<?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.Decode</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> :: Module Decode </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.Decode-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module Decode</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Decode-pysrc.html">source code</a></span></p> <!-- ==================== CLASSES ==================== --> <a name="section-Classes"></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 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width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="join_english"></a><span class="summary-sig-name">join_english</span>(<span class="summary-sig-arg">fields</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#join_english">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="chomp"></a><span class="summary-sig-name">chomp</span>(<span class="summary-sig-arg">s</span>, <span class="summary-sig-arg">c</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#chomp">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="lchomp"></a><span class="summary-sig-name">lchomp</span>(<span class="summary-sig-arg">s</span>, <span class="summary-sig-arg">c</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#lchomp">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="chompchomp"></a><span class="summary-sig-name">chompchomp</span>(<span class="summary-sig-arg">s</span>, <span class="summary-sig-arg">c</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#chompchomp">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="fixspaces"></a><span class="summary-sig-name">fixspaces</span>(<span class="summary-sig-arg">s</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#fixspaces">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="join_fixspaces"></a><span class="summary-sig-name">join_fixspaces</span>(<span class="summary-sig-arg">lines</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#join_fixspaces">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="tr"></a><span class="summary-sig-name">tr</span>(<span class="summary-sig-arg">s</span>, <span class="summary-sig-arg">frm</span>, <span class="summary-sig-arg">to</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#tr">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="safe_int"></a><span class="summary-sig-name">safe_int</span>(<span class="summary-sig-arg">s</span>)</span><br /> converts to int if the number is small, long if it's large</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#safe_int">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="_fixup_defs"></a><span class="summary-sig-name">_fixup_defs</span>()</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#_fixup_defs">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="scan"></a><span class="summary-sig-name">scan</span>(<span class="summary-sig-arg">input</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#scan">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">tokens</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#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 name="make_decoder"></a><span class="summary-sig-name">make_decoder</span>(<span class="summary-sig-arg">s</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#make_decoder">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="_verify_subtypes"></a><span class="summary-sig-name">_verify_subtypes</span>(<span class="summary-sig-arg">subset</span>, <span class="summary-sig-arg">total</span>, <span class="summary-sig-arg">old_name</span>, <span class="summary-sig-arg">new_name</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#_verify_subtypes">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_typechecked_decoder"></a><span class="summary-sig-name">make_typechecked_decoder</span>(<span class="summary-sig-arg">s</span>, <span class="summary-sig-arg">input_types</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">output_types</span>=<span class="summary-sig-default">None</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#make_typechecked_decoder">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="test"></a><span class="summary-sig-name">test</span>()</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Decode-pysrc.html#test">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== VARIABLES ==================== --> <a name="section-Variables"></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">Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Variables" 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"> <a href="Bio.Decode-module.html#decode_functions" class="summary-name">decode_functions</a> = <code title="{'add': (<function <lambda> at 0xcfc488>, (<type 'int'>), (<type 'int'>)), 'chomp': (<function chomp at 0xcf4f50>, (<type 'str'>), (<type 'str'>)), 'chompchomp': (<function chompchomp at 0xcf8050>, (<type 'str'>), ..."><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">add</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-group">(</code><function <lambda> at 0xcfc488><code class="variable-op">, </code><code class="variable-group">(</code><code class="variable-ellipsis">...</code></code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_decoder_cache"></a><span class="summary-name">_decoder_cache</span> = <code title="{}"><code class="variable-group">{</code><code class="variable-group">}</code></code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_typechecked_decoder_cache"></a><span class="summary-name">_typechecked_decoder_cache</span> = <code title="{}"><code class="variable-group">{</code><code class="variable-group">}</code></code> </td> </tr> </table> <!-- ==================== VARIABLES DETAILS ==================== --> <a name="section-VariablesDetails"></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">Variables Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-VariablesDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="decode_functions"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">decode_functions</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">add</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-group">(</code><function <lambda> at 0xcfc488><code class="variable-op">,</code> <code class="variable-group">(</code><type 'int'><code class="variable-group">)</code><code class="variable-op">,</code> <code class="variable-group">(</code><type 'int'><code class="variable-group">)</code><code class="variable-group">)</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">chomp</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-group">(</code><function chomp at 0xcf4f50><code class="variable-op">,</code> <code class="variable-group">(</code><type 'str'><code class="variable-group">)</code><code class="variable-op">,</code> <code class="variable-group">(</code><type 'str'><code class="variable-group">)</code><code class="variable-group">)</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">chompchomp</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-group">(</code><function chompchomp at 0xcf8050><code class="variable-op">,</code> <code class="variable-group">(</code><type 'str'><code class="variable-group">)</code><code class="variable-op">,</code> <code class="variable-ellipsis">...</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" 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