<?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.Registry</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> :: Module Registry </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.Registry-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.config.Registry-module.html">Module Bio.config.Registry</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2002 by Jeffrey Chang, Andrew Dalke. All rights reserved.</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># This is based on some older code by Andrew Dalke.</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">"""This module implements some base classes used in the Registry</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">system for Biopython.</tt> </tt> <a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt> <a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">Registry Implements a Biopython Registry.</tt> </tt> <a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">RegisterableObject Base class for objects in the Registry.</tt> </tt> <a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">RegisterableGroup Base class for groups of objects in the Registry.</tt> </tt> <a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt> <a name="Registry"></a><div id="Registry-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="Registry-toggle" onclick="return toggle('Registry');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.config.Registry.Registry-class.html">Registry</a><tt class="py-op">:</tt> </tt> </div><div id="Registry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Registry-expanded"><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-docstring">"""This is a dictionary-like object for storing and retrieving</tt> </tt> <a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> objects in a registry.</tt> </tt> <a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> Methods:</tt> </tt> <a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> register Add a RegisterableObject into the Registry.</tt> </tt> <a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> Dictionary interface:</tt> </tt> <a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> __getitem__</tt> </tt> <a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> get</tt> </tt> <a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> keys</tt> </tt> <a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> values</tt> </tt> <a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> items</tt> </tt> <a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="Registry.__init__"></a><div id="Registry.__init__-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="Registry.__init__-toggle" onclick="return toggle('Registry.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.Registry-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">load_path</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Registry.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Registry.__init__-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-docstring">"""Registry(name[, load_path])</tt> </tt> <a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> Create a new registry. name is the name of the registry.</tt> </tt> <a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> load_path is an optional path (e.g. Bio.config.dbdefs) that</tt> </tt> <a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> contains objects for the registry.</tt> </tt> <a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.KEGG.Compound.Record._name()=Bio.KEGG.Compound.Record-class.html#_name,Method Bio.KEGG.Enzyme.Record._name()=Bio.KEGG.Enzyme.Record-class.html#_name,Method Bio.MEME.Motif.Motif._name()=Bio.MEME.Motif.Motif-class.html#_name,Variable Bio.Mindy.XPath._name=Bio.Mindy.XPath-module.html#_name"><a title="Bio.KEGG.Compound.Record._name Bio.KEGG.Enzyme.Record._name Bio.MEME.Motif.Motif._name Bio.Mindy.XPath._name" class="py-name" href="#" onclick="return doclink('link-0', '_name', 'link-0');">_name</a></tt> <tt class="py-op">=</tt> <tt id="link-1" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-1', 'name', 'link-1');">name</a></tt> </tt> <a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_load_path</tt> <tt class="py-op">=</tt> <tt class="py-name">load_path</tt> </tt> <a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_name_table</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_abbrev_table</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_autoloaded</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_autoloading</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> </div><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt> <a name="Registry._autoload"></a><div id="Registry._autoload-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="Registry._autoload-toggle" onclick="return toggle('Registry._autoload');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.Registry-class.html#_autoload">_autoload</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Registry._autoload-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Registry._autoload-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_autoloaded</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_autoloading</tt><tt class="py-op">:</tt> </tt> <a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_autoloading</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt> <a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.config.Registry.Registry._load()=Bio.config.Registry.Registry-class.html#_load,Method Bio.config.SeqDBRegistry.SeqDBRegistry._load()=Bio.config.SeqDBRegistry.SeqDBRegistry-class.html#_load"><a title="Bio.config.Registry.Registry._load Bio.config.SeqDBRegistry.SeqDBRegistry._load" class="py-name" href="#" onclick="return doclink('link-2', '_load', 'link-2');">_load</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_load_path</tt><tt class="py-op">)</tt> </tt> <a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_autoloading</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> <a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_autoloaded</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt> </div><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt> <a name="Registry._load"></a><div id="Registry._load-def"><a name="L53"></a><tt class="py-lineno"> 53</tt> <a class="py-toggle" href="#" id="Registry._load-toggle" onclick="return toggle('Registry._load');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.Registry-class.html#_load">_load</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">path</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Registry._load-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Registry._load-expanded"><a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">path</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt> <a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Module Bio.config._support=Bio.config._support-module.html,Module Bio.dbdefs._support=Bio.dbdefs._support-module.html"><a title="Bio.config._support Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-3', '_support', 'link-3');">_support</a></tt> </tt> <a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-comment"># Get a list of all the modules in that path.</tt> </tt> <a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">modulenames</tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name"><a title="Bio.config._support Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-4', '_support', 'link-3');">_support</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Function Bio.config._support.find_submodules()=Bio.config._support-module.html#find_submodules"><a title="Bio.config._support.find_submodules" class="py-name" href="#" onclick="return doclink('link-5', 'find_submodules', 'link-5');">find_submodules</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">)</tt> </tt> <a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">modulenames</tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter Bio.FilteredReader.FilteredReader.filter Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-6', 'filter', 'link-6');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-7" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-7', 'x', 'link-7');">x</a></tt><tt class="py-op">:</tt> <tt class="py-keyword">not</tt> <tt id="link-8" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-8', 'x', 'link-7');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"_"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">modulenames</tt><tt class="py-op">)</tt> </tt> <a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">modulenames</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort Bio.PDB.Residue.Residue.sort Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-9', 'sort', 'link-9');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt> <a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-comment"># Now load each one of the modules and look for</tt> </tt> <a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># RegisterableObject objects in them.</tt> </tt> <a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-10" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-1');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">modulenames</tt><tt class="py-op">:</tt> </tt> <a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Bio.config._support Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-11', '_support', 'link-3');">_support</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Function Bio.config._support.load_module()=Bio.config._support-module.html#load_module"><a title="Bio.config._support.load_module" class="py-name" href="#" onclick="return doclink('link-12', 'load_module', 'link-12');">load_module</a></tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-13', 'name', 'link-1');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-14" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-14', 'name', 'link-1');">name</a></tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.obj=Bio.Encodings.IUPACEncoding-module.html#obj"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-15', 'obj', 'link-15');">obj</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">module</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items Bio.EUtils.MultiDict._BaseMultiDict.items Bio.Entrez.SerialSet.items Bio.GenBank.NCBIDictionary.items Bio.Mindy.BaseDB.DictLookup.items Bio.Prosite.ExPASyDictionary.items Bio.Prosite.Prodoc.ExPASyDictionary.items Bio.PubMed.Dictionary.items Bio.SwissProt.SProt.ExPASyDictionary.items Bio.config.Registry.Registry.items Bio.listfns.items BioSQL.BioSeqDatabase.BioSeqDatabase.items BioSQL.BioSeqDatabase.DBServer.items Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-16', 'items', 'link-16');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-17" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-17', 'name', 'link-1');">name</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"_"</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-18', 'obj', 'link-15');">obj</a></tt><tt class="py-op">,</tt> <tt id="link-19" class="py-name" targets="Class Bio.config.Registry.RegisterableObject=Bio.config.Registry.RegisterableObject-class.html"><a title="Bio.config.Registry.RegisterableObject" class="py-name" href="#" onclick="return doclink('link-19', 'RegisterableObject', 'link-19');">RegisterableObject</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt> <a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.config.Registry.Registry.register()=Bio.config.Registry.Registry-class.html#register"><a title="Bio.config.Registry.Registry.register" class="py-name" href="#" onclick="return doclink('link-20', 'register', 'link-20');">register</a></tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-21', 'obj', 'link-15');">obj</a></tt><tt class="py-op">)</tt> </tt> </div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt> <a name="Registry.register"></a><div id="Registry.register-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="Registry.register-toggle" onclick="return toggle('Registry.register');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.Registry-class.html#register">register</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Registry.register-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Registry.register-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-docstring">"""S.register(obj)</tt> </tt> <a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> Add an object to the registry. obj must be a</tt> </tt> <a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> RegisterableObject object.</tt> </tt> <a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.config.Registry.Registry._autoload()=Bio.config.Registry.Registry-class.html#_autoload"><a title="Bio.config.Registry.Registry._autoload" class="py-name" href="#" onclick="return doclink('link-22', '_autoload', 'link-22');">_autoload</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt id="link-23" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-23', 'name', 'link-1');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-24', 'obj', 'link-15');">obj</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-25', 'name', 'link-1');">name</a></tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-26', 'obj', 'link-15');">obj</a></tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt> </tt> <a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-name">abbrev</tt> <tt class="py-keyword">or</tt> <tt id="link-27" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-27', 'name', 'link-1');">name</a></tt> </tt> <a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_name_table</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key Bio.EUtils.POM.ElementNode.has_key Bio.GenBank.NCBIDictionary.has_key Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key Bio.PDB.FragmentMapper'.FragmentMapper.has_key Bio.Prosite.ExPASyDictionary.has_key Bio.Prosite.Prodoc.ExPASyDictionary.has_key Bio.PubMed.Dictionary.has_key Bio.SwissProt.SProt.ExPASyDictionary.has_key Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-28', 'has_key', 'link-28');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-29', 'name', 'link-1');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"%r is a duplicate entry"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-30', 'name', 'link-1');">name</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_abbrev_table</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Crystal.Crystal.has_key Bio.EUtils.POM.ElementNode.has_key Bio.GenBank.NCBIDictionary.has_key Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key Bio.PDB.FragmentMapper'.FragmentMapper.has_key Bio.Prosite.ExPASyDictionary.has_key Bio.Prosite.Prodoc.ExPASyDictionary.has_key Bio.PubMed.Dictionary.has_key Bio.SwissProt.SProt.ExPASyDictionary.has_key Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-31', 'has_key', 'link-28');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">abbrev</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"%r is a duplicate entry"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">abbrev</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt> <a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_name_table</tt><tt class="py-op">[</tt><tt id="link-32" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-32', 'name', 'link-1');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-33', 'obj', 'link-15');">obj</a></tt> </tt> <a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_abbrev_table</tt><tt class="py-op">[</tt><tt class="py-name">abbrev</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-34', 'obj', 'link-15');">obj</a></tt> </tt> </div><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt> <a name="Registry.__getitem__"></a><div id="Registry.__getitem__-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="Registry.__getitem__-toggle" onclick="return toggle('Registry.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.Registry-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Registry.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Registry.__getitem__-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.config.Registry.Registry._autoload" class="py-name" href="#" onclick="return doclink('link-35', '_autoload', 'link-22');">_autoload</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_name_table</tt><tt class="py-op">[</tt><tt id="link-36" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-36', 'name', 'link-1');">name</a></tt><tt class="py-op">]</tt> <tt class="py-comment"># raises KeyError for unknown entries</tt> </tt> </div><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> </tt> <a name="Registry.get"></a><div id="Registry.get-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="Registry.get-toggle" onclick="return toggle('Registry.get');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.Registry-class.html#get">get</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">default</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Registry.get-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Registry.get-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.config.Registry.Registry._autoload" class="py-name" href="#" onclick="return doclink('link-37', '_autoload', 'link-22');">_autoload</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_name_table</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get Bio.Data.CodonTable.AmbiguousForwardTable.get Bio.EUtils.MultiDict._BaseMultiDict.get Bio.EUtils.POM.ElementNode.get Bio.GenBank.NCBIDictionary.get Bio.Mindy.BaseDB.DictLookup.get Bio.Prosite.ExPASyDictionary.get Bio.Prosite.Prodoc.ExPASyDictionary.get Bio.PubMed.Dictionary.get Bio.Restriction.Restriction.RestrictionBatch.get Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get Bio.SeqUtils.MissingTable.get Bio.SwissProt.SProt.ExPASyDictionary.get Bio.config.DBRegistry.DBGroup.get Bio.config.DBRegistry.DBObject.get Bio.config.Registry.Registry.get Martel.Parser.MartelAttributeList.get Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-38', 'get', 'link-38');">get</a></tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-39', 'name', 'link-1');">name</a></tt><tt class="py-op">,</tt> <tt id="link-40" class="py-name" targets="Method Bio.Parsers.spark.GenericASTTraversal.default()=Bio.Parsers.spark.GenericASTTraversal-class.html#default"><a title="Bio.Parsers.spark.GenericASTTraversal.default" class="py-name" href="#" onclick="return doclink('link-40', 'default', 'link-40');">default</a></tt><tt class="py-op">)</tt> </tt> </div><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt> <a name="Registry.keys"></a><div id="Registry.keys-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="Registry.keys-toggle" onclick="return toggle('Registry.keys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.Registry-class.html#keys">keys</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Registry.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Registry.keys-expanded"><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.config.Registry.Registry._autoload" class="py-name" href="#" onclick="return doclink('link-41', '_autoload', 'link-22');">_autoload</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_name_table</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" 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class="py-name" href="#" onclick="return doclink('link-45', '_autoload', 'link-22');">_autoload</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_name_table</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Crystal.Crystal.items Bio.EUtils.MultiDict._BaseMultiDict.items Bio.Entrez.SerialSet.items Bio.GenBank.NCBIDictionary.items Bio.Mindy.BaseDB.DictLookup.items Bio.Prosite.ExPASyDictionary.items Bio.Prosite.Prodoc.ExPASyDictionary.items Bio.PubMed.Dictionary.items Bio.SwissProt.SProt.ExPASyDictionary.items Bio.config.Registry.Registry.items Bio.listfns.items BioSQL.BioSeqDatabase.BioSeqDatabase.items BioSQL.BioSeqDatabase.DBServer.items Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-46', 'items', 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Martel.Parser.RecordParser.__str__" class="py-name" href="#" onclick="return doclink('link-53', '__str__', 'link-53');">__str__</a></tt> </tt> </div><a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt> <a name="RegisterableObject"></a><div id="RegisterableObject-def"><a name="L118"></a><tt class="py-lineno">118</tt> <a class="py-toggle" href="#" id="RegisterableObject-toggle" onclick="return toggle('RegisterableObject');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.config.Registry.RegisterableObject-class.html">RegisterableObject</a><tt class="py-op">:</tt> </tt> </div><div id="RegisterableObject-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RegisterableObject-expanded"><a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-docstring">"""This is a base class for objects that can be added to a registry.</tt> </tt> <a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> Members:</tt> </tt> <a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> name The name of the object.</tt> </tt> <a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> abbrev An abbreviation for the name</tt> </tt> <a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="RegisterableObject.__init__"></a><div id="RegisterableObject.__init__-def"><a name="L126"></a><tt class="py-lineno">126</tt> <a class="py-toggle" href="#" id="RegisterableObject.__init__-toggle" onclick="return toggle('RegisterableObject.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.RegisterableObject-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">abbrev</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="RegisterableObject.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RegisterableObject.__init__-expanded"><a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-docstring">"""RegisterableObject(name, abbrev, doc)"""</tt> </tt> <a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt> <a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt> <a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-54', 'name', 'link-1');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-55', 'name', 'link-1');">name</a></tt> </tt> <a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-name">abbrev</tt> <tt class="py-keyword">or</tt> <tt id="link-56" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-56', 'name', 'link-1');">name</a></tt> </tt> <a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">_legal_abbrev</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-57', 'compile', 'link-57');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"[a-zA-Z][a-zA-Z0-9_]*$"</tt><tt class="py-op">)</tt> </tt> <a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">check_abbrev</tt> <tt class="py-op">=</tt> <tt class="py-name">_legal_abbrev</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match Bio.Prosite.Pattern.Prosite.match Bio.triefind.match Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-58', 'match', 'link-58');">match</a></tt> </tt> <a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">check_abbrev</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"abbrev name of %r is not allowed"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt> </tt> <a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__ Bio.PDB.Atom.__doc__ Bio.PDB.Chain.__doc__ Bio.PDB.Entity.__doc__ Bio.PDB.HSExposure.__doc__ Bio.PDB.MMCIF2Dict.__doc__ Bio.PDB.MMCIFParser.__doc__ Bio.PDB.Model.__doc__ Bio.PDB.NACCESS.__doc__ Bio.PDB.NeighborSearch.__doc__ Bio.PDB.PDBExceptions.__doc__ Bio.PDB.Polypeptide.__doc__ Bio.PDB.Residue.__doc__ Bio.PDB.Selection.__doc__ Bio.PDB.Structure.__doc__ Bio.PDB.StructureBuilder.__doc__ Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-59', '__doc__', 'link-59');">__doc__</a></tt> <tt class="py-op">=</tt> <tt class="py-name">doc</tt> </tt> </div></div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt> <a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt> <a name="RegisterableGroup"></a><div id="RegisterableGroup-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="RegisterableGroup-toggle" onclick="return toggle('RegisterableGroup');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.config.Registry.RegisterableGroup-class.html">RegisterableGroup</a><tt class="py-op">(</tt><tt class="py-base-class">RegisterableObject</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="RegisterableGroup-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RegisterableGroup-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-docstring">"""This is a base class for a RegisterableObject that groups many</tt> </tt> <a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> objects together.</tt> </tt> <a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> Methods:</tt> </tt> <a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> add Add an object to the end of the group.</tt> </tt> <a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> add_after Add an object to the group after another object.</tt> </tt> <a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> add_before Add an object to the group before another object.</tt> </tt> <a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="RegisterableGroup.__init__"></a><div id="RegisterableGroup.__init__-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="RegisterableGroup.__init__-toggle" onclick="return toggle('RegisterableGroup.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.RegisterableGroup-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">abbrev</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="RegisterableGroup.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RegisterableGroup.__init__-expanded"><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt id="link-60" class="py-name"><a title="Bio.config.Registry.RegisterableObject" class="py-name" href="#" onclick="return doclink('link-60', 'RegisterableObject', 'link-19');">RegisterableObject</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIWWW.BlastParser.__init__()=Bio.Blast.NCBIWWW.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method Bio.Blast.Record.DatabaseReport.__init__()=Bio.Blast.Record.DatabaseReport-class.html#__init__,Method Bio.Blast.Record.Description.__init__()=Bio.Blast.Record.Description-class.html#__init__,Method Bio.Blast.Record.HSP.__init__()=Bio.Blast.Record.HSP-class.html#__init__,Method Bio.Blast.Record.Header.__init__()=Bio.Blast.Record.Header-class.html#__init__,Method Bio.Blast.Record.MultipleAlignment.__init__()=Bio.Blast.Record.MultipleAlignment-class.html#__init__,Method Bio.Blast.Record.PSIBlast.__init__()=Bio.Blast.Record.PSIBlast-class.html#__init__,Method Bio.Blast.Record.Parameters.__init__()=Bio.Blast.Record.Parameters-class.html#__init__,Method Bio.Blast.Record.Round.__init__()=Bio.Blast.Record.Round-class.html#__init__,Method Bio.CAPS.CAPSMap.__init__()=Bio.CAPS.CAPSMap-class.html#__init__,Method Bio.CAPS.DifferentialCutsite.__init__()=Bio.CAPS.DifferentialCutsite-class.html#__init__,Method Bio.CDD.Iterator.__init__()=Bio.CDD.Iterator-class.html#__init__,Method Bio.CDD.Record.Record.__init__()=Bio.CDD.Record.Record-class.html#__init__,Method Bio.CDD.RecordParser.__init__()=Bio.CDD.RecordParser-class.html#__init__,Method Bio.CDD._RecordConsumer.__init__()=Bio.CDD._RecordConsumer-class.html#__init__,Method Bio.CDD._Scanner.__init__()=Bio.CDD._Scanner-class.html#__init__,Method Bio.Clustalw.ClustalAlignment.__init__()=Bio.Clustalw.ClustalAlignment-class.html#__init__,Method Bio.Clustalw.MultipleAlignCL.__init__()=Bio.Clustalw.MultipleAlignCL-class.html#__init__,Method Bio.Cluster.DataFile.__init__()=Bio.Cluster.DataFile-class.html#__init__,Method Bio.Cluster.Record.__init__()=Bio.Cluster.Record-class.html#__init__,Method Bio.Compass.Iterator.__init__()=Bio.Compass.Iterator-class.html#__init__,Method Bio.Compass.Record.__init__()=Bio.Compass.Record-class.html#__init__,Method Bio.Compass.RecordParser.__init__()=Bio.Compass.RecordParser-class.html#__init__,Method Bio.Compass._Consumer.__init__()=Bio.Compass._Consumer-class.html#__init__,Method Bio.Crystal.Chain.__init__()=Bio.Crystal.Chain-class.html#__init__,Method Bio.Crystal.Crystal.__init__()=Bio.Crystal.Crystal-class.html#__init__,Method Bio.Crystal.CrystalError.__init__()=Bio.Crystal.CrystalError-class.html#__init__,Method Bio.Crystal.Error.__init__()=Bio.Crystal.Error-class.html#__init__,Method Bio.Crystal.Hetero.__init__()=Bio.Crystal.Hetero-class.html#__init__,Method Bio.DBXRef.DBXRef.__init__()=Bio.DBXRef.DBXRef-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousCodonTable.__init__()=Bio.Data.CodonTable.AmbiguousCodonTable-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__init__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__init__,Method Bio.Data.CodonTable.CodonTable.__init__()=Bio.Data.CodonTable.CodonTable-class.html#__init__,Method Bio.Data.CodonTable.NCBICodonTable.__init__()=Bio.Data.CodonTable.NCBICodonTable-class.html#__init__,Method Bio.Decode.DecodeParser.__init__()=Bio.Decode.DecodeParser-class.html#__init__,Method Bio.Decode.DecodeScanner.__init__()=Bio.Decode.DecodeScanner-class.html#__init__,Method Bio.Decode.Float.__init__()=Bio.Decode.Float-class.html#__init__,Method Bio.Decode.Function.__init__()=Bio.Decode.Function-class.html#__init__,Method Bio.Decode.FunctionCall.__init__()=Bio.Decode.FunctionCall-class.html#__init__,Method Bio.Decode.FunctionCallChain.__init__()=Bio.Decode.FunctionCallChain-class.html#__init__,Method Bio.Decode.FunctionName.__init__()=Bio.Decode.FunctionName-class.html#__init__,Method Bio.Decode.Integer.__init__()=Bio.Decode.Integer-class.html#__init__,Method Bio.Decode.String.__init__()=Bio.Decode.String-class.html#__init__,Method Bio.Decode.Token.__init__()=Bio.Decode.Token-class.html#__init__,Method Bio.Decode.ValueToken.__init__()=Bio.Decode.ValueToken-class.html#__init__,Method Bio.DocSQL.Create.__init__()=Bio.DocSQL.Create-class.html#__init__,Method Bio.DocSQL.Insert.__init__()=Bio.DocSQL.Insert-class.html#__init__,Method Bio.DocSQL.IterationCursor.__init__()=Bio.DocSQL.IterationCursor-class.html#__init__,Method Bio.DocSQL.Query.__init__()=Bio.DocSQL.Query-class.html#__init__,Method Bio.DocSQL.QueryAll.__init__()=Bio.DocSQL.QueryAll-class.html#__init__,Method Bio.DocSQL.QueryGeneric.__init__()=Bio.DocSQL.QueryGeneric-class.html#__init__,Method Bio.DocSQL.QueryRow.__init__()=Bio.DocSQL.QueryRow-class.html#__init__,Method Bio.DocSQL.QuerySingle.__init__()=Bio.DocSQL.QuerySingle-class.html#__init__,Method Bio.ECell.ECellError.__init__()=Bio.ECell.ECellError-class.html#__init__,Method Bio.ECell.Error.__init__()=Bio.ECell.Error-class.html#__init__,Method Bio.ECell.Iterator.__init__()=Bio.ECell.Iterator-class.html#__init__,Method Bio.ECell.Record.Record.__init__()=Bio.ECell.Record.Record-class.html#__init__,Method Bio.ECell.RecordParser.__init__()=Bio.ECell.RecordParser-class.html#__init__,Method Bio.ECell._RecordConsumer.__init__()=Bio.ECell._RecordConsumer-class.html#__init__,Method Bio.ECell._Scanner.__init__()=Bio.ECell._Scanner-class.html#__init__,Method Bio.EUtils.Config.DatabaseInfo.__init__()=Bio.EUtils.Config.DatabaseInfo-class.html#__init__,Method Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__()=Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsClient.__init__()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsLookup.__init__()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#__init__,Method Bio.EUtils.Datatypes.BinaryOp.__init__()=Bio.EUtils.Datatypes.BinaryOp-class.html#__init__,Method Bio.EUtils.Datatypes.CheckLinkSet.__init__()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.DBIds.__init__()=Bio.EUtils.Datatypes.DBIds-class.html#__init__,Method Bio.EUtils.Datatypes.Date.__init__()=Bio.EUtils.Datatypes.Date-class.html#__init__,Method Bio.EUtils.Datatypes.DateRange.__init__()=Bio.EUtils.Datatypes.DateRange-class.html#__init__,Method 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Martel.Iterator.RecordEventStream.__init__ Martel.Iterator.StoreEvents.__init__ Martel.LAX.ElementInfo.__init__ Martel.LAX.LAX.__init__ Martel.Parser.HeaderFooterParser.__init__ Martel.Parser.Parser.__init__ Martel.Parser.ParserIncompleteException.__init__ Martel.Parser.ParserPositionException.__init__ Martel.Parser.RecordParser.__init__ Martel.RecordReader.CountLines.__init__ Martel.RecordReader.EndsWith.__init__ Martel.RecordReader.Everything.__init__ Martel.RecordReader.Nothing.__init__ Martel.RecordReader.RecordReader.__init__ Martel.RecordReader.StartsWith.__init__ Martel.RecordReader.Until.__init__ Martel.convert_re.GroupNames.__init__ Martel.msre_parse.Pattern.__init__ Martel.msre_parse.SubPattern.__init__ Martel.msre_parse.Tokenizer.__init__ Martel.test.support.CheckGood.__init__ Martel.test.support.Dump.__init__ Martel.test.support.Storage.__init__ Martel.test.test_Parser.CountErrors.__init__ Martel.test.test_Parser.CountRecords.__init__ Martel.test.test_delimiter.CatchFields.__init__ Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-61', '__init__', 'link-61');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-62" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-62', 'name', 'link-1');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">abbrev</tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">)</tt> </tt> <a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">objs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> </div><a name="RegisterableGroup.add"></a><div id="RegisterableGroup.add-def"><a name="L152"></a><tt class="py-lineno">152</tt> <a class="py-toggle" href="#" id="RegisterableGroup.add-toggle" onclick="return toggle('RegisterableGroup.add');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.RegisterableGroup-class.html#add">add</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="RegisterableGroup.add-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RegisterableGroup.add-expanded"><a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-63" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index Bio.EUtils.POM.ElementNode.index Bio.SCOP.Raf.SeqMap.index Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-63', 'index', 'link-63');">index</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt> <a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt id="link-64" class="py-name"><a title="Bio.Crystal.Chain.index Bio.EUtils.POM.ElementNode.index Bio.SCOP.Raf.SeqMap.index Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-64', 'index', 'link-63');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">objs</tt><tt class="py-op">)</tt> </tt> <a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">objs</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name" targets="Method Bio.Crystal.Chain.insert()=Bio.Crystal.Chain-class.html#insert,Method Bio.EUtils.POM.Comment.insert()=Bio.EUtils.POM.Comment-class.html#insert,Method Bio.EUtils.POM.ElementNode.insert()=Bio.EUtils.POM.ElementNode-class.html#insert,Method Bio.EUtils.POM.IndentedText.insert()=Bio.EUtils.POM.IndentedText-class.html#insert,Method Bio.Seq.MutableSeq.insert()=Bio.Seq.MutableSeq-class.html#insert,Method Martel.msre_parse.SubPattern.insert()=Martel.msre_parse.SubPattern-class.html#insert"><a title="Bio.Crystal.Chain.insert Bio.EUtils.POM.Comment.insert Bio.EUtils.POM.ElementNode.insert Bio.EUtils.POM.IndentedText.insert Bio.Seq.MutableSeq.insert Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-65', 'insert', 'link-65');">insert</a></tt><tt class="py-op">(</tt><tt id="link-66" class="py-name"><a title="Bio.Crystal.Chain.index Bio.EUtils.POM.ElementNode.index Bio.SCOP.Raf.SeqMap.index Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-66', 'index', 'link-63');">index</a></tt><tt class="py-op">,</tt> <tt id="link-67" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-67', 'obj', 'link-15');">obj</a></tt><tt class="py-op">)</tt> </tt> </div><a name="RegisterableGroup.add_after"></a><div id="RegisterableGroup.add_after-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="RegisterableGroup.add_after-toggle" onclick="return toggle('RegisterableGroup.add_after');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.RegisterableGroup-class.html#add_after">add_after</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">,</tt> <tt class="py-param">after</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="RegisterableGroup.add_after-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RegisterableGroup.add_after-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-68" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-68', 'i', 'link-68');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">objs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">objs</tt><tt class="py-op">[</tt><tt id="link-69" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-69', 'i', 'link-68');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">after</tt><tt class="py-op">:</tt> </tt> <a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt> <a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I couldn't find the insertion point"</tt> </tt> <a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add Bio.EUtils.POM.ElementNode.add Bio.GFF.easy.Location.add Bio.Graphics.BasicChromosome._ChromosomeComponent.add Bio.LogisticRegression.add Bio.MarkovModel.add Bio.MaxEntropy.add Bio.NaiveBayes.add Bio.Nexus.Nexus.StepMatrix.add Bio.Nexus.Nodes.Chain.add Bio.PDB.Entity.Entity.add Bio.PDB.Residue.DisorderedResidue.add Bio.PDB.Residue.Residue.add Bio.Pathway.Rep.HashSet.HashSet.add Bio.Restriction.Restriction.RestrictionBatch.add Bio.Statistics.lowess.add Bio.config.FormatRegistry.FormatGroup.add Bio.config.Registry.RegisterableGroup.add Bio.distance.add Bio.kNN.add Martel.Dispatch.MulticallEnd.add Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-70', 'add', 'link-70');">add</a></tt><tt class="py-op">(</tt><tt id="link-71" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-71', 'obj', 'link-15');">obj</a></tt><tt class="py-op">,</tt> <tt id="link-72" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-72', 'i', 'link-68');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt> </div><a name="RegisterableGroup.add_before"></a><div id="RegisterableGroup.add_before-def"><a name="L163"></a><tt class="py-lineno">163</tt> <a class="py-toggle" href="#" id="RegisterableGroup.add_before-toggle" onclick="return toggle('RegisterableGroup.add_before');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.Registry.RegisterableGroup-class.html#add_before">add_before</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">,</tt> <tt class="py-param">before</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="RegisterableGroup.add_before-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RegisterableGroup.add_before-expanded"><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-73" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-73', 'i', 'link-68');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">objs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">objs</tt><tt class="py-op">[</tt><tt id="link-74" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-74', 'i', 'link-68');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">before</tt><tt class="py-op">:</tt> </tt> <a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt> <a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I couldn't find the insertion point"</tt> </tt> <a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.Affy.CelFile.add Bio.EUtils.POM.ElementNode.add Bio.GFF.easy.Location.add Bio.Graphics.BasicChromosome._ChromosomeComponent.add Bio.LogisticRegression.add Bio.MarkovModel.add Bio.MaxEntropy.add Bio.NaiveBayes.add Bio.Nexus.Nexus.StepMatrix.add Bio.Nexus.Nodes.Chain.add Bio.PDB.Entity.Entity.add Bio.PDB.Residue.DisorderedResidue.add Bio.PDB.Residue.Residue.add Bio.Pathway.Rep.HashSet.HashSet.add Bio.Restriction.Restriction.RestrictionBatch.add Bio.Statistics.lowess.add Bio.config.FormatRegistry.FormatGroup.add Bio.config.Registry.RegisterableGroup.add Bio.distance.add Bio.kNN.add Martel.Dispatch.MulticallEnd.add Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-75', 'add', 'link-70');">add</a></tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-76', 'obj', 'link-15');">obj</a></tt><tt class="py-op">,</tt> <tt id="link-77" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-77', 'i', 'link-68');">i</a></tt><tt class="py-op">)</tt> </tt> </div></div><a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> </tt><script type="text/javascript"> <!-- expandto(location.href); // --> </script> </pre> <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 09:28:10 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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