> :: <a href="Bio.GenBank.LocationParser-module.html">Module LocationParser</a> :: Class LocationParser </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.GenBank.LocationParser.LocationParser-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class LocationParser</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser">source code</a></span></p> <pre class="base-tree"> object --+ | <a href="Bio.Parsers.spark.GenericParser-class.html">Parsers.spark.GenericParser</a> --+ | <strong class="uidshort">LocationParser</strong> </pre> <hr /> <!-- ==================== 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.GenBank.LocationParser.LocationParser-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">start</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">location</code><code class="variable-quote">'</code></span>)</span><br /> x.__init__(...) initializes x; see help(type(x)) for signature</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.__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 name="p_location"></a><span class="summary-sig-name">p_location</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> location ::= absolute_location location ::= feature_name location ::= function</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_location">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="p_function"></a><span class="summary-sig-name">p_function</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> function ::= functional_operator open_paren location_list close_paren</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_function">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="p_absolute_location"></a><span class="summary-sig-name">p_absolute_location</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> absolute_location ::= local_location absolute_location ::= path colon local_location</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_absolute_location">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="p_path"></a><span class="summary-sig-name">p_path</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> path ::= database double_colon primary_accession path ::= primary_accession</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_path">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="p_feature_name"></a><span class="summary-sig-name">p_feature_name</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> feature_name ::= path colon feature_label feature_name ::= feature_label</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_feature_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 name="p_feature_label"></a><span class="summary-sig-name">p_feature_label</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> label ::= symbol</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_feature_label">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="p_local_location"></a><span class="summary-sig-name">p_local_location</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> local_location ::= base_position local_location ::= between_position local_location ::= base_range</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_local_location">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="p_location_list"></a><span class="summary-sig-name">p_location_list</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> location_list ::= location location_list ::= location_list comma location</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_location_list">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="p_functional_operator"></a><span class="summary-sig-name">p_functional_operator</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> functional_operator ::= symbol</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_functional_operator">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="p_base_position"></a><span class="summary-sig-name">p_base_position</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> base_position ::= integer base_position ::= low_base_bound base_position ::= high_base_bound base_position ::= two_base_bound</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_base_position">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="p_low_base_bound"></a><span class="summary-sig-name">p_low_base_bound</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> low_base_bound ::= greater_than integer</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_low_base_bound">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="p_high_base_bound"></a><span class="summary-sig-name">p_high_base_bound</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> high_base_bound ::= less_than integer</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_high_base_bound">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="p_two_base_bound_1"></a><span class="summary-sig-name">p_two_base_bound_1</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> two_base_bound ::= open_paren base_position dot base_position close_paren</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_two_base_bound_1">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="p_two_base_bound_2"></a><span class="summary-sig-name">p_two_base_bound_2</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> two_base_bound ::= base_position dot base_position</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_two_base_bound_2">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="p_between_position"></a><span class="summary-sig-name">p_between_position</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> between_position ::= base_position caret base_position</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_between_position">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="p_base_range"></a><span class="summary-sig-name">p_base_range</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> base_range ::= base_position double_dot base_position base_range ::= function double_dot base_position base_range ::= base_position double_dot function base_range ::= function double_dot function</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_base_range">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="p_database"></a><span class="summary-sig-name">p_database</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> database ::= symbol</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_database">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="p_primary_accession"></a><span class="summary-sig-name">p_primary_accession</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">args</span>)</span><br /> primary_accession ::= symbol</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.p_primary_accession">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.Parsers.spark.GenericParser-class.html">Parsers.spark.GenericParser</a></code></b>: <code><a href="Bio.Parsers.spark.GenericParser-class.html#addRule">addRule</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#ambiguity">ambiguity</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#augment">augment</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#buildState">buildState</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#buildTree">buildTree</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#buildTree_r">buildTree_r</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#collectRules">collectRules</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#error">error</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#makeFIRST">makeFIRST</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#parse">parse</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#preprocess">preprocess</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#resolve">resolve</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#typestring">typestring</a></code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>: <code>__delattr__</code>, <code>__format__</code>, <code>__getattribute__</code>, <code>__hash__</code>, <code>__new__</code>, <code>__reduce__</code>, <code>__reduce_ex__</code>, <code>__repr__</code>, <code>__setattr__</code>, <code>__sizeof__</code>, <code>__str__</code>, <code>__subclasshook__</code> </p> </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"> <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Parsers.spark.GenericParser-class.html">Parsers.spark.GenericParser</a></code></b> (private): <code><a href="Bio.Parsers.spark.GenericParser-class.html#_EOF" onclick="show_private();">_EOF</a></code>, <code><a href="Bio.Parsers.spark.GenericParser-class.html#_START" onclick="show_private();">_START</a></code> </p></div> </td> </tr> </table> <!-- ==================== PROPERTIES ==================== --> <a name="section-Properties"></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">Properties</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Properties" 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>object</code></b>: <code>__class__</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">start</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">location</code><code class="variable-quote">'</code></span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.GenBank.LocationParser-pysrc.html#LocationParser.__init__">source code</a></span> </td> </tr></table> <p>x.__init__(...) initializes x; see help(type(x)) for signature</p> <dl class="fields"> <dt>Overrides: object.__init__ <dd><em class="note">(inherited documentation)</em></dd> </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 Thu Aug 18 18:19:25 2011 </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 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