Sophie

Sophie

distrib > Mandriva > 2008.1 > x86_64 > by-pkgid > 763d6289e1351f2d34257ce697a3ccb7 > files > 1262

biopython-doc-1.47-2mdv2008.1.x86_64.rpm

<?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.Restriction.PrintFormat</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>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</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&nbsp;Bio</a> ::
        <a href="Bio.Restriction-module.html">Package&nbsp;Restriction</a> ::
        Module&nbsp;PrintFormat
      </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&nbsp;private</a>]</span></td></tr>
        <tr><td align="right"><span class="options"
            >[<a href="frames.html" target="_top">frames</a
            >]&nbsp;|&nbsp;<a href="Bio.Restriction.PrintFormat-pysrc.html"
            target="_top">no&nbsp;frames</a>]</span></td></tr>
      </table>
    </td>
  </tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.Restriction.PrintFormat-module.html">Module Bio.Restriction.PrintFormat</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</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">#</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">#      Restriction Analysis Libraries.</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">#      Copyright (C) 2004. Frederic Sohm.</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</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="L7"></a><tt class="py-lineno">  7</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="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">itertools</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Restriction=Bio.Restriction-module.html,Module Bio.Restriction.Restriction=Bio.Restriction.Restriction-module.html"><a title="Bio.Restriction
Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-1', 'Restriction', 'link-1');">Restriction</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Bio.Restriction.RanaConfig=Bio.Restriction.RanaConfig-module.html"><a title="Bio.Restriction.RanaConfig" class="py-name" href="#" onclick="return doclink('link-2', 'RanaConfig', 'link-2');">RanaConfig</a></tt> <tt class="py-keyword">as</tt> <tt class="py-name">RanaConf</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.Restriction
Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-4', 'Restriction', 'link-1');">Restriction</a></tt><tt class="py-op">.</tt><tt class="py-name">DNAUtils</tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Method Bio.Seq.MutableSeq.complement()=Bio.Seq.MutableSeq-class.html#complement,Method Bio.Seq.Seq.complement()=Bio.Seq.Seq-class.html#complement"><a title="Bio.Seq.MutableSeq.complement
Bio.Seq.Seq.complement" class="py-name" href="#" onclick="return doclink('link-5', 'complement', 'link-5');">complement</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-string">Usage :</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-string">    PrintFormat allow to print the results from restriction analysis in 3</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-string">    different format.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-string">    List, column or map.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-string">    the easiest way to use it is :</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-string">    </tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-string">    &gt;&gt;&gt; from Rana.PrintFormat import PrintFormat</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-string">    &gt;&gt;&gt; from Rana.Restriction import AllEnzymes</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-string">    &gt;&gt;&gt; from Rana.fts import fts</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-string">    &gt;&gt;&gt; seq = fts(pBR322)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-string">    &gt;&gt;&gt; dct = AllEnzymes.search(seq)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-string">    &gt;&gt;&gt; new = PrintFormat()</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-string">    &gt;&gt;&gt; new.print_that(dct, '\n my pBR322 analysis\n\n','\n no site :\n\n')</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-string">     my pBR322 analysis</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-string">     </tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-string">    AasI       :  2169, 2582.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-string">    AatII      :  4289.</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-string">    ...</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-string">            More enzymes.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-string">    ...</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-string">    ZraI       :  4287.</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-string">    ZrmI       :  3847.</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-string">    </tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-string">     no site :</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-string">     </tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-string">    AarI      AatI      Acc65I    AcsI      AcvI      AdeI      AflII     AgeI    </tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-string">    ...</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-string">            More enzymes.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-string">    ...</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-string">    Vha464I   XapI      XbaI      XcmI      XhoI      XmaCI     XmaI      XmaJI     </tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-string">    Zsp2I </tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-string">    &gt;&gt;&gt;</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt class="py-string">    </tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-string">    Some of the methods of PrintFormat are meant to be overriden by derived</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-string">    class.</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"> </tt>
<a name="PrintFormat"></a><div id="PrintFormat-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="PrintFormat-toggle" onclick="return toggle('PrintFormat');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html">PrintFormat</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrintFormat-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-docstring">"""PrintFormat allow the printing of results of restriction analysis."""</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    <tt id="link-6" class="py-name" targets="Variable Bio.Restriction.PrintFormat.PrintFormat.ConsoleWidth=Bio.Restriction.PrintFormat.PrintFormat-class.html#ConsoleWidth,Variable Bio.Restriction.RanaConfig.ConsoleWidth=Bio.Restriction.RanaConfig-module.html#ConsoleWidth"><a title="Bio.Restriction.PrintFormat.PrintFormat.ConsoleWidth
Bio.Restriction.RanaConfig.ConsoleWidth" class="py-name" href="#" onclick="return doclink('link-6', 'ConsoleWidth', 'link-6');">ConsoleWidth</a></tt> <tt class="py-op">=</tt> <tt class="py-name">RanaConf</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.ConsoleWidth
Bio.Restriction.RanaConfig.ConsoleWidth" class="py-name" href="#" onclick="return doclink('link-7', 'ConsoleWidth', 'link-6');">ConsoleWidth</a></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt id="link-8" class="py-name" targets="Variable Bio.Restriction.PrintFormat.PrintFormat.NameWidth=Bio.Restriction.PrintFormat.PrintFormat-class.html#NameWidth,Variable Bio.Restriction.RanaConfig.NameWidth=Bio.Restriction.RanaConfig-module.html#NameWidth"><a title="Bio.Restriction.PrintFormat.PrintFormat.NameWidth
Bio.Restriction.RanaConfig.NameWidth" class="py-name" href="#" onclick="return doclink('link-8', 'NameWidth', 'link-8');">NameWidth</a></tt>    <tt class="py-op">=</tt> <tt class="py-name">RanaConf</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.NameWidth
Bio.Restriction.RanaConfig.NameWidth" class="py-name" href="#" onclick="return doclink('link-9', 'NameWidth', 'link-8');">NameWidth</a></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt id="link-10" class="py-name" targets="Variable Bio.Restriction.PrintFormat.PrintFormat.MaxSize=Bio.Restriction.PrintFormat.PrintFormat-class.html#MaxSize,Variable Bio.Restriction.RanaConfig.MaxSize=Bio.Restriction.RanaConfig-module.html#MaxSize"><a title="Bio.Restriction.PrintFormat.PrintFormat.MaxSize
Bio.Restriction.RanaConfig.MaxSize" class="py-name" href="#" onclick="return doclink('link-10', 'MaxSize', 'link-10');">MaxSize</a></tt>      <tt class="py-op">=</tt> <tt class="py-name">RanaConf</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.MaxSize
Bio.Restriction.RanaConfig.MaxSize" class="py-name" href="#" onclick="return doclink('link-11', 'MaxSize', 'link-10');">MaxSize</a></tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">    <tt id="link-12" class="py-name" targets="Variable Bio.Restriction.PrintFormat.PrintFormat.Cmodulo=Bio.Restriction.PrintFormat.PrintFormat-class.html#Cmodulo"><a title="Bio.Restriction.PrintFormat.PrintFormat.Cmodulo" class="py-name" href="#" onclick="return doclink('link-12', 'Cmodulo', 'link-12');">Cmodulo</a></tt>      <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.ConsoleWidth
Bio.Restriction.RanaConfig.ConsoleWidth" class="py-name" href="#" onclick="return doclink('link-13', 'ConsoleWidth', 'link-6');">ConsoleWidth</a></tt><tt class="py-op">%</tt><tt id="link-14" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.NameWidth
Bio.Restriction.RanaConfig.NameWidth" class="py-name" href="#" onclick="return doclink('link-14', 'NameWidth', 'link-8');">NameWidth</a></tt>        </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt id="link-15" class="py-name" targets="Variable Bio.Restriction.PrintFormat.PrintFormat.PrefWidth=Bio.Restriction.PrintFormat.PrintFormat-class.html#PrefWidth"><a title="Bio.Restriction.PrintFormat.PrintFormat.PrefWidth" class="py-name" href="#" onclick="return doclink('link-15', 'PrefWidth', 'link-15');">PrefWidth</a></tt>    <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.ConsoleWidth
Bio.Restriction.RanaConfig.ConsoleWidth" class="py-name" href="#" onclick="return doclink('link-16', 'ConsoleWidth', 'link-6');">ConsoleWidth</a></tt> <tt class="py-op">-</tt> <tt id="link-17" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.Cmodulo" class="py-name" href="#" onclick="return doclink('link-17', 'Cmodulo', 'link-12');">Cmodulo</a></tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt id="link-18" class="py-name" targets="Variable Bio.Restriction.PrintFormat.PrintFormat.Indent=Bio.Restriction.PrintFormat.PrintFormat-class.html#Indent,Variable Bio.Restriction.RanaConfig.Indent=Bio.Restriction.RanaConfig-module.html#Indent"><a title="Bio.Restriction.PrintFormat.PrintFormat.Indent
Bio.Restriction.RanaConfig.Indent" class="py-name" href="#" onclick="return doclink('link-18', 'Indent', 'link-18');">Indent</a></tt>       <tt class="py-op">=</tt> <tt class="py-name">RanaConf</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.Indent
Bio.Restriction.RanaConfig.Indent" class="py-name" href="#" onclick="return doclink('link-19', 'Indent', 'link-18');">Indent</a></tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">    <tt id="link-20" class="py-name" targets="Variable Bio.Restriction.PrintFormat.PrintFormat.linesize=Bio.Restriction.PrintFormat.PrintFormat-class.html#linesize"><a title="Bio.Restriction.PrintFormat.PrintFormat.linesize" class="py-name" href="#" onclick="return doclink('link-20', 'linesize', 'link-20');">linesize</a></tt>     <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.PrefWidth" class="py-name" href="#" onclick="return doclink('link-21', 'PrefWidth', 'link-15');">PrefWidth</a></tt> <tt class="py-op">-</tt> <tt id="link-22" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.NameWidth
Bio.Restriction.RanaConfig.NameWidth" class="py-name" href="#" onclick="return doclink('link-22', 'NameWidth', 'link-8');">NameWidth</a></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"> </tt>
<a name="PrintFormat.__init__"></a><div id="PrintFormat.__init__-def"><a name="L69"></a><tt class="py-lineno"> 69</tt> <a class="py-toggle" href="#" id="PrintFormat.__init__-toggle" onclick="return toggle('PrintFormat.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#__init__">__init__</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="PrintFormat.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat.__init__-expanded"><a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">        <tt class="py-docstring">"""PrintFormat() -&gt; new PrintFormat Instance"""</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"> </tt>
<a name="PrintFormat.print_as"></a><div id="PrintFormat.print_as-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="PrintFormat.print_as-toggle" onclick="return toggle('PrintFormat.print_as');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#print_as">print_as</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">what</tt><tt class="py-op">=</tt><tt class="py-string">'list'</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat.print_as-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat.print_as-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF.print_as([what='list']) -&gt; print the results as specified.</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">        Valid format are :</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-docstring">            'list'      -&gt; alphabetical order</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-docstring">            'number'    -&gt; number of sites in the sequence</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-docstring">            'map'       -&gt; a map representation of the sequence with the sites.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-docstring">        If you want more flexibility over-ride the virtual method make_format.</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-docstring">        """</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">what</tt> <tt class="py-op">==</tt> <tt class="py-string">'map'</tt> <tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Restriction.PrintFormat.PrintFormat.make_format()=Bio.Restriction.PrintFormat.PrintFormat-class.html#make_format"><a title="Bio.Restriction.PrintFormat.PrintFormat.make_format" class="py-name" href="#" onclick="return doclink('link-23', 'make_format', 'link-23');">make_format</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Restriction.PrintFormat.PrintFormat._make_map()=Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_map"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_map" class="py-name" href="#" onclick="return doclink('link-24', '_make_map', 'link-24');">_make_map</a></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">what</tt> <tt class="py-op">==</tt> <tt class="py-string">'number'</tt> <tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.make_format" class="py-name" href="#" onclick="return doclink('link-25', 'make_format', 'link-23');">make_format</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Restriction.PrintFormat.PrintFormat._make_number()=Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_number"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_number" class="py-name" href="#" onclick="return doclink('link-26', '_make_number', 'link-26');">_make_number</a></tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </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 id="link-27" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.make_format" class="py-name" href="#" onclick="return doclink('link-27', 'make_format', 'link-23');">make_format</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.Restriction.PrintFormat.PrintFormat._make_list()=Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_list"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_list" class="py-name" href="#" onclick="return doclink('link-28', '_make_list', 'link-28');">_make_list</a></tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">             </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> </tt>
</div><a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">             </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"> </tt>
<a name="PrintFormat.print_that"></a><div id="PrintFormat.print_that-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="PrintFormat.print_that-toggle" onclick="return toggle('PrintFormat.print_that');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#print_that">print_that</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dct</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">,</tt>  <tt class="py-param">s1</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat.print_that-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat.print_that-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF.print_that(dct, [title[, s1]]) -&gt; Print dct nicely formatted.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"><tt class="py-docstring">        dct is a dictionary as returned by a RestrictionBatch.search()</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-docstring">        title is the title of the map.</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring">        It must be a formated string, i.e. you must include the line break.</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-docstring">        s1 is the title separating the list of enzymes that have sites from</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"><tt class="py-docstring">        those without sites.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"><tt class="py-docstring">        s1 must be a formatted string as well.</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"><tt class="py-docstring">        The format of print_that is a list."""</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">dct</tt> <tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">            <tt class="py-name">dct</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">results</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-name">ls</tt><tt class="py-op">,</tt> <tt class="py-name">nc</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="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-29" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-29', 'v', 'link-29');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">dct</tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-30" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-30', 'v', 'link-29');">v</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">                <tt class="py-name">ls</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-31', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt><tt id="link-32" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-32', 'v', 'link-29');">v</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">                <tt class="py-name">nc</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-33', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.make_format" class="py-name" href="#" onclick="return doclink('link-34', 'make_format', 'link-23');">make_format</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-35', 'title', 'link-35');">title</a></tt><tt class="py-op">,</tt> <tt class="py-name">nc</tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name" targets="Variable Martel.test.test_swissprot38.s1=Martel.test.test_swissprot38-module.html#s1"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-36', 's1', 'link-36');">s1</a></tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        </tt>
<a name="PrintFormat.make_format"></a><div id="PrintFormat.make_format-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="PrintFormat.make_format-toggle" onclick="return toggle('PrintFormat.make_format');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#make_format">make_format</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cut</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">,</tt> <tt class="py-param">nc</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">s1</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat.make_format-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat.make_format-expanded"><a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF.make_format(cut, nc, title, s) -&gt; string</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"><tt class="py-docstring">        Virtual method.</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"><tt class="py-docstring">        Here to be pointed to one of the _make_* methods.</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"><tt class="py-docstring">        You can as well create a new method and point make_format to it."""</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_list" class="py-name" href="#" onclick="return doclink('link-37', '_make_list', 'link-28');">_make_list</a></tt><tt class="py-op">(</tt><tt class="py-name">cut</tt><tt class="py-op">,</tt><tt id="link-38" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-38', 'title', 'link-35');">title</a></tt><tt class="py-op">,</tt> <tt class="py-name">nc</tt><tt class="py-op">,</tt><tt id="link-39" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-39', 's1', 'link-36');">s1</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-comment">###### _make_* methods to be used with the virtual method make_format</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="PrintFormat._make_list"></a><div id="PrintFormat._make_list-def"><a name="L127"></a><tt class="py-lineno">127</tt> <a class="py-toggle" href="#" id="PrintFormat._make_list-toggle" onclick="return toggle('PrintFormat._make_list');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_list">_make_list</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ls</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">,</tt> <tt class="py-param">nc</tt><tt class="py-op">,</tt><tt class="py-param">s1</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat._make_list-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat._make_list-expanded"><a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF._make_number(ls,title, nc,s1) -&gt; string.</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line"><tt class="py-docstring">        return a string of form :</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"><tt class="py-docstring">        title.</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme1     :   position1, position2.</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme2     :   position1, position2, position3.</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-docstring">        ls is a list of cutting enzymes.</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"><tt class="py-docstring">        title is the title.</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"><tt class="py-docstring">        nc is a list of non cutting enzymes.</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"><tt class="py-docstring">        s1 is the sentence before the non cutting enzymes."""</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.Restriction.PrintFormat.PrintFormat._make_list_only()=Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_list_only"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_list_only" class="py-name" href="#" onclick="return doclink('link-40', '_make_list_only', 'link-40');">_make_list_only</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">,</tt> <tt id="link-41" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-41', 'title', 'link-35');">title</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.Restriction.PrintFormat.PrintFormat._make_nocut_only()=Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_nocut_only"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_nocut_only" class="py-name" href="#" onclick="return doclink('link-42', '_make_nocut_only', 'link-42');">_make_nocut_only</a></tt><tt class="py-op">(</tt><tt class="py-name">nc</tt><tt class="py-op">,</tt> <tt id="link-43" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-43', 's1', 'link-36');">s1</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"> </tt>
<a name="PrintFormat._make_map"></a><div id="PrintFormat._make_map-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="PrintFormat._make_map-toggle" onclick="return toggle('PrintFormat._make_map');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_map">_make_map</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ls</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">,</tt> <tt class="py-param">nc</tt><tt class="py-op">,</tt><tt class="py-param">s1</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat._make_map-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat._make_map-expanded"><a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF._make_number(ls,title, nc,s1) -&gt; string.</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"><tt class="py-docstring">        return a string of form :</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">        title.</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"><tt class="py-docstring">            enzyme1, position</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line"><tt class="py-docstring">            |</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line"><tt class="py-docstring">        AAAAAAAAAAAAAAAAAAAAA...</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line"><tt class="py-docstring">        |||||||||||||||||||||</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line"><tt class="py-docstring">        TTTTTTTTTTTTTTTTTTTTT...</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line"><tt class="py-docstring">        ls is a list of cutting enzymes.</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line"><tt class="py-docstring">        title is the title.</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line"><tt class="py-docstring">        nc is a list of non cutting enzymes.</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line"><tt class="py-docstring">        s1 is the sentence before the non cutting enzymes."""</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.Restriction.PrintFormat.PrintFormat._make_map_only()=Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_map_only"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_map_only" class="py-name" href="#" onclick="return doclink('link-44', '_make_map_only', 'link-44');">_make_map_only</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">,</tt> <tt id="link-45" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-45', 'title', 'link-35');">title</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_nocut_only" class="py-name" href="#" onclick="return doclink('link-46', '_make_nocut_only', 'link-42');">_make_nocut_only</a></tt><tt class="py-op">(</tt><tt class="py-name">nc</tt><tt class="py-op">,</tt> <tt id="link-47" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-47', 's1', 'link-36');">s1</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line"> </tt>
<a name="PrintFormat._make_number"></a><div id="PrintFormat._make_number-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="PrintFormat._make_number-toggle" onclick="return toggle('PrintFormat._make_number');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_number">_make_number</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ls</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">,</tt> <tt class="py-param">nc</tt><tt class="py-op">,</tt><tt class="py-param">s1</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat._make_number-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat._make_number-expanded"><a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF._make_number(ls,title, nc,s1) -&gt; string.</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line"><tt class="py-docstring">        title.</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme which cut 1 time :</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme1     :   position1.</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme which cut 2 times :</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme2     :   position1, position2.</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-docstring">        ...</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-docstring">        ls is a list of cutting enzymes.</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"><tt class="py-docstring">        title is the title.</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"><tt class="py-docstring">        nc is a list of non cutting enzymes.</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line"><tt class="py-docstring">        s1 is the sentence before the non cutting enzymes."""</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name" targets="Method Bio.Restriction.PrintFormat.PrintFormat._make_number_only()=Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_number_only"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_number_only" class="py-name" href="#" onclick="return doclink('link-48', '_make_number_only', 'link-48');">_make_number_only</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">,</tt> <tt id="link-49" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-49', 'title', 'link-35');">title</a></tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_nocut_only" class="py-name" href="#" onclick="return doclink('link-50', '_make_nocut_only', 'link-42');">_make_nocut_only</a></tt><tt class="py-op">(</tt><tt class="py-name">nc</tt><tt class="py-op">,</tt><tt id="link-51" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-51', 's1', 'link-36');">s1</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">     </tt>
<a name="PrintFormat._make_nocut"></a><div id="PrintFormat._make_nocut-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="PrintFormat._make_nocut-toggle" onclick="return toggle('PrintFormat._make_nocut');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_nocut">_make_nocut</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ls</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">,</tt> <tt class="py-param">nc</tt><tt class="py-op">,</tt><tt class="py-param">s1</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat._make_nocut-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat._make_nocut-expanded"><a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF._make_nocut(ls,title, nc,s1) -&gt; string.</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"><tt class="py-docstring">        return a formatted string of the non cutting enzymes.</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line"><tt class="py-docstring">        ls is a list of cutting enzymes -&gt; will not be used.</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line"><tt class="py-docstring">        Here for compatibility with make_format.</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line"><tt class="py-docstring">        title is the title.</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"><tt class="py-docstring">        nc is a list of non cutting enzymes.</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"><tt class="py-docstring">        s1 is the sentence before the non cutting enzymes."""</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-52" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-52', 'title', 'link-35');">title</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat._make_nocut_only" class="py-name" href="#" onclick="return doclink('link-53', '_make_nocut_only', 'link-42');">_make_nocut_only</a></tt><tt class="py-op">(</tt><tt class="py-name">nc</tt><tt class="py-op">,</tt> <tt id="link-54" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-54', 's1', 'link-36');">s1</a></tt><tt class="py-op">)</tt>  </tt>
</div><a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line"> </tt>
<a name="PrintFormat._make_nocut_only"></a><div id="PrintFormat._make_nocut_only-def"><a name="L195"></a><tt class="py-lineno">195</tt> <a class="py-toggle" href="#" id="PrintFormat._make_nocut_only-toggle" onclick="return toggle('PrintFormat._make_nocut_only');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_nocut_only">_make_nocut_only</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">nc</tt><tt class="py-op">,</tt> <tt class="py-param">s1</tt><tt class="py-op">,</tt> <tt class="py-param">ls</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat._make_nocut_only-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat._make_nocut_only-expanded"><a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF._make_nocut_only(nc, s1) -&gt; string.</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line"><tt class="py-docstring">        return a formatted string of the non cutting enzymes.</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"><tt class="py-docstring">        nc is a list of non cutting enzymes.</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line"><tt class="py-docstring">        s1 is the sentence before the non cutting enzymes.</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">nc</tt> <tt class="py-op">:</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-55" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-55', 's1', 'link-36');">s1</a></tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-name">nc</tt><tt class="py-op">.</tt><tt id="link-56" 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-56', 'sort', 'link-56');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">        <tt class="py-name">st</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">        <tt class="py-name">stringsite</tt> <tt class="py-op">=</tt> <tt id="link-57" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-57', 's1', 'link-36');">s1</a></tt> <tt class="py-keyword">or</tt> <tt class="py-string">'\n   Enzymes which do not cut the sequence.\n\n'</tt>     </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">        <tt class="py-name">Join</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-58" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-58', 'key', 'link-58');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">nc</tt> <tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">            <tt class="py-name">st</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">st</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">.</tt><tt class="py-name">ljust</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-59" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-59', 'key', 'link-58');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.NameWidth
Bio.Restriction.RanaConfig.NameWidth" class="py-name" href="#" onclick="return doclink('link-60', 'NameWidth', 'link-8');">NameWidth</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">st</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.linesize" class="py-name" href="#" onclick="return doclink('link-61', 'linesize', 'link-20');">linesize</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">                <tt class="py-name">stringsite</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">stringsite</tt><tt class="py-op">,</tt> <tt class="py-name">st</tt><tt class="py-op">,</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">                <tt class="py-name">st</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">        <tt class="py-name">stringsite</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">stringsite</tt><tt class="py-op">,</tt> <tt class="py-name">st</tt><tt class="py-op">,</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">stringsite</tt> </tt>
</div><a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">     </tt>
<a name="PrintFormat._make_list_only"></a><div id="PrintFormat._make_list_only-def"><a name="L217"></a><tt class="py-lineno">217</tt> <a class="py-toggle" href="#" id="PrintFormat._make_list_only-toggle" onclick="return toggle('PrintFormat._make_list_only');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_list_only">_make_list_only</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ls</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">,</tt> <tt class="py-param">nc</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">s1</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat._make_list_only-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat._make_list_only-expanded"><a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF._make_list_only(ls, title) -&gt; string.</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line"><tt class="py-docstring">        return a string of form :</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"><tt class="py-docstring">        title.</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme1     :   position1, position2.</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme2     :   position1, position2, position3.</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"><tt class="py-docstring">        ...</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"><tt class="py-docstring">        ls is a list of results.</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"><tt class="py-docstring">        title is a string.</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line"><tt class="py-docstring">        Non cutting enzymes are not included."""</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">ls</tt> <tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-62" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-62', 'title', 'link-35');">title</a></tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name" targets="Method Bio.Restriction.PrintFormat.PrintFormat.__next_section()=Bio.Restriction.PrintFormat.PrintFormat-class.html#__next_section"><a title="Bio.Restriction.PrintFormat.PrintFormat.__next_section" class="py-name" href="#" onclick="return doclink('link-63', '__next_section', 'link-63');">__next_section</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">,</tt> <tt id="link-64" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-64', 'title', 'link-35');">title</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line"> </tt>
<a name="PrintFormat._make_number_only"></a><div id="PrintFormat._make_number_only-def"><a name="L235"></a><tt class="py-lineno">235</tt> <a class="py-toggle" href="#" id="PrintFormat._make_number_only-toggle" onclick="return toggle('PrintFormat._make_number_only');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_number_only">_make_number_only</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ls</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">,</tt> <tt class="py-param">nc</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">s1</tt> <tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat._make_number_only-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat._make_number_only-expanded"><a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF._make_number_only(ls, title) -&gt; string.</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line"><tt class="py-docstring">        return a string of form :</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line"><tt class="py-docstring">        title.</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme which cut 1 time :</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme1     :   position1.</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme which cut 2 times :</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme2     :   position1, position2.</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line"><tt class="py-docstring">        ...</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line"><tt class="py-docstring">                </tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line"><tt class="py-docstring">        ls is a list of results.</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line"><tt class="py-docstring">        title is a string.</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line"><tt class="py-docstring">        Non cutting enzymes are not included."""</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">ls</tt> <tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-65" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-65', 'title', 'link-35');">title</a></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">        <tt class="py-name">ls</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><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-66', 'sort', 'link-56');">sort</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-67" 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-67', 'x', 'link-67');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt> <tt class="py-op">:</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-68" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-68', 'x', 'link-67');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">        <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">        <tt class="py-name">cur_len</tt>  <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">        <tt class="py-name">new_sect</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-69" 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-69', 'name', 'link-69');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">sites</tt> <tt class="py-keyword">in</tt> <tt class="py-name">iterator</tt> <tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">            <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sites</tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">l</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">cur_len</tt> <tt class="py-op">:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">                <tt id="link-70" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-70', 'title', 'link-35');">title</a></tt> <tt class="py-op">+=</tt> <tt class="py-string">"\n\nenzymes which cut %i times :\n\n"</tt><tt class="py-op">%</tt><tt class="py-name">cur_len</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">                <tt id="link-71" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-71', 'title', 'link-35');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.__next_section" class="py-name" href="#" onclick="return doclink('link-72', '__next_section', 'link-63');">__next_section</a></tt><tt class="py-op">(</tt><tt class="py-name">new_sect</tt><tt class="py-op">,</tt> <tt id="link-73" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-73', 'title', 'link-35');">title</a></tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">                <tt class="py-name">new_sect</tt><tt class="py-op">,</tt> <tt class="py-name">cur_len</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-74', 'name', 'link-69');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">sites</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">l</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">            <tt class="py-name">new_sect</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-75', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-76', 'name', 'link-69');">name</a></tt><tt class="py-op">,</tt><tt class="py-name">sites</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">        <tt id="link-77" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-77', 'title', 'link-35');">title</a></tt> <tt class="py-op">+=</tt> <tt class="py-string">"\n\nenzymes which cut %i times :\n\n"</tt><tt class="py-op">%</tt><tt class="py-name">cur_len</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.__next_section" class="py-name" href="#" onclick="return doclink('link-78', '__next_section', 'link-63');">__next_section</a></tt><tt class="py-op">(</tt><tt class="py-name">new_sect</tt><tt class="py-op">,</tt> <tt id="link-79" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-79', 'title', 'link-35');">title</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">             </tt>
<a name="PrintFormat._make_map_only"></a><div id="PrintFormat._make_map_only-def"><a name="L272"></a><tt class="py-lineno">272</tt> <a class="py-toggle" href="#" id="PrintFormat._make_map_only-toggle" onclick="return toggle('PrintFormat._make_map_only');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_map_only">_make_map_only</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ls</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">,</tt> <tt class="py-param">nc</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  <tt class="py-param">s1</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat._make_map_only-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat._make_map_only-expanded"><a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">        <tt class="py-docstring">"""PF._make_map_only(ls, title) -&gt; string.</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line"><tt class="py-docstring">        return a string of form :</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line"><tt class="py-docstring">        title.</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line"><tt class="py-docstring">            enzyme1, position</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line"><tt class="py-docstring">            |</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line"><tt class="py-docstring">        AAAAAAAAAAAAAAAAAAAAA...</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line"><tt class="py-docstring">        |||||||||||||||||||||</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line"><tt class="py-docstring">        TTTTTTTTTTTTTTTTTTTTT...</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line"><tt class="py-docstring">                </tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line"><tt class="py-docstring">        ls is a list of results.</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line"><tt class="py-docstring">        title is a string.</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line"><tt class="py-docstring">        Non cutting enzymes are not included.</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">ls</tt> <tt class="py-op">:</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-80" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-80', 'title', 'link-35');">title</a></tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">        <tt class="py-name">resultKeys</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-81" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-81', 'x', 'link-67');">x</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-82" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-82', 'x', 'link-67');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ls</tt><tt class="py-op">]</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">        <tt class="py-name">resultKeys</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><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-83', 'sort', 'link-56');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">        <tt id="link-84" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-84', 'map', 'link-84');">map</a></tt> <tt class="py-op">=</tt> <tt id="link-85" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-85', 'title', 'link-35');">title</a></tt> <tt class="py-keyword">or</tt> <tt class="py-string">''</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">        <tt class="py-name">enzymemap</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt id="link-86" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.enzyme()=Bio.MetaTool._RecordConsumer-class.html#enzyme,Variable Bio.MetaTool.metatool_format.enzyme=Bio.MetaTool.metatool_format-module.html#enzyme"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-86', 'enzyme', 'link-86');">enzyme</a></tt><tt class="py-op">,</tt> <tt class="py-name">cut</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ls</tt> <tt class="py-op">:</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cut</tt> <tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">enzymemap</tt><tt class="py-op">.</tt><tt id="link-87" 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-87', 'has_key', 'link-87');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">                    <tt class="py-name">enzymemap</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-88', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-89', 'enzyme', 'link-86');">enzyme</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">                    <tt class="py-name">enzymemap</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-90" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-90', 'enzyme', 'link-86');">enzyme</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">        <tt id="link-91" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.mapping()=Bio.Prosite.Pattern.PrositeMatch-class.html#mapping"><a title="Bio.Prosite.Pattern.PrositeMatch.mapping" class="py-name" href="#" onclick="return doclink('link-91', 'mapping', 'link-91');">mapping</a></tt> <tt class="py-op">=</tt> <tt class="py-name">enzymemap</tt><tt class="py-op">.</tt><tt id="link-92" 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" href="#" onclick="return doclink('link-92', 'keys', 'link-92');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">        <tt id="link-93" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.mapping" class="py-name" href="#" onclick="return doclink('link-93', 'mapping', 'link-91');">mapping</a></tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><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-94', 'sort', 'link-56');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line">        <tt class="py-name">cutloc</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">        <tt id="link-95" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-95', 'x', 'link-67');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">counter</tt><tt class="py-op">,</tt> <tt id="link-96" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-96', 'length', 'link-96');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</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 id="link-97" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-97', 'sequence', 'link-97');">sequence</a></tt><tt class="py-op">)</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-98" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-98', 'x', 'link-67');">x</a></tt> <tt class="py-keyword">in</tt> <tt id="link-99" class="py-name" targets="Method Bio.GFF.Feature.xrange()=Bio.GFF.Feature-class.html#xrange"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-99', 'xrange', 'link-99');">xrange</a></tt><tt class="py-op">(</tt><tt class="py-number">60</tt><tt class="py-op">,</tt> <tt id="link-100" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-100', 'length', 'link-96');">length</a></tt><tt class="py-op">,</tt> <tt class="py-number">60</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">            <tt class="py-name">counter</tt> <tt class="py-op">=</tt> <tt id="link-101" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-101', 'x', 'link-67');">x</a></tt> <tt class="py-op">-</tt> <tt class="py-number">60</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">            <tt class="py-name">l</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt id="link-102" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-102', 'key', 'link-58');">key</a></tt> <tt class="py-keyword">in</tt> <tt id="link-103" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.mapping" class="py-name" href="#" onclick="return doclink('link-103', 'mapping', 'link-91');">mapping</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-104" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-104', 'key', 'link-58');">key</a></tt> <tt class="py-op">&lt;=</tt> <tt id="link-105" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-105', 'x', 'link-67');">x</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">                    <tt class="py-name">l</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-106', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt id="link-107" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-107', 'key', 'link-58');">key</a></tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">                    <tt class="py-name">cutloc</tt><tt class="py-op">[</tt><tt class="py-name">counter</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">l</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line">                    <tt id="link-108" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.mapping" class="py-name" href="#" onclick="return doclink('link-108', 'mapping', 'link-91');">mapping</a></tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.mapping" class="py-name" href="#" onclick="return doclink('link-109', 'mapping', 'link-91');">mapping</a></tt><tt class="py-op">[</tt><tt id="link-110" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.mapping" class="py-name" href="#" onclick="return doclink('link-110', 'mapping', 'link-91');">mapping</a></tt><tt class="py-op">.</tt><tt id="link-111" 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-111', 'index', 'link-111');">index</a></tt><tt class="py-op">(</tt><tt id="link-112" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-112', 'key', 'link-58');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">                    <tt class="py-keyword">break</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">            <tt class="py-name">cutloc</tt><tt class="py-op">[</tt><tt id="link-113" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-113', 'x', 'link-67');">x</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">l</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">        <tt class="py-name">cutloc</tt><tt class="py-op">[</tt><tt id="link-114" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-114', 'x', 'link-67');">x</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-115" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.mapping" class="py-name" href="#" onclick="return doclink('link-115', 'mapping', 'link-91');">mapping</a></tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">        <tt id="link-116" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-116', 'sequence', 'link-97');">sequence</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-117', 'sequence', 'link-97');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-118" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.EUtils.POM.ElementNode.tostring()=Bio.EUtils.POM.ElementNode-class.html#tostring,Method Bio.Prosite.Pattern.Prosite.tostring()=Bio.Prosite.Pattern.Prosite-class.html#tostring,Method Bio.Seq.MutableSeq.tostring()=Bio.Seq.MutableSeq-class.html#tostring,Method Bio.Seq.Seq.tostring()=Bio.Seq.Seq-class.html#tostring,Method BioSQL.BioSeq.DBSeq.tostring()=BioSQL.BioSeq.DBSeq-class.html#tostring"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-118', 'tostring', 'link-118');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line">        <tt class="py-name">revsequence</tt> <tt class="py-op">=</tt> <tt id="link-119" class="py-name"><a title="Bio.Seq.MutableSeq.complement
Bio.Seq.Seq.complement" class="py-name" href="#" onclick="return doclink('link-119', 'complement', 'link-5');">complement</a></tt><tt class="py-op">(</tt><tt id="link-120" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-120', 'sequence', 'link-97');">sequence</a></tt><tt class="py-op">)</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line">        <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-string">'|'</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line">        <tt class="py-name">base</tt><tt class="py-op">,</tt> <tt class="py-name">counter</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line">        <tt class="py-name">emptyline</tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt> <tt class="py-op">*</tt> <tt class="py-number">60</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line">        <tt class="py-name">Join</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">base</tt> <tt class="py-keyword">in</tt> <tt id="link-121" class="py-name"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-121', 'xrange', 'link-99');">xrange</a></tt><tt class="py-op">(</tt><tt class="py-number">60</tt><tt class="py-op">,</tt> <tt id="link-122" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-122', 'length', 'link-96');">length</a></tt><tt class="py-op">,</tt> <tt class="py-number">60</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">            <tt class="py-name">counter</tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt> <tt class="py-op">-</tt> <tt class="py-number">60</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">emptyline</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt id="link-123" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-123', 'key', 'link-58');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">cutloc</tt><tt class="py-op">[</tt><tt class="py-name">counter</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line">                <tt id="link-124" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-124', 's', 'link-124');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-125" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-125', 'key', 'link-58');">key</a></tt> <tt class="py-op">==</tt> <tt class="py-name">base</tt> <tt class="py-op">:</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line">                    <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enzymemap</tt><tt class="py-op">[</tt><tt id="link-126" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-126', 'key', 'link-58');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> <tt id="link-127" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-127', 's', 'link-124');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-128" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-128', 's', 'link-124');">s</a></tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">                    <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">59</tt><tt class="py-op">]</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">                    <tt class="py-name">lineo</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-129" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-129', 'key', 'link-58');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-130" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-130', 's', 'link-124');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">                    <tt class="py-name">line2</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">,</tt> <tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">                    <tt class="py-name">linetot</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">lineo</tt><tt class="py-op">,</tt> <tt class="py-name">line2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">                    <tt id="link-131" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-131', 'map', 'link-84');">map</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-132" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-132', 'map', 'link-84');">map</a></tt><tt class="py-op">,</tt> <tt class="py-name">linetot</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">                    <tt class="py-keyword">break</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enzymemap</tt><tt class="py-op">[</tt><tt id="link-133" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-133', 'key', 'link-58');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> <tt id="link-134" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-134', 's', 'link-124');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-135" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-135', 's', 'link-124');">s</a></tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">                <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-136', 'key', 'link-58');">key</a></tt><tt class="py-op">%</tt><tt class="py-number">60</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line">                <tt class="py-name">lineo</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-137', 'key', 'link-58');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-138" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-138', 's', 'link-124');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line">                <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">                <tt class="py-name">line2</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">                <tt class="py-name">linetot</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">lineo</tt><tt class="py-op">,</tt><tt class="py-name">line2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">                <tt id="link-139" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-139', 'map', 'link-84');">map</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-140" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-140', 'map', 'link-84');">map</a></tt><tt class="py-op">,</tt><tt class="py-name">linetot</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">            <tt class="py-name">mapunit</tt> <tt class="py-op">=</tt> <tt class="py-string">'\n'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-141" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-141', 'sequence', 'link-97');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-name">counter</tt> <tt class="py-op">:</tt> <tt class="py-name">base</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">a</tt> <tt class="py-op">*</tt> <tt class="py-number">60</tt><tt class="py-op">,</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">                                 <tt class="py-name">revsequence</tt><tt class="py-op">[</tt><tt class="py-name">counter</tt> <tt class="py-op">:</tt> <tt class="py-name">base</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line">                                 <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">.</tt><tt class="py-name">ljust</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">counter</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">15</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt><tt class="py-op">*</tt> <tt class="py-number">30</tt><tt class="py-op">,</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">                                        <tt class="py-name">str</tt><tt class="py-op">.</tt><tt class="py-name">rjust</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">15</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'\n\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line">                                 <tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line">            <tt id="link-142" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-142', 'map', 'link-84');">map</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-143" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-143', 'map', 'link-84');">map</a></tt><tt class="py-op">,</tt> <tt class="py-name">mapunit</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>  </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt><tt class="py-op">*</tt> <tt class="py-number">60</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-144" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-144', 'key', 'link-58');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">cutloc</tt><tt class="py-op">[</tt><tt class="py-name">base</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">            <tt id="link-145" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-145', 's', 'link-124');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-146" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-146', 'key', 'link-58');">key</a></tt> <tt class="py-op">==</tt> <tt id="link-147" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-147', 'length', 'link-96');">length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enzymemap</tt><tt class="py-op">[</tt><tt id="link-148" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-148', 'key', 'link-58');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">                    <tt id="link-149" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-149', 's', 'link-124');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-150" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-150', 's', 'link-124');">s</a></tt><tt class="py-op">,</tt><tt class="py-string">' '</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">                <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt id="link-151" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-151', 'length', 'link-96');">length</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">                <tt class="py-name">lineo</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-152" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-152', 'key', 'link-58');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-153" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-153', 's', 'link-124');">s</a></tt><tt class="py-op">,</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">                <tt class="py-name">line2</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">,</tt><tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">                <tt class="py-name">linetot</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">lineo</tt><tt class="py-op">,</tt> <tt class="py-name">line2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">                <tt id="link-154" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-154', 'map', 'link-84');">map</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-155" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-155', 'map', 'link-84');">map</a></tt><tt class="py-op">,</tt> <tt class="py-name">linetot</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enzymemap</tt><tt class="py-op">[</tt><tt id="link-156" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-156', 'key', 'link-58');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> <tt id="link-157" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-157', 's', 'link-124');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-158" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-158', 's', 'link-124');">s</a></tt><tt class="py-op">,</tt><tt class="py-string">' '</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">            <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt id="link-159" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-159', 'key', 'link-58');">key</a></tt><tt class="py-op">%</tt><tt class="py-number">60</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">            <tt class="py-name">lineo</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-160" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-160', 'key', 'link-58');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-161" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-161', 's', 'link-124');">s</a></tt><tt class="py-op">,</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">            <tt class="py-name">line2</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">            <tt class="py-name">linetot</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">lineo</tt><tt class="py-op">,</tt><tt class="py-name">line2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line">            <tt id="link-162" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-162', 'map', 'link-84');">map</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-163" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-163', 'map', 'link-84');">map</a></tt><tt class="py-op">,</tt><tt class="py-name">linetot</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">        <tt class="py-name">mapunit</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">        <tt class="py-name">mapunit</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-164" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-164', 'sequence', 'link-97');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-name">base</tt> <tt class="py-op">:</tt> <tt id="link-165" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-165', 'length', 'link-96');">length</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line">        <tt class="py-name">mapunit</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">mapunit</tt><tt class="py-op">,</tt> <tt class="py-name">a</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt id="link-166" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-166', 'length', 'link-96');">length</a></tt><tt class="py-op">-</tt><tt class="py-name">base</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">        <tt class="py-name">mapunit</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">mapunit</tt><tt class="py-op">,</tt><tt class="py-name">revsequence</tt><tt class="py-op">[</tt><tt class="py-name">base</tt><tt class="py-op">:</tt><tt id="link-167" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-167', 'length', 'link-96');">length</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line">        <tt class="py-name">mapunit</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">mapunit</tt><tt class="py-op">,</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">.</tt><tt class="py-name">ljust</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">15</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt><tt class="py-op">*</tt><tt class="py-op">(</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line">            <tt id="link-168" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-168', 'length', 'link-96');">length</a></tt><tt class="py-op">-</tt><tt class="py-name">base</tt><tt class="py-op">-</tt><tt class="py-number">30</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">.</tt><tt class="py-name">rjust</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-169" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-169', 'length', 'link-96');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">15</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">                                       <tt class="py-string">'\n\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">        <tt id="link-170" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-170', 'map', 'link-84');">map</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-171" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-171', 'map', 'link-84');">map</a></tt><tt class="py-op">,</tt><tt class="py-name">mapunit</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-172" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-172', 'map', 'link-84');">map</a></tt> </tt>
</div><a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line">     </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line"><tt class="py-comment">###### private method to do lists :</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line"><tt class="py-comment"></tt>     </tt>
<a name="PrintFormat.__next_section"></a><div id="PrintFormat.__next_section-def"><a name="L381"></a><tt class="py-lineno">381</tt> <a class="py-toggle" href="#" id="PrintFormat.__next_section-toggle" onclick="return toggle('PrintFormat.__next_section');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction.PrintFormat.PrintFormat-class.html#__next_section">__next_section</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ls</tt><tt class="py-op">,</tt> <tt class="py-param">into</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="PrintFormat.__next_section-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrintFormat.__next_section-expanded"><a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line">        <tt class="py-docstring">"""FP.__next_section(ls, into) -&gt; string.</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line"><tt class="py-docstring">        ls is a list of tuple (string, [int, int]).</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line"><tt class="py-docstring">        into is a string to which the formatted ls will be added.</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line"><tt class="py-docstring">        Format ls as a string of lines :</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line"><tt class="py-docstring">        The form is :</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme1     :   position1.</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line"><tt class="py-docstring">        enzyme2     :   position2, position3.</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line"><tt class="py-docstring">        then add the formatted ls to tot</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line"><tt class="py-docstring">        return tot."""</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line">        <tt class="py-name">ls</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><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-173', 'sort', 'link-56');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line">        <tt class="py-name">indentation</tt> <tt class="py-op">=</tt> <tt class="py-string">'\n'</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.NameWidth
Bio.Restriction.RanaConfig.NameWidth" class="py-name" href="#" onclick="return doclink('link-174', 'NameWidth', 'link-8');">NameWidth</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.Indent
Bio.Restriction.RanaConfig.Indent" class="py-name" href="#" onclick="return doclink('link-175', 'Indent', 'link-18');">Indent</a></tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-string">' '</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line">        <tt id="link-176" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.linesize" class="py-name" href="#" onclick="return doclink('link-176', 'linesize', 'link-20');">linesize</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.linesize" class="py-name" href="#" onclick="return doclink('link-177', 'linesize', 'link-20');">linesize</a></tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.MaxSize
Bio.Restriction.RanaConfig.MaxSize" class="py-name" href="#" onclick="return doclink('link-178', 'MaxSize', 'link-10');">MaxSize</a></tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line">        <tt id="link-179" class="py-name" targets="Variable Martel.Time.pat=Martel.Time-module.html#pat"><a title="Martel.Time.pat" class="py-name" href="#" onclick="return doclink('link-179', 'pat', 'link-179');">pat</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-180" 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-180', 'compile', 'link-180');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">"([\w,\s()]){1,%i}[,\.]"</tt><tt class="py-op">%</tt><tt id="link-181" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.linesize" class="py-name" href="#" onclick="return doclink('link-181', 'linesize', 'link-20');">linesize</a></tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line">        <tt class="py-name">several</tt><tt class="py-op">,</tt> <tt class="py-name">Join</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-182" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-182', 'name', 'link-69');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">sites</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ls</tt> <tt class="py-op">:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line">            <tt class="py-name">stringsite</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line">            <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">', '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">site</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">site</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sites</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'.'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt id="link-183" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.linesize" class="py-name" href="#" onclick="return doclink('link-183', 'linesize', 'link-20');">linesize</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line">                <tt class="py-comment">#</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#   cut where appropriate and add the indentation</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-184" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-184', 'x', 'link-67');">x</a></tt><tt class="py-op">.</tt><tt id="link-185" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.group()=Bio.Prosite.Pattern.PrositeMatch-class.html#group"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-185', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-186" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-186', 'x', 'link-67');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-187" class="py-name" targets="Method Bio.Restriction.Restriction.FormattedSeq.finditer()=Bio.Restriction.Restriction.FormattedSeq-class.html#finditer"><a title="Bio.Restriction.Restriction.FormattedSeq.finditer" class="py-name" href="#" onclick="return doclink('link-187', 'finditer', 'link-187');">finditer</a></tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Martel.Time.pat" class="py-name" href="#" onclick="return doclink('link-188', 'pat', 'link-179');">pat</a></tt><tt class="py-op">,</tt> <tt class="py-name">l</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line">                <tt class="py-name">stringsite</tt> <tt class="py-op">=</tt> <tt class="py-name">indentation</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt>  </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line">                <tt class="py-name">stringsite</tt> <tt class="py-op">=</tt> <tt class="py-name">l</tt>     </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line">            <tt class="py-name">into</tt> <tt class="py-op">=</tt> <tt class="py-name">Join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">into</tt><tt class="py-op">,</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line">                         <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-189" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-189', 'name', 'link-69');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">ljust</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="Bio.Restriction.PrintFormat.PrintFormat.NameWidth
Bio.Restriction.RanaConfig.NameWidth" class="py-name" href="#" onclick="return doclink('link-190', 'NameWidth', 'link-8');">NameWidth</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">' :  '</tt><tt class="py-op">,</tt><tt class="py-name">stringsite</tt><tt class="py-op">,</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">into</tt> </tt>
</div></div><a name="L414"></a><tt class="py-lineno">414</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>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</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 09:28:06 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.  So hide
  // them unless we have a cookie that says to show them.
  checkCookie();
  // -->
</script>
</body>
</html>