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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.EUtils-module.html">Package EUtils</a> ::
Module HistoryClient
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<h1 class="epydoc">Source Code for <a href="Bio.EUtils.HistoryClient-module.html">Module Bio.EUtils.HistoryClient</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Search and retreive information using the EUtils history.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">EUtils has two major modes. One uses history while the other uses</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">database identifiers. This is a high-level interface for working with</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">the history. You should use this module if you expect to work with</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">large or an unknown number of identifiers.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">See DBIdsClient if you want to get information about a set of known</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">database identifiers.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">>>> from Bio.EUtils import HistoryClient</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">>>> client = HistoryClient.HistoryClient()</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">>>> cancer = client.search("cancer")</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">>>> print len(cancer)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">1458353</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">>>> </tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">That's quite a few hits. Most people would like to see the first few</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">records then try to refine the search.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">>>> print cancer[:5].efetch(retmode = "text", rettype = "docsum").read()</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">1: Seow-Choen F.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">Author's reply: Adjuvant therapy for rectal cancer cannot be based on the</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">results of other surgeons (Br J Surg 2002; 89: 946-947).</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">Br J Surg. 2003 Jan;90(1):121-122.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">PMID: 12520589 [PubMed - as supplied by publisher]</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">2: Mortensen N, Lindsey I.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">Adjuvant therapy for rectal cancer cannot be based on the results of other</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">surgeons (Br J Surg 2002; 89: 946-947).</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">Br J Surg. 2003 Jan;90(1):121.</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring">PMID: 12520588 [PubMed - as supplied by publisher]</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring">3: Osugi H, Takemura M, Higashino M, Takada N, Lee S, Kinoshita H.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring">A comparison of video-assisted thoracoscopic oesophagectomy and radical lymph</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring">node dissection for squamous cell cancer of the oesophagus with open operation.</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring">Br J Surg. 2003 Jan;90(1):108-13.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring">PMID: 12520585 [PubMed - in process]</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring">4: Tanaka M, Kitajima Y, Sato S, Miyazaki K.</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring">Combined evaluation of mucin antigen and E-cadherin expression may help select</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring">patients with gastric cancer suitable for minimally invasive therapy.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring">Br J Surg. 2003 Jan;90(1):95-101.</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring">PMID: 12520583 [PubMed - in process]</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring">5: Diaz De Liano A, Oteiza Martinez F, Ciga MA, Aizcorbe M, Cobo F, Trujillo R.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring">Impact of surgical procedure for gastric cancer on quality of life.</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring">Br J Surg. 2003 Jan;90(1):91-4.</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring">PMID: 12520582 [PubMed - in process]</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring">>>></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring">Now refine the query to publications in the last day</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring">>>> from Bio import EUtils</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring">>>> recent_cancer = client.search("#%s" % (cancer.query_key,),</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring">... daterange = EUtils.WithinNDays(1))</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring">>>> len(recent_cancer)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring">106</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring">>>></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring">Still quite a few. What's the last one about?</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring">>>> for k, v in recent_cancer[-1].summary().dataitems.allitems():</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring">... print k, "=", v</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring">...</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring">PubDate = 2002/12/01</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring">Source = Nippon Shokakibyo Gakkai Zasshi</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring">Authors = Kuroki T</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring">Title = [Strategy against cancer in 21 century, with emphasis of cancer prevention and refractory cancer]</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring">Volume = 99</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring">Pages = 1423-7</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring">EntrezDate = 2003/01/10</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring">PubMedId = 12518389</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring">MedlineId = 22406828</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring">Lang = Japanese</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring">PubType =</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring">RecordStatus = PubMed - in process</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring">Issue = 12</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring">SO = 2002 Dec;99(12):1423-7</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring">DOI =</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring">JTA = KJY</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring">ISSN = 0446-6586</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring">PubId =</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring">PubStatus = 4</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring">Status = 6</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring">HasAbstract = 0</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring">ArticleIds = {'MedlineUID': u'22406828', 'PubMedId': u'12518389'}</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring">>>> </tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring">Here's an interesting one. Which articles are related to this one but</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring">are not about cancer? First, get the related articles.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"></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">>>> neighbors = recent_cancer[-1].neighbor_links()</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring">>>> dbids = neighbors.linksetdbs["pubmed_pubmed"].dbids</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring">>>> len(dbids)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring">10296</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"></tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring">Upload that back to the server</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring">>>> related_result = client.post(dbids)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring">>>></tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring">>>> non_cancer = client.search("#%s NOT #%s" % (related_result.query_key,</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring">... cancer.query_key))</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring">>>> len(non_cancer)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring">4000</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring">>>></tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring">The HistoryClient instance has an attribute named 'query_history'</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring">which stores the searches done so far, keyed by the query_key value</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring">assigned by the server. The history on the server can expire. If</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring">that is detected during a search then previous results are invalidated</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring">and removed from the query_history. Future requests from invalidated</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring">results will raise an error.</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring">If a request is made from a search which has not been invalidated but</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring">whose history has expired then queries like 'summary' will raise an</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring">error. Some other request (like 'dbids') may return success but</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring">contain undefined information.</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> <tt class="py-comment">#"</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">types</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module Bio.EUtils.ThinClient=Bio.EUtils.ThinClient-module.html,Class Bio.EUtils.ThinClient.ThinClient=Bio.EUtils.ThinClient.ThinClient-class.html"><a title="Bio.EUtils.ThinClient
Bio.EUtils.ThinClient.ThinClient" class="py-name" href="#" onclick="return doclink('link-0', 'ThinClient', 'link-0');">ThinClient</a></tt><tt class="py-op">,</tt> <tt id="link-1" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-1', 'parse', 'link-1');">parse</a></tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Module Bio.EUtils.Datatypes=Bio.EUtils.Datatypes-module.html"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-2', 'Datatypes', 'link-2');">Datatypes</a></tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Module Bio.EUtils.Mixins=Bio.EUtils.Mixins-module.html"><a title="Bio.EUtils.Mixins" class="py-name" href="#" onclick="return doclink('link-3', 'Mixins', 'link-3');">Mixins</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Module Bio.EUtils.Config=Bio.EUtils.Config-module.html"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-4', 'Config', 'link-4');">Config</a></tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> </tt>
<a name="HistoryCookie"></a><div id="HistoryCookie-def"><a name="L129"></a><tt class="py-lineno">129</tt> <a class="py-toggle" href="#" id="HistoryCookie-toggle" onclick="return toggle('HistoryCookie');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryCookie-class.html">HistoryCookie</a><tt class="py-op">:</tt> </tt>
</div><div id="HistoryCookie-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="HistoryCookie-expanded"><a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-docstring">"""Data needed to get back to the history"""</tt> </tt>
<a name="HistoryCookie.__init__"></a><div id="HistoryCookie.__init__-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="HistoryCookie.__init__-toggle" onclick="return toggle('HistoryCookie.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryCookie-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">webenv_ref</tt><tt class="py-op">,</tt> <tt class="py-param">query_key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HistoryCookie.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryCookie.__init__-expanded"><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Variable Bio.LocusLink.locus_format.db=Bio.LocusLink.locus_format-module.html#db,Variable Bio.config.DBRegistry.db=Bio.config.DBRegistry-module.html#db"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-5', 'db', 'link-5');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-6', 'db', 'link-5');">db</a></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt> <tt class="py-op">=</tt> <tt class="py-name">webenv_ref</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">query_key</tt> </tt>
</div></div><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="HistoryLookup"></a><div id="HistoryLookup-def"><a name="L136"></a><tt class="py-lineno">136</tt> <a class="py-toggle" href="#" id="HistoryLookup-toggle" onclick="return toggle('HistoryLookup');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryLookup-class.html">HistoryLookup</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="HistoryLookup-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="HistoryLookup-expanded"><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-docstring">"""Look up information about a search in history</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> To get the list of dbids by fetching the server's "uilist",</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> use the "dbids" attribute.</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="HistoryLookup.__init__"></a><div id="HistoryLookup.__init__-def"><a name="L142"></a><tt class="py-lineno">142</tt> <a class="py-toggle" href="#" id="HistoryLookup.__init__-toggle" onclick="return toggle('HistoryLookup.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryLookup-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">eutils</tt><tt class="py-op">,</tt> <tt class="py-param">cookie</tt><tt class="py-op">,</tt> <tt class="py-param">retstart</tt><tt class="py-op">,</tt> <tt class="py-param">retmax</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HistoryLookup.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryLookup.__init__-expanded"><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt> <tt class="py-op">=</tt> <tt class="py-name">eutils</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt> <tt class="py-op">=</tt> <tt class="py-name">cookie</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-name">retstart</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt class="py-name">retmax</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-7', 'db', 'link-5');">db</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-8', 'db', 'link-5');">db</a></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt> </tt>
</div><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="HistoryLookup._check_invalid"></a><div id="HistoryLookup._check_invalid-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="HistoryLookup._check_invalid-toggle" onclick="return toggle('HistoryLookup._check_invalid');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryLookup-class.html#_check_invalid">_check_invalid</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="HistoryLookup._check_invalid-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryLookup._check_invalid-expanded"><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-comment"># Check if we can get data from this history</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"empty data set"</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-9" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-9', 'Datatypes', 'link-2');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Class Bio.EUtils.Datatypes.EUtilsError=Bio.EUtils.Datatypes.EUtilsError-class.html"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-10', 'EUtilsError', 'link-10');">EUtilsError</a></tt><tt class="py-op">(</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-string">"query history no longer available on server"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="HistoryLookup.esummary"></a><div id="HistoryLookup.esummary-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="HistoryLookup.esummary-toggle" onclick="return toggle('HistoryLookup.esummary');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryLookup-class.html#esummary">esummary</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">retmode</tt> <tt class="py-op">=</tt> <tt class="py-string">'xml'</tt><tt class="py-op">,</tt> <tt class="py-param">rettype</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HistoryLookup.esummary-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryLookup.esummary-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-docstring">"""Request the eSummary for this history; returns the socket handle"""</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.EUtils.HistoryClient.HistoryLookup._check_invalid()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#_check_invalid"><a title="Bio.EUtils.HistoryClient.HistoryLookup._check_invalid" class="py-name" href="#" onclick="return doclink('link-11', '_check_invalid', 'link-11');">_check_invalid</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.esummary_using_history()=Bio.EUtils.ThinClient.ThinClient-class.html#esummary_using_history"><a title="Bio.EUtils.ThinClient.ThinClient.esummary_using_history" class="py-name" href="#" onclick="return doclink('link-12', 'esummary_using_history', 'link-12');">esummary_using_history</a></tt><tt class="py-op">(</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">webenv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-13', 'db', 'link-5');">db</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-14', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">,</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retstart</tt><tt class="py-op">,</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">infile</tt> </tt>
</div><a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
<a name="HistoryLookup.summary"></a><div id="HistoryLookup.summary-def"><a name="L169"></a><tt class="py-lineno">169</tt> <a class="py-toggle" href="#" id="HistoryLookup.summary-toggle" onclick="return toggle('HistoryLookup.summary');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryLookup-class.html#summary">summary</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="HistoryLookup.summary-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryLookup.summary-expanded"><a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-docstring">"""the Datatypes.Summary for this history"""</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-15" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-15', 'parse', 'link-1');">parse</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Function Bio.EUtils.parse.parse_summary_xml()=Bio.EUtils.parse-module.html#parse_summary_xml"><a title="Bio.EUtils.parse.parse_summary_xml" class="py-name" href="#" onclick="return doclink('link-16', 'parse_summary_xml', 'link-16');">parse_summary_xml</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsLookup.esummary()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#esummary,Method Bio.EUtils.HistoryClient.HistoryLookup.esummary()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#esummary,Function Bio.Entrez.esummary()=Bio.Entrez-module.html#esummary"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.esummary
Bio.EUtils.HistoryClient.HistoryLookup.esummary
Bio.Entrez.esummary" class="py-name" href="#" onclick="return doclink('link-17', 'esummary', 'link-17');">esummary</a></tt><tt class="py-op">(</tt><tt class="py-string">"xml"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="HistoryLookup.elink"></a><div id="HistoryLookup.elink-def"><a name="L173"></a><tt class="py-lineno">173</tt> <a class="py-toggle" href="#" id="HistoryLookup.elink-toggle" onclick="return toggle('HistoryLookup.elink');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryLookup-class.html#elink">elink</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-param">db</tt> <tt class="py-op">=</tt> <tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-param">cmd</tt> <tt class="py-op">=</tt> <tt class="py-string">"neighbor"</tt><tt class="py-op">,</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-param">term</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-param">field</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-param">daterange</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HistoryLookup.elink-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryLookup.elink-expanded"><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-docstring">"""Request an eLink for this history; returns the socket handle"""</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.EUtils.HistoryClient.HistoryLookup._check_invalid" class="py-name" href="#" onclick="return doclink('link-18', '_check_invalid', 'link-11');">_check_invalid</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.elink_using_history()=Bio.EUtils.ThinClient.ThinClient-class.html#elink_using_history"><a title="Bio.EUtils.ThinClient.ThinClient.elink_using_history" class="py-name" href="#" onclick="return doclink('link-19', 'elink_using_history', 'link-19');">elink_using_history</a></tt><tt class="py-op">(</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">webenv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">,</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt id="link-20" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-20', 'db', 'link-5');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-21', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">dbfrom</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-22', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">=</tt> <tt class="py-name">cmd</tt><tt class="py-op">,</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retstart</tt><tt class="py-op">,</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt><tt class="py-op">,</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">daterange</tt> <tt class="py-op">=</tt> <tt class="py-name">daterange</tt><tt class="py-op">,</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</tt><tt class="py-op">,</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">field</tt> <tt class="py-op">=</tt> <tt class="py-name">field</tt><tt class="py-op">,</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
</div><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> </tt>
<a name="HistoryLookup._get_dbids"></a><div id="HistoryLookup._get_dbids-def"><a name="L194"></a><tt class="py-lineno">194</tt> <a class="py-toggle" href="#" id="HistoryLookup._get_dbids-toggle" onclick="return toggle('HistoryLookup._get_dbids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryLookup-class.html#_get_dbids">_get_dbids</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="HistoryLookup._get_dbids-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryLookup._get_dbids-expanded"><a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin.efetch()=Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin-class.html#efetch,Method Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin.efetch()=Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin-class.html#efetch,Method Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin.efetch()=Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin-class.html#efetch,Method Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin.efetch()=Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin-class.html#efetch,Function Bio.Entrez.efetch()=Bio.Entrez-module.html#efetch,Function Bio.WWW.NCBI.efetch()=Bio.WWW.NCBI-module.html#efetch"><a title="Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin.efetch
Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin.efetch
Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin.efetch
Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin.efetch
Bio.Entrez.efetch
Bio.WWW.NCBI.efetch" class="py-name" href="#" onclick="return doclink('link-23', 'efetch', 'link-23');">efetch</a></tt><tt class="py-op">(</tt><tt class="py-name">retmode</tt> <tt class="py-op">=</tt> <tt class="py-string">"text"</tt><tt class="py-op">,</tt> <tt class="py-name">rettype</tt> <tt class="py-op">=</tt> <tt class="py-string">"uilist"</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt id="link-24" class="py-name" targets="Variable Bio.expressions.fasta.ids=Bio.expressions.fasta-module.html#ids"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-24', 'ids', 'link-24');">ids</a></tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-25', 'parse', 'link-1');">parse</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Function Bio.EUtils.parse.parse_fetch_identifiers()=Bio.EUtils.parse-module.html#parse_fetch_identifiers"><a title="Bio.EUtils.parse.parse_fetch_identifiers" class="py-name" href="#" onclick="return doclink('link-26', 'parse_fetch_identifiers', 'link-26');">parse_fetch_identifiers</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-27" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-27', 'Datatypes', 'link-2');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Class Bio.EUtils.Datatypes.DBIds=Bio.EUtils.Datatypes.DBIds-class.html"><a title="Bio.EUtils.Datatypes.DBIds" class="py-name" href="#" onclick="return doclink('link-28', 'DBIds', 'link-28');">DBIds</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-29', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> <tt id="link-30" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-30', 'ids', 'link-24');">ids</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt id="link-31" class="py-name" targets="Variable Bio.EUtils.DBIdsClient.DBIdsLookup.dbids=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#dbids,Variable Bio.EUtils.Datatypes.CheckLinkSet.dbids=Bio.EUtils.Datatypes.CheckLinkSet-class.html#dbids,Variable Bio.EUtils.Datatypes.LinkSetDb.dbids=Bio.EUtils.Datatypes.LinkSetDb-class.html#dbids,Variable Bio.EUtils.HistoryClient.HistoryLookup.dbids=Bio.EUtils.HistoryClient.HistoryLookup-class.html#dbids"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-31', 'dbids', 'link-31');">dbids</a></tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.property=Bio.Encodings.IUPACEncoding-module.html#property"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-32', 'property', 'link-32');">property</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsLookup._get_dbids()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#_get_dbids,Method Bio.EUtils.Datatypes.CheckLinkSet._get_dbids()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#_get_dbids,Method Bio.EUtils.Datatypes.LinkSetDb._get_dbids()=Bio.EUtils.Datatypes.LinkSetDb-class.html#_get_dbids,Method Bio.EUtils.HistoryClient.HistoryLookup._get_dbids()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#_get_dbids"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup._get_dbids
Bio.EUtils.Datatypes.CheckLinkSet._get_dbids
Bio.EUtils.Datatypes.LinkSetDb._get_dbids
Bio.EUtils.HistoryClient.HistoryLookup._get_dbids" class="py-name" href="#" onclick="return doclink('link-33', '_get_dbids', 'link-33');">_get_dbids</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-string">"The DBIds for this results set, fetched from the server's 'uilist'"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="HistoryRecord"></a><div id="HistoryRecord-def"><a name="L201"></a><tt class="py-lineno">201</tt> <a class="py-toggle" href="#" id="HistoryRecord-toggle" onclick="return toggle('HistoryRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryRecord-class.html">HistoryRecord</a><tt class="py-op">(</tt><tt class="py-base-class">HistoryLookup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HistoryRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="HistoryRecord-expanded"><a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-docstring">"""Get information about a single record in a history"""</tt> </tt>
<a name="HistoryRecord.__init__"></a><div id="HistoryRecord.__init__-def"><a name="L203"></a><tt class="py-lineno">203</tt> <a class="py-toggle" href="#" id="HistoryRecord.__init__-toggle" onclick="return toggle('HistoryRecord.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryRecord-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">eutils</tt><tt class="py-op">,</tt> <tt class="py-param">cookie</tt><tt class="py-op">,</tt> <tt class="py-param">offset</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-35', '__init__', 'link-35');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt class="py-name">cookie</tt><tt class="py-op">,</tt> <tt class="py-name">offset</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="HistoryRecord.summary"></a><div id="HistoryRecord.summary-def"><a name="L205"></a><tt class="py-lineno">205</tt> <a class="py-toggle" href="#" id="HistoryRecord.summary-toggle" onclick="return toggle('HistoryRecord.summary');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryRecord-class.html#summary">summary</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="HistoryRecord.summary-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryRecord.summary-expanded"><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-docstring">"""the Datatypes.Summary for this history record"""</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-36" class="py-name"><a title="Bio.EUtils.HistoryClient.HistoryLookup" class="py-name" href="#" onclick="return doclink('link-36', 'HistoryLookup', 'link-34');">HistoryLookup</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsLookup.summary()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#summary,Method Bio.EUtils.DBIdsClient.DBIdsRecord.summary()=Bio.EUtils.DBIdsClient.DBIdsRecord-class.html#summary,Method Bio.EUtils.HistoryClient.HistoryLookup.summary()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#summary,Method Bio.EUtils.HistoryClient.HistoryRecord.summary()=Bio.EUtils.HistoryClient.HistoryRecord-class.html#summary"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.summary
Bio.EUtils.DBIdsClient.DBIdsRecord.summary
Bio.EUtils.HistoryClient.HistoryLookup.summary
Bio.EUtils.HistoryClient.HistoryRecord.summary" class="py-name" href="#" onclick="return doclink('link-37', 'summary', 'link-37');">summary</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="SequenceHistoryFetchMixin"></a><div id="SequenceHistoryFetchMixin-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="SequenceHistoryFetchMixin-toggle" onclick="return toggle('SequenceHistoryFetchMixin');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin-class.html">SequenceHistoryFetchMixin</a><tt class="py-op">:</tt> </tt>
</div><div id="SequenceHistoryFetchMixin-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SequenceHistoryFetchMixin-expanded"><a name="SequenceHistoryFetchMixin.efetch"></a><div id="SequenceHistoryFetchMixin.efetch-def"><a name="L210"></a><tt class="py-lineno">210</tt> <a class="py-toggle" href="#" id="SequenceHistoryFetchMixin.efetch-toggle" onclick="return toggle('SequenceHistoryFetchMixin.efetch');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin-class.html#efetch">efetch</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">retmode</tt> <tt class="py-op">=</tt> <tt class="py-string">'xml'</tt><tt class="py-op">,</tt> <tt class="py-param">rettype</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-param">seq_start</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">seq_stop</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">strand</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-param">complexity</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequenceHistoryFetchMixin.efetch-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequenceHistoryFetchMixin.efetch-expanded"><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.EUtils.HistoryClient.HistoryLookup._check_invalid" class="py-name" href="#" onclick="return doclink('link-38', '_check_invalid', 'link-11');">_check_invalid</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-39" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.strand()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#strand,Variable Bio.expressions.blast.ncbiblast.strand=Bio.expressions.blast.ncbiblast-module.html#strand"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-39', 'strand', 'link-39');">strand</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">2</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">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Strand can only be 1 (plus, default) or 2 (minus)"</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.efetch_using_history()=Bio.EUtils.ThinClient.ThinClient-class.html#efetch_using_history"><a title="Bio.EUtils.ThinClient.ThinClient.efetch_using_history" class="py-name" href="#" onclick="return doclink('link-40', 'efetch_using_history', 'link-40');">efetch_using_history</a></tt><tt class="py-op">(</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">webenv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt id="link-41" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-41', 'db', 'link-5');">db</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-42', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">,</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retstart</tt><tt class="py-op">,</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt><tt class="py-op">,</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">retmode</tt> <tt class="py-op">=</tt> <tt class="py-name">retmode</tt><tt class="py-op">,</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">rettype</tt> <tt class="py-op">=</tt> <tt class="py-name">rettype</tt><tt class="py-op">,</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">seq_start</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_start</tt><tt class="py-op">,</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">seq_stop</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_stop</tt><tt class="py-op">,</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-43', 'strand', 'link-39');">strand</a></tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-44', 'strand', 'link-39');">strand</a></tt><tt class="py-op">,</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">complexity</tt> <tt class="py-op">=</tt> <tt class="py-name">complexity</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> </tt>
<a name="SequenceHistoryRecord"></a><div id="SequenceHistoryRecord-def"><a name="L229"></a><tt class="py-lineno">229</tt> <a class="py-toggle" href="#" id="SequenceHistoryRecord-toggle" onclick="return toggle('SequenceHistoryRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.SequenceHistoryRecord-class.html">SequenceHistoryRecord</a><tt class="py-op">(</tt><tt class="py-base-class">Mixins</tt><tt class="py-op">.</tt><tt class="py-base-class">SequenceFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-base-class">SequenceHistoryFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-base-class">HistoryRecord</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequenceHistoryRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SequenceHistoryRecord-expanded"><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="PublicationHistoryFetchMixin"></a><div id="PublicationHistoryFetchMixin-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="PublicationHistoryFetchMixin-toggle" onclick="return toggle('PublicationHistoryFetchMixin');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin-class.html">PublicationHistoryFetchMixin</a><tt class="py-op">:</tt> </tt>
</div><div id="PublicationHistoryFetchMixin-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PublicationHistoryFetchMixin-expanded"><a name="PublicationHistoryFetchMixin.efetch"></a><div id="PublicationHistoryFetchMixin.efetch-def"><a name="L235"></a><tt class="py-lineno">235</tt> <a class="py-toggle" href="#" id="PublicationHistoryFetchMixin.efetch-toggle" onclick="return toggle('PublicationHistoryFetchMixin.efetch');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin-class.html#efetch">efetch</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">retmode</tt> <tt class="py-op">=</tt> <tt class="py-string">"xml"</tt><tt class="py-op">,</tt> <tt class="py-param">rettype</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PublicationHistoryFetchMixin.efetch-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PublicationHistoryFetchMixin.efetch-expanded"><a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.EUtils.HistoryClient.HistoryLookup._check_invalid" class="py-name" href="#" onclick="return doclink('link-45', '_check_invalid', 'link-11');">_check_invalid</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.EUtils.ThinClient.ThinClient.efetch_using_history" class="py-name" href="#" onclick="return doclink('link-46', 'efetch_using_history', 'link-40');">efetch_using_history</a></tt><tt class="py-op">(</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">webenv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt id="link-47" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-47', 'db', 'link-5');">db</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-48', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">,</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retstart</tt><tt class="py-op">,</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt><tt class="py-op">,</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">retmode</tt> <tt class="py-op">=</tt> <tt class="py-name">retmode</tt><tt class="py-op">,</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">rettype</tt> <tt class="py-op">=</tt> <tt class="py-name">rettype</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="PublicationHistoryRecord"></a><div id="PublicationHistoryRecord-def"><a name="L246"></a><tt class="py-lineno">246</tt> <a class="py-toggle" href="#" id="PublicationHistoryRecord-toggle" onclick="return toggle('PublicationHistoryRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.PublicationHistoryRecord-class.html">PublicationHistoryRecord</a><tt class="py-op">(</tt><tt class="py-base-class">Mixins</tt><tt class="py-op">.</tt><tt class="py-base-class">PublicationFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-base-class">PublicationHistoryFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-base-class">HistoryRecord</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PublicationHistoryRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PublicationHistoryRecord-expanded"><a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> </tt>
<a name="BaseHistoryRecordSet"></a><div id="BaseHistoryRecordSet-def"><a name="L251"></a><tt class="py-lineno">251</tt> <a class="py-toggle" href="#" id="BaseHistoryRecordSet-toggle" onclick="return toggle('BaseHistoryRecordSet');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html">BaseHistoryRecordSet</a><tt class="py-op">(</tt><tt class="py-base-class">HistoryLookup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BaseHistoryRecordSet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BaseHistoryRecordSet-expanded"><a name="BaseHistoryRecordSet.__init__"></a><div id="BaseHistoryRecordSet.__init__-def"><a name="L252"></a><tt class="py-lineno">252</tt> <a class="py-toggle" href="#" id="BaseHistoryRecordSet.__init__-toggle" onclick="return toggle('BaseHistoryRecordSet.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">eutils</tt><tt class="py-op">,</tt> <tt class="py-param">cookie</tt><tt class="py-op">,</tt> <tt class="py-param">retstart</tt><tt class="py-op">,</tt> <tt class="py-param">retmax</tt><tt class="py-op">,</tt> <tt class="py-param">metadata</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BaseHistoryRecordSet.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BaseHistoryRecordSet.__init__-expanded"><a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt id="link-49" class="py-name"><a title="Bio.EUtils.HistoryClient.HistoryLookup" class="py-name" href="#" onclick="return doclink('link-49', 'HistoryLookup', 'link-34');">HistoryLookup</a></tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-50', '__init__', 'link-35');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt class="py-name">cookie</tt><tt class="py-op">,</tt> <tt class="py-name">retstart</tt><tt class="py-op">,</tt> <tt class="py-name">retmax</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">metadata</tt> <tt class="py-op">=</tt> <tt class="py-name">metadata</tt> </tt>
</div><a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> </tt>
<a name="BaseHistoryRecordSet.__len__"></a><div id="BaseHistoryRecordSet.__len__-def"><a name="L256"></a><tt class="py-lineno">256</tt> <a class="py-toggle" href="#" id="BaseHistoryRecordSet.__len__-toggle" onclick="return toggle('BaseHistoryRecordSet.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__len__">__len__</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="BaseHistoryRecordSet.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BaseHistoryRecordSet.__len__-expanded"><a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt> </tt>
</div><a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> </tt>
<a name="BaseHistoryRecordSet.__getitem__"></a><div id="BaseHistoryRecordSet.__getitem__-def"><a name="L259"></a><tt class="py-lineno">259</tt> <a class="py-toggle" href="#" id="BaseHistoryRecordSet.__getitem__-toggle" onclick="return toggle('BaseHistoryRecordSet.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BaseHistoryRecordSet.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BaseHistoryRecordSet.__getitem__-expanded"><a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-51" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-51', 'i', 'link-51');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">types</tt><tt class="py-op">.</tt><tt class="py-name">SliceType</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">if</tt> <tt id="link-52" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-52', 'i', 'link-51');">i</a></tt><tt class="py-op">.</tt><tt class="py-name">step</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"cannot set step size in slice"</tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-comment"># Don't pass metadata downwards</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-53" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-53', 'start', 'link-53');">start</a></tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-54', 'i', 'link-51');">i</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-55', 'start', 'link-53');">start</a></tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-56" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-56', 'start', 'link-53');">start</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt id="link-57" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-57', 'start', 'link-53');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-name">stop</tt> <tt class="py-op">=</tt> <tt id="link-58" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-58', 'i', 'link-51');">i</a></tt><tt class="py-op">.</tt><tt class="py-name">stop</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stop</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">stop</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-comment"># Potentially expensive, but this is the easy way</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># to get the semantics correct.</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-59" 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-59', 'x', 'link-59');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retstart</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retstart</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt id="link-60" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-60', 'start', 'link-53');">start</a></tt><tt class="py-op">:</tt><tt class="py-name">stop</tt><tt class="py-op">]</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-61" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-61', 'x', 'link-59');">x</a></tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-62', 'x', 'link-59');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-63', 'x', 'link-59');">x</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt id="link-64" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-64', 'x', 'link-59');">x</a></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-number">1</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">,</tt> <tt class="py-name">retstart</tt><tt class="py-op">,</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">retmax</tt><tt class="py-op">)</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-number">0</tt> <tt class="py-op"><=</tt> <tt id="link-65" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-65', 'i', 'link-51');">i</a></tt> <tt class="py-op"><</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt><tt class="py-op">:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retstart</tt> <tt class="py-op">+</tt> <tt id="link-66" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-66', 'i', 'link-51');">i</a></tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-number">1</tt> <tt class="py-op"><=</tt> <tt class="py-op">-</tt><tt id="link-67" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-67', 'i', 'link-51');">i</a></tt> <tt class="py-op"><=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt><tt class="py-op">:</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retstart</tt> <tt class="py-op">+</tt> <tt id="link-68" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-68', 'i', 'link-51');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">retmax</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt id="link-69" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-69', 'i', 'link-51');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_record_class</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cookie</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> </tt>
<a name="SequenceHistoryRecordSet"></a><div id="SequenceHistoryRecordSet-def"><a name="L287"></a><tt class="py-lineno">287</tt> <a class="py-toggle" href="#" id="SequenceHistoryRecordSet-toggle" onclick="return toggle('SequenceHistoryRecordSet');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.SequenceHistoryRecordSet-class.html">SequenceHistoryRecordSet</a><tt class="py-op">(</tt><tt class="py-base-class">Mixins</tt><tt class="py-op">.</tt><tt class="py-base-class">SequenceFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-base-class">SequenceHistoryFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-base-class">BaseHistoryRecordSet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequenceHistoryRecordSet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SequenceHistoryRecordSet-expanded"><a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">_record_class</tt> <tt class="py-op">=</tt> <tt id="link-70" class="py-name" targets="Class Bio.EUtils.HistoryClient.SequenceHistoryRecord=Bio.EUtils.HistoryClient.SequenceHistoryRecord-class.html"><a title="Bio.EUtils.HistoryClient.SequenceHistoryRecord" class="py-name" href="#" onclick="return doclink('link-70', 'SequenceHistoryRecord', 'link-70');">SequenceHistoryRecord</a></tt> </tt>
</div><a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> </tt>
<a name="PublicationHistoryRecordSet"></a><div id="PublicationHistoryRecordSet-def"><a name="L292"></a><tt class="py-lineno">292</tt> <a class="py-toggle" href="#" id="PublicationHistoryRecordSet-toggle" onclick="return toggle('PublicationHistoryRecordSet');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.PublicationHistoryRecordSet-class.html">PublicationHistoryRecordSet</a><tt class="py-op">(</tt><tt class="py-base-class">Mixins</tt><tt class="py-op">.</tt><tt class="py-base-class">PublicationFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-base-class">PublicationHistoryFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-base-class">BaseHistoryRecordSet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PublicationHistoryRecordSet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PublicationHistoryRecordSet-expanded"><a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">_record_class</tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name" targets="Class Bio.EUtils.HistoryClient.PublicationHistoryRecord=Bio.EUtils.HistoryClient.PublicationHistoryRecord-class.html"><a title="Bio.EUtils.HistoryClient.PublicationHistoryRecord" class="py-name" href="#" onclick="return doclink('link-71', 'PublicationHistoryRecord', 'link-71');">PublicationHistoryRecord</a></tt> </tt>
</div><a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> </tt>
<a name="_get_recordset_constructor"></a><div id="_get_recordset_constructor-def"><a name="L297"></a><tt class="py-lineno">297</tt> <a class="py-toggle" href="#" id="_get_recordset_constructor-toggle" onclick="return toggle('_get_recordset_constructor');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient-module.html#_get_recordset_constructor">_get_recordset_constructor</a><tt class="py-op">(</tt><tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">dbtype</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_get_recordset_constructor-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_get_recordset_constructor-expanded"><a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">dbtype</tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-72', 'Config', 'link-4');">Config</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Variable Bio.EUtils.Config.databases=Bio.EUtils.Config-module.html#databases"><a title="Bio.EUtils.Config.databases" class="py-name" href="#" onclick="return doclink('link-73', 'databases', 'link-73');">databases</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name" targets="Method Bio.EUtils.Config.DatabaseDict.gettype()=Bio.EUtils.Config.DatabaseDict-class.html#gettype"><a title="Bio.EUtils.Config.DatabaseDict.gettype" class="py-name" href="#" onclick="return doclink('link-74', 'gettype', 'link-74');">gettype</a></tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-75', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">dbtype</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dbtype</tt> <tt class="py-op">==</tt> <tt id="link-76" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-76', 'Config', 'link-4');">Config</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name" targets="Variable Bio.EUtils.Config.SEQUENCE_TYPE=Bio.EUtils.Config-module.html#SEQUENCE_TYPE"><a title="Bio.EUtils.Config.SEQUENCE_TYPE" class="py-name" href="#" onclick="return doclink('link-77', 'SEQUENCE_TYPE', 'link-77');">SEQUENCE_TYPE</a></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">return</tt> <tt id="link-78" class="py-name" targets="Class Bio.EUtils.HistoryClient.SequenceHistoryRecordSet=Bio.EUtils.HistoryClient.SequenceHistoryRecordSet-class.html"><a title="Bio.EUtils.HistoryClient.SequenceHistoryRecordSet" class="py-name" href="#" onclick="return doclink('link-78', 'SequenceHistoryRecordSet', 'link-78');">SequenceHistoryRecordSet</a></tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">dbtype</tt> <tt class="py-op">==</tt> <tt id="link-79" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-79', 'Config', 'link-4');">Config</a></tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Variable Bio.EUtils.Config.PUBLICATION_TYPE=Bio.EUtils.Config-module.html#PUBLICATION_TYPE"><a title="Bio.EUtils.Config.PUBLICATION_TYPE" class="py-name" href="#" onclick="return doclink('link-80', 'PUBLICATION_TYPE', 'link-80');">PUBLICATION_TYPE</a></tt><tt class="py-op">:</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-81" class="py-name" targets="Class Bio.EUtils.HistoryClient.PublicationHistoryRecordSet=Bio.EUtils.HistoryClient.PublicationHistoryRecordSet-class.html"><a title="Bio.EUtils.HistoryClient.PublicationHistoryRecordSet" class="py-name" href="#" onclick="return doclink('link-81', 'PublicationHistoryRecordSet', 'link-81');">PublicationHistoryRecordSet</a></tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"unknown database type: %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">dbtype</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 class="py-keyword">return</tt> <tt class="py-name">Hrec_set</tt><tt class="py-op">,</tt> <tt class="py-name">Hrec</tt> </tt>
</div><a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="HistoryClient"></a><div id="HistoryClient-def"><a name="L307"></a><tt class="py-lineno">307</tt> <a class="py-toggle" href="#" id="HistoryClient-toggle" onclick="return toggle('HistoryClient');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryClient-class.html">HistoryClient</a><tt class="py-op">:</tt> </tt>
</div><div id="HistoryClient-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="HistoryClient-expanded"><a name="HistoryClient.__init__"></a><div id="HistoryClient.__init__-def"><a name="L308"></a><tt class="py-lineno">308</tt> <a class="py-toggle" href="#" id="HistoryClient.__init__-toggle" onclick="return toggle('HistoryClient.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryClient-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">eutils</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HistoryClient.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryClient.__init__-expanded"><a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">eutils</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">eutils</tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="Bio.EUtils.ThinClient
Bio.EUtils.ThinClient.ThinClient" class="py-name" href="#" onclick="return doclink('link-82', 'ThinClient', 'link-0');">ThinClient</a></tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.EUtils.ThinClient
Bio.EUtils.ThinClient.ThinClient" class="py-name" href="#" onclick="return doclink('link-83', 'ThinClient', 'link-0');">ThinClient</a></tt><tt class="py-op">(</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">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt> <tt class="py-op">=</tt> <tt class="py-name">eutils</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">None</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">self</tt><tt class="py-op">.</tt><tt class="py-name">query_history</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> </tt>
<a name="HistoryClient._check_for_cache_reset"></a><div id="HistoryClient._check_for_cache_reset-def"><a name="L315"></a><tt class="py-lineno">315</tt> <a class="py-toggle" href="#" id="HistoryClient._check_for_cache_reset-toggle" onclick="return toggle('HistoryClient._check_for_cache_reset');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryClient-class.html#_check_for_cache_reset">_check_for_cache_reset</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">query_key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HistoryClient._check_for_cache_reset-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryClient._check_for_cache_reset-expanded"><a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-comment"># If this is a repeat then it's because the history</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># has expired. Set the existing results to have a</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># query_key of None and reset the cache.</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">query_key</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">query_history</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-comment"># New value, so there was no reset</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-84" 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-84', 'v', 'link-84');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">query_history</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-85', 'values', 'link-85');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt id="link-86" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-86', 'v', 'link-84');">v</a></tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">query_history</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name" targets="Method Bio.Crystal.Crystal.clear()=Bio.Crystal.Crystal-class.html#clear,Method Bio.GenBank.NCBIDictionary.clear()=Bio.GenBank.NCBIDictionary-class.html#clear,Method Bio.Index._InMemoryIndex.clear()=Bio.Index._InMemoryIndex-class.html#clear,Method Bio.Prosite.ExPASyDictionary.clear()=Bio.Prosite.ExPASyDictionary-class.html#clear,Method Bio.Prosite.Prodoc.ExPASyDictionary.clear()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#clear,Method Bio.PubMed.Dictionary.clear()=Bio.PubMed.Dictionary-class.html#clear,Method Bio.SwissProt.SProt.ExPASyDictionary.clear()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#clear"><a title="Bio.Crystal.Crystal.clear
Bio.GenBank.NCBIDictionary.clear
Bio.Index._InMemoryIndex.clear
Bio.Prosite.ExPASyDictionary.clear
Bio.Prosite.Prodoc.ExPASyDictionary.clear
Bio.PubMed.Dictionary.clear
Bio.SwissProt.SProt.ExPASyDictionary.clear" class="py-name" href="#" onclick="return doclink('link-87', 'clear', 'link-87');">clear</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="HistoryClient.search"></a><div id="HistoryClient.search-def"><a name="L328"></a><tt class="py-lineno">328</tt> <a class="py-toggle" href="#" id="HistoryClient.search-toggle" onclick="return toggle('HistoryClient.search');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryClient-class.html#search">search</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-param">term</tt><tt class="py-op">,</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-param">db</tt> <tt class="py-op">=</tt> <tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-param">field</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-param">daterange</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-param">dbtype</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HistoryClient.search-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryClient.search-expanded"><a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">set_klass</tt> <tt class="py-op">=</tt> <tt id="link-88" class="py-name" targets="Function Bio.EUtils.DBIdsClient._get_recordset_constructor()=Bio.EUtils.DBIdsClient-module.html#_get_recordset_constructor,Function Bio.EUtils.HistoryClient._get_recordset_constructor()=Bio.EUtils.HistoryClient-module.html#_get_recordset_constructor"><a title="Bio.EUtils.DBIdsClient._get_recordset_constructor
Bio.EUtils.HistoryClient._get_recordset_constructor" class="py-name" href="#" onclick="return doclink('link-88', '_get_recordset_constructor', 'link-88');">_get_recordset_constructor</a></tt><tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-89', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">dbtype</tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.esearch()=Bio.EUtils.ThinClient.ThinClient-class.html#esearch,Function Bio.Entrez.esearch()=Bio.Entrez-module.html#esearch,Function Bio.WWW.NCBI.esearch()=Bio.WWW.NCBI-module.html#esearch"><a title="Bio.EUtils.ThinClient.ThinClient.esearch
Bio.Entrez.esearch
Bio.WWW.NCBI.esearch" class="py-name" href="#" onclick="return doclink('link-90', 'esearch', 'link-90');">esearch</a></tt><tt class="py-op">(</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</tt><tt class="py-op">,</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt id="link-91" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-91', 'db', 'link-5');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-92" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-92', 'db', 'link-5');">db</a></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">field</tt> <tt class="py-op">=</tt> <tt class="py-name">field</tt><tt class="py-op">,</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-number">0</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">retmax</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-name">daterange</tt> <tt class="py-op">=</tt> <tt class="py-name">daterange</tt><tt class="py-op">,</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-name">usehistory</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-name">webenv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">[</tt><tt class="py-number">0</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-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-name">searchinfo</tt> <tt class="py-op">=</tt> <tt id="link-93" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-93', 'parse', 'link-1');">parse</a></tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Function Bio.EUtils.parse.parse_search()=Bio.EUtils.parse-module.html#parse_search"><a title="Bio.EUtils.parse.parse_search" class="py-name" href="#" onclick="return doclink('link-94', 'parse_search', 'link-94');">parse_search</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">searchinfo</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-name">cookie</tt> <tt class="py-op">=</tt> <tt id="link-95" class="py-name" targets="Class Bio.EUtils.HistoryClient.HistoryCookie=Bio.EUtils.HistoryClient.HistoryCookie-class.html"><a title="Bio.EUtils.HistoryClient.HistoryCookie" class="py-name" href="#" onclick="return doclink('link-95', 'HistoryCookie', 'link-95');">HistoryCookie</a></tt><tt class="py-op">(</tt><tt id="link-96" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-96', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">,</tt> <tt class="py-name">searchinfo</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">)</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">searchinfo</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-97', 'count', 'link-97');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-name">cookie</tt> <tt class="py-op">=</tt> <tt id="link-98" class="py-name"><a title="Bio.EUtils.HistoryClient.HistoryCookie" class="py-name" href="#" onclick="return doclink('link-98', 'HistoryCookie', 'link-95');">HistoryCookie</a></tt><tt class="py-op">(</tt><tt id="link-99" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-99', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">recordset</tt> <tt class="py-op">=</tt> <tt class="py-name">set_klass</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt class="py-name">cookie</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">searchinfo</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-100', 'count', 'link-97');">count</a></tt><tt class="py-op">,</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">searchinfo</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-comment"># won't have a query_key if the search turned up empty</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">searchinfo</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</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">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name" targets="Method Bio.EUtils.HistoryClient.HistoryClient._check_for_cache_reset()=Bio.EUtils.HistoryClient.HistoryClient-class.html#_check_for_cache_reset"><a title="Bio.EUtils.HistoryClient.HistoryClient._check_for_cache_reset" class="py-name" href="#" onclick="return doclink('link-101', '_check_for_cache_reset', 'link-101');">_check_for_cache_reset</a></tt><tt class="py-op">(</tt><tt class="py-name">searchinfo</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">query_history</tt><tt class="py-op">[</tt><tt class="py-name">searchinfo</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">recordset</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">recordset</tt> </tt>
</div><a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> </tt>
<a name="HistoryClient.post"></a><div id="HistoryClient.post-def"><a name="L368"></a><tt class="py-lineno">368</tt> <a class="py-toggle" href="#" id="HistoryClient.post-toggle" onclick="return toggle('HistoryClient.post');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.HistoryClient.HistoryClient-class.html#post">post</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbids</tt><tt class="py-op">,</tt> <tt class="py-param">dbtype</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HistoryClient.post-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HistoryClient.post-expanded"><a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-name">set_klass</tt> <tt class="py-op">=</tt> <tt id="link-102" class="py-name"><a title="Bio.EUtils.DBIdsClient._get_recordset_constructor
Bio.EUtils.HistoryClient._get_recordset_constructor" class="py-name" href="#" onclick="return doclink('link-102', '_get_recordset_constructor', 'link-88');">_get_recordset_constructor</a></tt><tt class="py-op">(</tt><tt id="link-103" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-103', 'dbids', 'link-31');">dbids</a></tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-104', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">dbtype</tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.epost()=Bio.EUtils.ThinClient.ThinClient-class.html#epost,Function Bio.Entrez.epost()=Bio.Entrez-module.html#epost,Function Bio.WWW.NCBI.epost()=Bio.WWW.NCBI-module.html#epost"><a title="Bio.EUtils.ThinClient.ThinClient.epost
Bio.Entrez.epost
Bio.WWW.NCBI.epost" class="py-name" href="#" onclick="return doclink('link-105', 'epost', 'link-105');">epost</a></tt><tt class="py-op">(</tt><tt id="link-106" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-106', 'dbids', 'link-31');">dbids</a></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">webenv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">[</tt><tt class="py-number">0</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-comment"># Extract the webenv_ref since it may change.</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">postinfo</tt> <tt class="py-op">=</tt> <tt id="link-107" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-107', 'parse', 'link-1');">parse</a></tt><tt class="py-op">.</tt><tt id="link-108" class="py-name" targets="Function Bio.EUtils.parse.parse_post()=Bio.EUtils.parse-module.html#parse_post"><a title="Bio.EUtils.parse.parse_post" class="py-name" href="#" onclick="return doclink('link-108', 'parse_post', 'link-108');">parse_post</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">)</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-comment"># Were there any invalid identifiers?</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-109" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-109', 'dbids', 'link-31');">dbids</a></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">postinfo</tt><tt class="py-op">.</tt><tt class="py-name">invalid_ids</tt><tt class="py-op">)</tt> </tt>
<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-name">cookie</tt> <tt class="py-op">=</tt> <tt id="link-110" class="py-name"><a title="Bio.EUtils.HistoryClient.HistoryCookie" class="py-name" href="#" onclick="return doclink('link-110', 'HistoryCookie', 'link-95');">HistoryCookie</a></tt><tt class="py-op">(</tt><tt id="link-111" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-111', 'dbids', 'link-31');">dbids</a></tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-112', 'db', 'link-5');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">webenv_ref</tt><tt class="py-op">,</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">postinfo</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">)</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-name">recordset</tt> <tt class="py-op">=</tt> <tt class="py-name">set_klass</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt class="py-name">cookie</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt> <tt class="py-name">postinfo</tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.EUtils.HistoryClient.HistoryClient._check_for_cache_reset" class="py-name" href="#" onclick="return doclink('link-113', '_check_for_cache_reset', 'link-101');">_check_for_cache_reset</a></tt><tt class="py-op">(</tt><tt class="py-name">postinfo</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">)</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">query_history</tt><tt class="py-op">[</tt><tt class="py-name">postinfo</tt><tt class="py-op">.</tt><tt class="py-name">query_key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">recordset</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">recordset</tt> </tt>
</div><a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt id="link-114" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.from_dbids()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#from_dbids,Function Bio.EUtils.DBIdsClient.from_dbids()=Bio.EUtils.DBIdsClient-module.html#from_dbids"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.from_dbids
Bio.EUtils.DBIdsClient.from_dbids" class="py-name" href="#" onclick="return doclink('link-114', 'from_dbids', 'link-114');">from_dbids</a></tt> <tt class="py-op">=</tt> <tt id="link-115" class="py-name" targets="Method Bio.EUtils.HistoryClient.HistoryClient.post()=Bio.EUtils.HistoryClient.HistoryClient-class.html#post"><a title="Bio.EUtils.HistoryClient.HistoryClient.post" class="py-name" href="#" onclick="return doclink('link-115', 'post', 'link-115');">post</a></tt> <tt class="py-comment"># alias for similarity to DBIdsClient</tt> </tt>
</div><a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt><script type="text/javascript">
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