<?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.Data.CodonTable</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.Data-module.html">Package Data</a> :: Module CodonTable </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.Data.CodonTable-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module CodonTable</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Data.CodonTable-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 border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Classes</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Classes" 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.Data.CodonTable.TranslationError-class.html" class="summary-name">TranslationError</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Data.CodonTable.CodonTable-class.html" class="summary-name">CodonTable</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Data.CodonTable.NCBICodonTable-class.html" class="summary-name">NCBICodonTable</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Data.CodonTable.NCBICodonTableDNA-class.html" class="summary-name">NCBICodonTableDNA</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Data.CodonTable.NCBICodonTableRNA-class.html" class="summary-name">NCBICodonTableRNA</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Data.CodonTable.AmbiguousCodonTable-class.html" class="summary-name">AmbiguousCodonTable</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Data.CodonTable.AmbiguousForwardTable-class.html" class="summary-name">AmbiguousForwardTable</a> </td> </tr> </table> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></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">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" 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 name="make_back_table"></a><span class="summary-sig-name">make_back_table</span>(<span class="summary-sig-arg">table</span>, <span class="summary-sig-arg">default_stop_codon</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Data.CodonTable-pysrc.html#make_back_table">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="register_ncbi_table"></a><span class="summary-sig-name">register_ncbi_table</span>(<span class="summary-sig-arg">name</span>, <span class="summary-sig-arg">alt_name</span>, <span class="summary-sig-arg">id</span>, <span class="summary-sig-arg">table</span>, <span class="summary-sig-arg">start_codons</span>, <span class="summary-sig-arg">stop_codons</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Data.CodonTable-pysrc.html#register_ncbi_table">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="list_possible_proteins"></a><span class="summary-sig-name">list_possible_proteins</span>(<span class="summary-sig-arg">codon</span>, <span class="summary-sig-arg">forward_table</span>, <span class="summary-sig-arg">ambiguous_nucleotide_values</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Data.CodonTable-pysrc.html#list_possible_proteins">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="list_ambiguous_codons"></a><span class="summary-sig-name">list_ambiguous_codons</span>(<span class="summary-sig-arg">codons</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Data.CodonTable-pysrc.html#list_ambiguous_codons">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 name="unambiguous_dna_by_name"></a><span class="summary-name">unambiguous_dna_by_name</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="unambiguous_dna_by_id"></a><span class="summary-name">unambiguous_dna_by_id</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="unambiguous_rna_by_name"></a><span class="summary-name">unambiguous_rna_by_name</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="unambiguous_rna_by_id"></a><span class="summary-name">unambiguous_rna_by_id</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="generic_by_name"></a><span class="summary-name">generic_by_name</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="generic_by_id"></a><span class="summary-name">generic_by_id</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="ambiguous_generic_by_name"></a><span class="summary-name">ambiguous_generic_by_name</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="ambiguous_generic_by_id"></a><span class="summary-name">ambiguous_generic_by_id</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="standard_dna_table"></a><span class="summary-name">standard_dna_table</span> = <code title="None">None</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="standard_rna_table"></a><span class="summary-name">standard_rna_table</span> = <code title="None">None</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="ambiguous_dna_by_name"></a><span class="summary-name">ambiguous_dna_by_name</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="ambiguous_dna_by_id"></a><span class="summary-name">ambiguous_dna_by_id</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="ambiguous_rna_by_name"></a><span class="summary-name">ambiguous_rna_by_name</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="ambiguous_rna_by_id"></a><span class="summary-name">ambiguous_rna_by_id</span> = <code title="{}">{}</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="id"></a><span class="summary-name">id</span> = <code title="15">15</code> </td> </tr> </table> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> 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