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<a href="Bio-module.html">Package Bio</a> ::
Module pairwise2
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<h1 class="epydoc">Source Code for <a href="Bio.pairwise2-module.html">Module Bio.pairwise2</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2002 by Jeffrey Chang. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""This package implements pairwise sequence alignment using a dynamic</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">programming algorithm.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">This provides functions to get global and local alignments between two</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">sequences. A global alignment finds the best concordance between all</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">characters in two sequences. A local alignment finds just the</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">subsequences that align the best.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">When doing alignments, you can specify the match score and gap</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">penalties. The match score indicates the compatibility between an</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">alignment of two characters in the sequences. Highly compatible</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">characters should be given positive scores, and incompatible ones</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">should be given negative scores or 0. The gap penalties should be</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">negative.</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">The names of the alignment functions in this module follow the</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">convention</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"><alignment type>XX</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">where <alignment type> is either "global" or "local" and XX is a 2</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">character code indicating the parameters it takes. The first</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">character indicates the parameters for matches (and mismatches), and</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">the second indicates the parameters for gap penalties.</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">The match parameters are</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">CODE DESCRIPTION</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">x No parameters. Identical characters have score of 1, otherwise 0.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">m A match score is the score of identical chars, otherwise mismatch score.</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring">d A dictionary returns the score of any pair of characters.</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring">c A callback function returns scores.</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring">The gap penalty parameters are</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring">CODE DESCRIPTION</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring">x No gap penalties.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring">s Same open and extend gap penalties for both sequences.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring">d The sequences have different open and extend gap penalties.</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring">c A callback function returns the gap penalties.</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring">All the different alignment functions are contained in an object</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring">"align". For example:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import pairwise2</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> >>> alignments = pairwise2.align.globalxx("ACCGT", "ACG")</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring">will return a list of the alignments between the two strings. The</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring">parameters of the alignment function depends on the function called.</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring">Some examples:</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">>>> pairwise2.align.globalxx("ACCGT", "ACG")</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> # Find the best global alignment between the two sequences.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> # Identical characters are given 1 point. No points are deducted</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> # for mismatches or gaps.</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring">>>> pairwise2.align.localxx("ACCGT", "ACG")</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> # Same thing as before, but with a local alignment.</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring">>>> pairwise2.align.globalmx("ACCGT", "ACG", 2, -1)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> # Do a global alignment. Identical characters are given 2 points,</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> # 1 point is deducted for each non-identical character.</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring">>>> pairwise2.align.globalms("ACCGT", "ACG", 2, -1, -.5, -.1)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> # Same as above, except now 0.5 points are deducted when opening a</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> # gap, and 0.1 points are deducted when extending it.</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring">To see a description of the parameters for a function, please look at</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring">the docstring for the function.</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring">>>> print newalign.align.localds.__doc__</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring">localds(sequenceA, sequenceB, match_dict, open, extend) -> alignments</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-comment"># The alignment functions take some undocumented keyword parameters:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - penalize_extend_when_opening: boolean</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Whether to count an extension penalty when opening a gap. If</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># false, a gap of 1 is only penalize an "open" penalty, otherwise it</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># is penalized "open+extend".</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - penalize_end_gaps: boolean</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Whether to count the gaps at the ends of an alignment. By</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># default, they are counted for global alignments but not for local</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># ones.</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - gap_char: string</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Which character to use as a gap character in the alignment</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># returned. By default, uses '-'.</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - force_generic: boolean</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Always use the generic, non-cached, dynamic programming function.</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># For debugging.</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - score_only: boolean</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Only get the best score, don't recover any alignments. The return</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># value of the function is the score.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - one_alignment_only: boolean</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Only recover one alignment.</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">types</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.listfns=Bio.listfns-module.html"><a title="Bio.listfns" class="py-name" href="#" onclick="return doclink('link-1', 'listfns', 'link-1');">listfns</a></tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable Bio.pairwise2.MAX_ALIGNMENTS=Bio.pairwise2-module.html#MAX_ALIGNMENTS"><a title="Bio.pairwise2.MAX_ALIGNMENTS" class="py-name" href="#" onclick="return doclink('link-2', 'MAX_ALIGNMENTS', 'link-2');">MAX_ALIGNMENTS</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1000</tt> <tt class="py-comment"># maximum alignments recovered in traceback</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
<a name="align"></a><div id="align-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="align-toggle" onclick="return toggle('align');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.pairwise2.align-class.html">align</a><tt class="py-op">:</tt> </tt>
</div><div id="align-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="align-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-docstring">"""This class provides functions that do alignments."""</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="align.alignment_function"></a><div id="align.alignment_function-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="align.alignment_function-toggle" onclick="return toggle('align.alignment_function');">-</a><tt class="py-line"> <tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.pairwise2.align.alignment_function-class.html">alignment_function</a><tt class="py-op">:</tt> </tt>
</div><div id="align.alignment_function-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="align.alignment_function-expanded"><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-docstring">"""This class is callable impersonates an alignment function.</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> The constructor takes the name of the function. This class</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> will decode the name of the function to figure out how to</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> interpret the parameters.</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-comment"># match code -> tuple of (parameters, docstring)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">match2args</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-string">'x'</tt> <tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-string">'m'</tt> <tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'match'</tt><tt class="py-op">,</tt> <tt class="py-string">'mismatch'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-string">"""match is the score to given to identical characters. mismatch is</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-string">the score given to non-identical ones."""</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-string">'d'</tt> <tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'match_dict'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-string">"""match_dict is a dictionary where the keys are tuples of pairs of</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-string">characters and the values are the scores, e.g. ("A", "C") : 2.5."""</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-string">'c'</tt> <tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'match_fn'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-string">"""match_fn is a callback function that takes two characters and</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-string">returns the score between them."""</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-comment"># penalty code -> tuple of (parameters, docstring)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">penalty2args</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-string">'x'</tt> <tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-string">'s'</tt> <tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'open'</tt><tt class="py-op">,</tt> <tt class="py-string">'extend'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-string">"""open and extend are the gap penalties when a gap is opened and</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-string">extended. They should be negative."""</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-string">'d'</tt> <tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'openA'</tt><tt class="py-op">,</tt> <tt class="py-string">'extendA'</tt><tt class="py-op">,</tt> <tt class="py-string">'openB'</tt><tt class="py-op">,</tt> <tt class="py-string">'extendB'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-string">"""openA and extendA are the gap penalties for sequenceA, and openB</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-string">and extendB for sequeneB. The penalties should be negative."""</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-string">'c'</tt> <tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'gap_A_fn'</tt><tt class="py-op">,</tt> <tt class="py-string">'gap_B_fn'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-string">"""gap_A_fn and gap_B_fn are callback functions that takes 1) the</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-string">index where the gap is opened, and 2) the length of the gap. They</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-string">should return a gap penalty."""</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="align.alignment_function.__init__"></a><div id="align.alignment_function.__init__-def"><a name="L142"></a><tt class="py-lineno">142</tt> <a class="py-toggle" href="#" id="align.alignment_function.__init__-toggle" onclick="return toggle('align.alignment_function.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.align.alignment_function-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="align.alignment_function.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="align.alignment_function.__init__-expanded"><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-comment"># Check to make sure the name of the function is</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># reasonable.</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-3" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-3', 'name', 'link-3');">name</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"global"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-4" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-4', 'name', 'link-3');">name</a></tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">8</tt><tt class="py-op">:</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">,</tt> <tt class="py-string">"function should be globalXX"</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-5" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-5', 'name', 'link-3');">name</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"local"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-6', 'name', 'link-3');">name</a></tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">7</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">,</tt> <tt class="py-string">"function should be localXX"</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">,</tt> <tt id="link-7" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-3');">name</a></tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">align_type</tt><tt class="py-op">,</tt> <tt class="py-name">match_type</tt><tt class="py-op">,</tt> <tt class="py-name">penalty_type</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt id="link-8" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-8', 'name', 'link-3');">name</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-9" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-9', 'name', 'link-3');">name</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-10" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-3');">name</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</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">try</tt><tt class="py-op">:</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">match_args</tt><tt class="py-op">,</tt> <tt class="py-name">match_doc</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">match2args</tt><tt class="py-op">[</tt><tt class="py-name">match_type</tt><tt class="py-op">]</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt id="link-11" 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-11', 'x', 'link-11');">x</a></tt><tt class="py-op">:</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">,</tt> <tt class="py-string">"unknown match type %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">match_type</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">penalty_args</tt><tt class="py-op">,</tt> <tt class="py-name">penalty_doc</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">penalty2args</tt><tt class="py-op">[</tt><tt class="py-name">penalty_type</tt><tt class="py-op">]</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-12', 'x', 'link-11');">x</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-keyword">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">,</tt> <tt class="py-string">"unknown penalty type %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">penalty_type</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-comment"># Now get the names of the parameters to this function.</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">param_names</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'sequenceA'</tt><tt class="py-op">,</tt> <tt class="py-string">'sequenceB'</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">param_names</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-13', 'extend', 'link-13');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">match_args</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">param_names</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-14', 'extend', 'link-13');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">penalty_args</tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">function_name</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-15', 'name', 'link-3');">name</a></tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">align_type</tt> <tt class="py-op">=</tt> <tt class="py-name">align_type</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt> <tt class="py-op">=</tt> <tt class="py-name">param_names</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">function_name</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-comment"># Set the doc string.</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">doc</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s(%s) -> alignments\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> <tt class="py-string">', '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">match_doc</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">doc</tt> <tt class="py-op">+=</tt> <tt class="py-string">"\n%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">match_doc</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">penalty_doc</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">doc</tt> <tt class="py-op">+=</tt> <tt class="py-string">"\n%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">penalty_doc</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">doc</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-string">"""\nalignments is a list of tuples (seqA, seqB, score, begin, end).</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-string">seqA and seqB are strings showing the alignment between the</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-string">sequences. score is the score of the alignment. begin and end</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-string">are indexes into seqA and seqB that indicate the where the</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-string">alignment occurs.</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-string">"""</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">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-16', '__doc__', 'link-16');">__doc__</a></tt> <tt class="py-op">=</tt> <tt class="py-name">doc</tt> </tt>
</div><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> </tt>
<a name="align.alignment_function.decode"></a><div id="align.alignment_function.decode-def"><a name="L189"></a><tt class="py-lineno">189</tt> <a class="py-toggle" href="#" id="align.alignment_function.decode-toggle" onclick="return toggle('align.alignment_function.decode');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.align.alignment_function-class.html#decode">decode</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="align.alignment_function.decode-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="align.alignment_function.decode-expanded"><a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-comment"># Decode the arguments for the _align function. keywds</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># will get passed to it, so translate the arguments to</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># this function into forms appropriate for _align.</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">keywds</tt> <tt class="py-op">=</tt> <tt class="py-name">keywds</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-17', 'copy', 'link-17');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">args</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">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</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">"%s takes exactly %d argument (%d given)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">function_name</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</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">args</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt id="link-18" 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-18', 'i', 'link-18');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-19" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-19', 'i', 'link-18');">i</a></tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</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">param_names</tt><tt class="py-op">[</tt><tt id="link-20" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-20', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-string">'sequenceA'</tt><tt class="py-op">,</tt> <tt class="py-string">'sequenceB'</tt><tt class="py-op">,</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-string">'gap_A_fn'</tt><tt class="py-op">,</tt> <tt class="py-string">'gap_B_fn'</tt><tt class="py-op">,</tt> <tt class="py-string">'match_fn'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">keywds</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">[</tt><tt id="link-21" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-21', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt id="link-22" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-22', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt id="link-23" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-23', 'i', 'link-18');">i</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">[</tt><tt id="link-24" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-24', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'match'</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">[</tt><tt id="link-25" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-25', 'i', 'link-18');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'mismatch'</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt id="link-26" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-26', 'match', 'link-26');">match</a></tt><tt class="py-op">,</tt> <tt class="py-name">mismatch</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt id="link-28" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-28', 'i', 'link-18');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">keywds</tt><tt class="py-op">[</tt><tt class="py-string">'match_fn'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name" targets="Class Bio.pairwise2.identity_match=Bio.pairwise2.identity_match-class.html"><a title="Bio.pairwise2.identity_match" class="py-name" href="#" onclick="return doclink('link-29', 'identity_match', 'link-29');">identity_match</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-30', 'match', 'link-26');">match</a></tt><tt class="py-op">,</tt> <tt class="py-name">mismatch</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-31', 'i', 'link-18');">i</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">2</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">[</tt><tt id="link-32" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-32', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'match_dict'</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">keywds</tt><tt class="py-op">[</tt><tt class="py-string">'match_fn'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name" targets="Class Bio.pairwise2.dictionary_match=Bio.pairwise2.dictionary_match-class.html"><a title="Bio.pairwise2.dictionary_match" class="py-name" href="#" onclick="return doclink('link-33', 'dictionary_match', 'link-33');">dictionary_match</a></tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt id="link-34" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-34', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt id="link-35" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-35', 'i', 'link-18');">i</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">[</tt><tt id="link-36" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-36', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'open'</tt><tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">[</tt><tt id="link-37" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-37', 'i', 'link-18');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'extend'</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt id="link-38" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-38', 'open', 'link-38');">open</a></tt><tt class="py-op">,</tt> <tt id="link-39" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-39', 'extend', 'link-13');">extend</a></tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt id="link-40" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-40', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt id="link-41" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-41', 'i', 'link-18');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">pe</tt> <tt class="py-op">=</tt> <tt class="py-name">keywds</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-42', 'get', 'link-42');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'penalize_extend_when_opening'</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">keywds</tt><tt class="py-op">[</tt><tt class="py-string">'gap_A_fn'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name" targets="Class Bio.pairwise2.affine_penalty=Bio.pairwise2.affine_penalty-class.html"><a title="Bio.pairwise2.affine_penalty" class="py-name" href="#" onclick="return doclink('link-43', 'affine_penalty', 'link-43');">affine_penalty</a></tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-44', 'open', 'link-38');">open</a></tt><tt class="py-op">,</tt> <tt id="link-45" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-45', 'extend', 'link-13');">extend</a></tt><tt class="py-op">,</tt> <tt class="py-name">pe</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">keywds</tt><tt class="py-op">[</tt><tt class="py-string">'gap_B_fn'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio.pairwise2.affine_penalty" class="py-name" href="#" onclick="return doclink('link-46', 'affine_penalty', 'link-43');">affine_penalty</a></tt><tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-47', 'open', 'link-38');">open</a></tt><tt class="py-op">,</tt> <tt id="link-48" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-48', 'extend', 'link-13');">extend</a></tt><tt class="py-op">,</tt> <tt class="py-name">pe</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt id="link-49" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-49', 'i', 'link-18');">i</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">2</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-50', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'openA'</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</tt><tt class="py-op">[</tt><tt id="link-51" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-51', 'i', 'link-18');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'extendB'</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">openA</tt><tt class="py-op">,</tt> <tt class="py-name">extendA</tt><tt class="py-op">,</tt> <tt class="py-name">openB</tt><tt class="py-op">,</tt> <tt class="py-name">extendB</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</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-18');">i</a></tt><tt class="py-op">:</tt><tt id="link-53" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-53', 'i', 'link-18');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">4</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">pe</tt> <tt class="py-op">=</tt> <tt class="py-name">keywds</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-54', 'get', 'link-42');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'penalize_extend_when_opening'</tt><tt class="py-op">,</tt> <tt class="py-number">0</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">keywds</tt><tt class="py-op">[</tt><tt class="py-string">'gap_A_fn'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name"><a title="Bio.pairwise2.affine_penalty" class="py-name" href="#" onclick="return doclink('link-55', 'affine_penalty', 'link-43');">affine_penalty</a></tt><tt class="py-op">(</tt><tt class="py-name">openA</tt><tt class="py-op">,</tt> <tt class="py-name">extendA</tt><tt class="py-op">,</tt> <tt class="py-name">pe</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">keywds</tt><tt class="py-op">[</tt><tt class="py-string">'gap_B_fn'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="Bio.pairwise2.affine_penalty" class="py-name" href="#" onclick="return doclink('link-56', 'affine_penalty', 'link-43');">affine_penalty</a></tt><tt class="py-op">(</tt><tt class="py-name">openB</tt><tt class="py-op">,</tt> <tt class="py-name">extendB</tt><tt class="py-op">,</tt> <tt class="py-name">pe</tt><tt class="py-op">)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-57', 'i', 'link-18');">i</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">4</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"unknown parameter %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_names</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-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-comment"># Here are the default parameters for _align. Assign</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># these to keywds, unless already specified.</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">pe</tt> <tt class="py-op">=</tt> <tt class="py-name">keywds</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-59', 'get', 'link-42');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'penalize_extend_when_opening'</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">default_params</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'match_fn'</tt><tt class="py-op">,</tt> <tt id="link-60" class="py-name"><a title="Bio.pairwise2.identity_match" class="py-name" href="#" onclick="return doclink('link-60', 'identity_match', 'link-29');">identity_match</a></tt><tt class="py-op">(</tt><tt class="py-number">1</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-op">,</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'gap_A_fn'</tt><tt class="py-op">,</tt> <tt id="link-61" class="py-name"><a title="Bio.pairwise2.affine_penalty" class="py-name" href="#" onclick="return doclink('link-61', 'affine_penalty', 'link-43');">affine_penalty</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">pe</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'gap_B_fn'</tt><tt class="py-op">,</tt> <tt id="link-62" class="py-name"><a title="Bio.pairwise2.affine_penalty" class="py-name" href="#" onclick="return doclink('link-62', 'affine_penalty', 'link-43');">affine_penalty</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">pe</tt><tt class="py-op">)</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-op">(</tt><tt class="py-string">'penalize_extend_when_opening'</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="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'penalize_end_gaps'</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">align_type</tt> <tt class="py-op">==</tt> <tt class="py-string">'global'</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 class="py-op">(</tt><tt class="py-string">'align_globally'</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">align_type</tt> <tt class="py-op">==</tt> <tt class="py-string">'global'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'gap_char'</tt><tt class="py-op">,</tt> <tt class="py-string">'-'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'force_generic'</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="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'score_only'</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="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'one_alignment_only'</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-op">]</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-63" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-63', 'name', 'link-3');">name</a></tt><tt class="py-op">,</tt> <tt id="link-64" class="py-name" targets="Method Bio.Parsers.spark.GenericASTTraversal.default()=Bio.Parsers.spark.GenericASTTraversal-class.html#default"><a title="Bio.Parsers.spark.GenericASTTraversal.default" class="py-name" href="#" onclick="return doclink('link-64', 'default', 'link-64');">default</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">default_params</tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">keywds</tt><tt class="py-op">[</tt><tt id="link-65" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-65', 'name', 'link-3');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">keywds</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-66', 'get', 'link-42');">get</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-67', 'name', 'link-3');">name</a></tt><tt class="py-op">,</tt> <tt id="link-68" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversal.default" class="py-name" href="#" onclick="return doclink('link-68', 'default', 'link-64');">default</a></tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">keywds</tt> </tt>
</div><a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> </tt>
<a name="align.alignment_function.__call__"></a><div id="align.alignment_function.__call__-def"><a name="L249"></a><tt class="py-lineno">249</tt> <a class="py-toggle" href="#" id="align.alignment_function.__call__-toggle" onclick="return toggle('align.alignment_function.__call__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.align.alignment_function-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="align.alignment_function.__call__-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="align.alignment_function.__call__-expanded"><a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">keywds</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">decode</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-69" class="py-name" targets="Function Bio.pairwise2._align()=Bio.pairwise2-module.html#_align"><a title="Bio.pairwise2._align" class="py-name" href="#" onclick="return doclink('link-69', '_align', 'link-69');">_align</a></tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt>
<a name="align.__getattr__"></a><div id="align.__getattr__-def"><a name="L253"></a><tt class="py-lineno">253</tt> <a class="py-toggle" href="#" id="align.__getattr__-toggle" onclick="return toggle('align.__getattr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.align-class.html#__getattr__">__getattr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="align.__getattr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="align.__getattr__-expanded"><a name="L254"></a><tt class="py-lineno">254</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">alignment_function</tt><tt class="py-op">(</tt><tt class="py-name">attr</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt id="link-70" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.align()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#align,Class Bio.FSSP.fssp_rec.align=Bio.FSSP.fssp_rec.align-class.html,Function Bio.Wise.align()=Bio.Wise-module.html#align,Function Bio.Wise.dnal.align()=Bio.Wise.dnal-module.html#align,Function Bio.Wise.psw.align()=Bio.Wise.psw-module.html#align,Variable Bio.pairwise2.align=Bio.pairwise2-module.html#align"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-70', 'align', 'link-70');">align</a></tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-71', 'align', 'link-70');">align</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> </tt>
<a name="_align"></a><div id="_align-def"><a name="L258"></a><tt class="py-lineno">258</tt> <a class="py-toggle" href="#" id="_align-toggle" onclick="return toggle('_align');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_align">_align</a><tt class="py-op">(</tt><tt class="py-param">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-param">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-param">match_fn</tt><tt class="py-op">,</tt> <tt class="py-param">gap_A_fn</tt><tt class="py-op">,</tt> <tt class="py-param">gap_B_fn</tt><tt class="py-op">,</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-param">penalize_extend_when_opening</tt><tt class="py-op">,</tt> <tt class="py-param">penalize_end_gaps</tt><tt class="py-op">,</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-param">align_globally</tt><tt class="py-op">,</tt> <tt class="py-param">gap_char</tt><tt class="py-op">,</tt> <tt class="py-param">force_generic</tt><tt class="py-op">,</tt> <tt class="py-param">score_only</tt><tt class="py-op">,</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-param">one_alignment_only</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_align-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_align-expanded"><a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">sequenceA</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">:</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-name">force_generic</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt id="link-72" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-72', 'type', 'link-72');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">gap_A_fn</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">InstanceType</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">gap_A_fn</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt> <tt class="py-keyword">is</tt> <tt id="link-73" class="py-name"><a title="Bio.pairwise2.affine_penalty" class="py-name" href="#" onclick="return doclink('link-73', 'affine_penalty', 'link-43');">affine_penalty</a></tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt id="link-74" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-74', 'type', 'link-72');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">gap_B_fn</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">InstanceType</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">gap_B_fn</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt> <tt class="py-keyword">is</tt> <tt id="link-75" class="py-name"><a title="Bio.pairwise2.affine_penalty" class="py-name" href="#" onclick="return doclink('link-75', 'affine_penalty', 'link-43');">affine_penalty</a></tt><tt class="py-op">:</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">open_A</tt><tt class="py-op">,</tt> <tt class="py-name">extend_A</tt> <tt class="py-op">=</tt> <tt class="py-name">gap_A_fn</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-76', 'open', 'link-38');">open</a></tt><tt class="py-op">,</tt> <tt class="py-name">gap_A_fn</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-77', 'extend', 'link-13');">extend</a></tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">open_B</tt><tt class="py-op">,</tt> <tt class="py-name">extend_B</tt> <tt class="py-op">=</tt> <tt class="py-name">gap_B_fn</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-78', 'open', 'link-38');">open</a></tt><tt class="py-op">,</tt> <tt class="py-name">gap_B_fn</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-79', 'extend', 'link-13');">extend</a></tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt id="link-80" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-80', 'x', 'link-11');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name" targets="Function Bio.pairwise2._make_score_matrix_fast()=Bio.pairwise2-module.html#_make_score_matrix_fast"><a title="Bio.pairwise2._make_score_matrix_fast" class="py-name" href="#" onclick="return doclink('link-81', '_make_score_matrix_fast', 'link-81');">_make_score_matrix_fast</a></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">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-name">match_fn</tt><tt class="py-op">,</tt> <tt class="py-name">open_A</tt><tt class="py-op">,</tt> <tt class="py-name">extend_A</tt><tt class="py-op">,</tt> <tt class="py-name">open_B</tt><tt class="py-op">,</tt> <tt class="py-name">extend_B</tt><tt class="py-op">,</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">penalize_extend_when_opening</tt><tt class="py-op">,</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">,</tt> <tt class="py-name">align_globally</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">score_only</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt id="link-82" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-82', 'x', 'link-11');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-83" class="py-name" targets="Function Bio.pairwise2._make_score_matrix_generic()=Bio.pairwise2-module.html#_make_score_matrix_generic"><a title="Bio.pairwise2._make_score_matrix_generic" class="py-name" href="#" onclick="return doclink('link-83', '_make_score_matrix_generic', 'link-83');">_make_score_matrix_generic</a></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">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-name">match_fn</tt><tt class="py-op">,</tt> <tt class="py-name">gap_A_fn</tt><tt class="py-op">,</tt> <tt class="py-name">gap_B_fn</tt><tt class="py-op">,</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">penalize_extend_when_opening</tt><tt class="py-op">,</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">,</tt> <tt class="py-name">align_globally</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">score_only</tt><tt class="py-op">)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-name">trace_matrix</tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-84', 'x', 'link-11');">x</a></tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-comment">#print "SCORE"; print_matrix(score_matrix)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print "TRACEBACK"; print_matrix(trace_matrix)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-comment"># Look for the proper starting point. Get a list of all possible</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># starting points.</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">starts</tt> <tt class="py-op">=</tt> <tt id="link-85" class="py-name" targets="Function Bio.pairwise2._find_start()=Bio.pairwise2-module.html#_find_start"><a title="Bio.pairwise2._find_start" class="py-name" href="#" onclick="return doclink('link-85', '_find_start', 'link-85');">_find_start</a></tt><tt class="py-op">(</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">,</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">gap_A_fn</tt><tt class="py-op">,</tt> <tt class="py-name">gap_B_fn</tt><tt class="py-op">,</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">,</tt> <tt class="py-name">align_globally</tt><tt class="py-op">)</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-comment"># Find the highest score.</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">best_score</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-86" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-86', 'x', 'link-11');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-87" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-87', 'x', 'link-11');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">starts</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-comment"># If they only want the score, then return it.</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">score_only</tt><tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">best_score</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">tolerance</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># XXX do anything with this?</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-comment"># Now find all the positions within some tolerance of the best</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># score.</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-88" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-88', 'i', 'link-18');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-89" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-89', 'i', 'link-18');">i</a></tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">starts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt id="link-90" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.score()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#score,Variable Bio.expressions.blast.ncbiblast.score=Bio.expressions.blast.ncbiblast-module.html#score"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-90', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">starts</tt><tt class="py-op">[</tt><tt id="link-91" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-91', 'i', 'link-18');">i</a></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">if</tt> <tt id="link-92" class="py-name" targets="Function Bio.pairwise2.rint()=Bio.pairwise2-module.html#rint"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-92', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt id="link-93" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.abs()=Bio.FSSP.FSSPAlignDict-class.html#abs"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-93', 'abs', 'link-93');">abs</a></tt><tt class="py-op">(</tt><tt id="link-94" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-94', 'score', 'link-90');">score</a></tt><tt class="py-op">-</tt><tt class="py-name">best_score</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt id="link-95" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-95', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">tolerance</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">del</tt> <tt class="py-name">starts</tt><tt class="py-op">[</tt><tt id="link-96" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-96', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt id="link-97" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-97', 'i', 'link-18');">i</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-comment"># Recover the alignments and return them.</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-98" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-98', 'x', 'link-11');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-99" class="py-name" targets="Function Bio.pairwise2._recover_alignments()=Bio.pairwise2-module.html#_recover_alignments"><a title="Bio.pairwise2._recover_alignments" class="py-name" href="#" onclick="return doclink('link-99', '_recover_alignments', 'link-99');">_recover_alignments</a></tt><tt class="py-op">(</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-name">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-name">starts</tt><tt class="py-op">,</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-name">trace_matrix</tt><tt class="py-op">,</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">align_globally</tt><tt class="py-op">,</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">,</tt> <tt class="py-name">gap_char</tt><tt class="py-op">,</tt> <tt class="py-name">one_alignment_only</tt><tt class="py-op">)</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-100" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-100', 'x', 'link-11');">x</a></tt> </tt>
</div><a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> </tt>
<a name="_make_score_matrix_generic"></a><div id="_make_score_matrix_generic-def"><a name="L315"></a><tt class="py-lineno">315</tt> <a class="py-toggle" href="#" id="_make_score_matrix_generic-toggle" onclick="return toggle('_make_score_matrix_generic');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_make_score_matrix_generic">_make_score_matrix_generic</a><tt class="py-op">(</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-param">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-param">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-param">match_fn</tt><tt class="py-op">,</tt> <tt class="py-param">gap_A_fn</tt><tt class="py-op">,</tt> <tt class="py-param">gap_B_fn</tt><tt class="py-op">,</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-param">penalize_extend_when_opening</tt><tt class="py-op">,</tt> <tt class="py-param">penalize_end_gaps</tt><tt class="py-op">,</tt> <tt class="py-param">align_globally</tt><tt class="py-op">,</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-param">score_only</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_make_score_matrix_generic-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_make_score_matrix_generic-expanded"><a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-comment"># This is an implementation of the Needleman-Wunsch dynamic</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># programming algorithm for aligning sequences.</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-comment"># Create the score and traceback matrices. These should be in the</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># shape:</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequenceA (down) x sequenceB (across)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">lenA</tt><tt class="py-op">,</tt> <tt class="py-name">lenB</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sequenceA</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">sequenceB</tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-name">trace_matrix</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-101" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-101', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">lenA</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-102', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">lenB</tt><tt class="py-op">)</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">trace_matrix</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-103', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">lenB</tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-comment"># The top and left borders of the matrices are special cases</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># because there are no previously aligned characters. To simplify</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the main loop, handle these separately.</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-104" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-104', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">lenA</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-comment"># Align the first residue in sequenceB to the ith residue in</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequence A. This is like opening up i gaps at the beginning</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># of sequence B.</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-105" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-105', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">match_fn</tt><tt class="py-op">(</tt><tt class="py-name">sequenceA</tt><tt class="py-op">[</tt><tt id="link-106" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-106', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</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="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">:</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt id="link-107" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-107', 'score', 'link-90');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">gap_B_fn</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-108" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-108', 'i', 'link-18');">i</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">score_matrix</tt><tt class="py-op">[</tt><tt id="link-109" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-109', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-110" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-110', 'score', 'link-90');">score</a></tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-111" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-111', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">lenB</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt id="link-112" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-112', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">match_fn</tt><tt class="py-op">(</tt><tt class="py-name">sequenceA</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">[</tt><tt id="link-113" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-113', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">:</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt id="link-114" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-114', 'score', 'link-90');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">gap_A_fn</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-115" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-115', 'i', 'link-18');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-116" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-116', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-117" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-117', 'score', 'link-90');">score</a></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-comment"># Fill in the score matrix. Each position in the matrix</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># represents an alignment between a character from sequenceA to</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># one in sequence B. As I iterate through the matrix, find the</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># alignment by choose the best of:</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 1) extending a previous alignment without gaps</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 2) adding a gap in sequenceA</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 3) adding a gap in sequenceB</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">row</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">lenA</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">col</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">lenB</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-comment"># First, calculate the score that would occur by extending</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the alignment without gaps.</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">best_score</tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</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">best_score_rint</tt> <tt class="py-op">=</tt> <tt id="link-118" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-118', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">best_score</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-name">best_indexes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-comment"># Try to find a better score by opening gaps in sequenceA.</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Do this by checking alignments from each column in the</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># previous row. Each column represents a different</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># character to align from, and thus a different length</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># gap.</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-119" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-119', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt id="link-120" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-120', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</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-121" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-121', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">gap_A_fn</tt><tt class="py-op">(</tt><tt id="link-122" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-122', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt id="link-123" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-123', 'i', 'link-18');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-name">score_rint</tt> <tt class="py-op">=</tt> <tt id="link-124" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-124', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt id="link-125" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-125', 'score', 'link-90');">score</a></tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">score_rint</tt> <tt class="py-op">==</tt> <tt class="py-name">best_score_rint</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">best_score</tt><tt class="py-op">,</tt> <tt class="py-name">best_score_rint</tt> <tt class="py-op">=</tt> <tt id="link-126" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-126', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">score_rint</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">best_indexes</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-127', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt id="link-128" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-128', 'i', 'link-18');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">score_rint</tt> <tt class="py-op">></tt> <tt class="py-name">best_score_rint</tt><tt class="py-op">:</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-name">best_score</tt><tt class="py-op">,</tt> <tt class="py-name">best_score_rint</tt> <tt class="py-op">=</tt> <tt id="link-129" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-129', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">score_rint</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-name">best_indexes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt id="link-130" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-130', 'i', 'link-18');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-comment"># Try to find a better score by opening gaps in sequenceB.</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-131" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-131', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt id="link-132" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-132', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt id="link-133" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-133', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">gap_B_fn</tt><tt class="py-op">(</tt><tt id="link-134" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-134', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt id="link-135" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-135', 'i', 'link-18');">i</a></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">score_rint</tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-136', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-137', 'score', 'link-90');">score</a></tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">score_rint</tt> <tt class="py-op">==</tt> <tt class="py-name">best_score_rint</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">best_score</tt><tt class="py-op">,</tt> <tt class="py-name">best_score_rint</tt> <tt class="py-op">=</tt> <tt id="link-138" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-138', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">score_rint</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">best_indexes</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-139', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-140" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-140', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">score_rint</tt> <tt class="py-op">></tt> <tt class="py-name">best_score_rint</tt><tt class="py-op">:</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-name">best_score</tt><tt class="py-op">,</tt> <tt class="py-name">best_score_rint</tt> <tt class="py-op">=</tt> <tt id="link-141" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-141', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">score_rint</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-name">best_indexes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-142" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-142', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">best_score</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-name">match_fn</tt><tt class="py-op">(</tt><tt class="py-name">sequenceA</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">align_globally</tt> <tt class="py-keyword">and</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-name">trace_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">best_indexes</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-name">trace_matrix</tt> </tt>
</div><a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> </tt>
<a name="_make_score_matrix_fast"></a><div id="_make_score_matrix_fast-def"><a name="L396"></a><tt class="py-lineno">396</tt> <a class="py-toggle" href="#" id="_make_score_matrix_fast-toggle" onclick="return toggle('_make_score_matrix_fast');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_make_score_matrix_fast">_make_score_matrix_fast</a><tt class="py-op">(</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-param">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-param">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-param">match_fn</tt><tt class="py-op">,</tt> <tt class="py-param">open_A</tt><tt class="py-op">,</tt> <tt class="py-param">extend_A</tt><tt class="py-op">,</tt> <tt class="py-param">open_B</tt><tt class="py-op">,</tt> <tt class="py-param">extend_B</tt><tt class="py-op">,</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-param">penalize_extend_when_opening</tt><tt class="py-op">,</tt> <tt class="py-param">penalize_end_gaps</tt><tt class="py-op">,</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-param">align_globally</tt><tt class="py-op">,</tt> <tt class="py-param">score_only</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_make_score_matrix_fast-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_make_score_matrix_fast-expanded"><a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-name">first_A_gap</tt> <tt class="py-op">=</tt> <tt id="link-143" class="py-name" targets="Function Bio.pairwise2.calc_affine_penalty()=Bio.pairwise2-module.html#calc_affine_penalty"><a title="Bio.pairwise2.calc_affine_penalty" class="py-name" href="#" onclick="return doclink('link-143', 'calc_affine_penalty', 'link-143');">calc_affine_penalty</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">open_A</tt><tt class="py-op">,</tt> <tt class="py-name">extend_A</tt><tt class="py-op">,</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-name">penalize_extend_when_opening</tt><tt class="py-op">)</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-name">first_B_gap</tt> <tt class="py-op">=</tt> <tt id="link-144" class="py-name"><a title="Bio.pairwise2.calc_affine_penalty" class="py-name" href="#" onclick="return doclink('link-144', 'calc_affine_penalty', 'link-143');">calc_affine_penalty</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">open_B</tt><tt class="py-op">,</tt> <tt class="py-name">extend_B</tt><tt class="py-op">,</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-name">penalize_extend_when_opening</tt><tt class="py-op">)</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-comment"># Create the score and traceback matrices. These should be in the</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># shape:</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequenceA (down) x sequenceB (across)</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">lenA</tt><tt class="py-op">,</tt> <tt class="py-name">lenB</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sequenceA</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">sequenceB</tt><tt class="py-op">)</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-name">trace_matrix</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-145" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-145', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">lenA</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-146', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">lenB</tt><tt class="py-op">)</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-name">trace_matrix</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-147', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">lenB</tt><tt class="py-op">)</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-comment"># The top and left borders of the matrices are special cases</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># because there are no previously aligned characters. To simplify</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the main loop, handle these separately.</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-148" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-148', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">lenA</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-comment"># Align the first residue in sequenceB to the ith residue in</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequence A. This is like opening up i gaps at the beginning</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># of sequence B.</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-149" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-149', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">match_fn</tt><tt class="py-op">(</tt><tt class="py-name">sequenceA</tt><tt class="py-op">[</tt><tt id="link-150" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-150', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</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="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">:</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt id="link-151" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-151', 'score', 'link-90');">score</a></tt> <tt class="py-op">+=</tt> <tt id="link-152" class="py-name"><a title="Bio.pairwise2.calc_affine_penalty" class="py-name" href="#" onclick="return doclink('link-152', 'calc_affine_penalty', 'link-143');">calc_affine_penalty</a></tt><tt class="py-op">(</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt id="link-153" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-153', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">open_B</tt><tt class="py-op">,</tt> <tt class="py-name">extend_B</tt><tt class="py-op">,</tt> <tt class="py-name">penalize_extend_when_opening</tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt id="link-154" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-154', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-155" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-155', 'score', 'link-90');">score</a></tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-156" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-156', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">lenB</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt id="link-157" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-157', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">match_fn</tt><tt class="py-op">(</tt><tt class="py-name">sequenceA</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">[</tt><tt id="link-158" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-158', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">:</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt id="link-159" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-159', 'score', 'link-90');">score</a></tt> <tt class="py-op">+=</tt> <tt id="link-160" class="py-name"><a title="Bio.pairwise2.calc_affine_penalty" class="py-name" href="#" onclick="return doclink('link-160', 'calc_affine_penalty', 'link-143');">calc_affine_penalty</a></tt><tt class="py-op">(</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt id="link-161" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-161', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">open_A</tt><tt class="py-op">,</tt> <tt class="py-name">extend_A</tt><tt class="py-op">,</tt> <tt class="py-name">penalize_extend_when_opening</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-162" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-162', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-163" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-163', 'score', 'link-90');">score</a></tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-comment"># In the generic algorithm, at each row and column in the score</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># matrix, we had to scan all previous rows and columns to see</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># whether opening a gap might yield a higher score. Here, since</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># we know the penalties are affine, we can cache just the best</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># score in the previous rows and columns. Instead of scanning</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># through all the previous rows and cols, we can just look at the</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># cache for the best one. Whenever the row or col increments, the</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># best cached score just decreases by extending the gap longer.</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-comment"># The best score and indexes for each row (goes down all columns).</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># I don't need to store the last row because it's the end of the</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequence.</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">row_cache_score</tt><tt class="py-op">,</tt> <tt class="py-name">row_cache_index</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">lenA</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">lenA</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-comment"># The best score and indexes for each column (goes across rows).</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">col_cache_score</tt><tt class="py-op">,</tt> <tt class="py-name">col_cache_index</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">lenB</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">lenB</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-164" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-164', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">lenA</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-comment"># Initialize each row to be the alignment of sequenceA[i] to</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequenceB[0], plus opening a gap in sequenceA.</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">row_cache_score</tt><tt class="py-op">[</tt><tt id="link-165" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-165', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt id="link-166" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-166', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">first_A_gap</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-name">row_cache_index</tt><tt class="py-op">[</tt><tt id="link-167" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-167', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-168" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-168', 'i', 'link-18');">i</a></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="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-169" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-169', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">lenB</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt class="py-name">col_cache_score</tt><tt class="py-op">[</tt><tt id="link-170" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-170', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-171" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-171', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">first_B_gap</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-name">col_cache_index</tt><tt class="py-op">[</tt><tt id="link-172" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-172', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-173" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-173', 'i', 'link-18');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-comment"># Fill in the score_matrix.</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">row</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">lenA</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">col</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">lenB</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-comment"># Calculate the score that would occur by extending the</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># alignment without gaps.</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">nogap_score</tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-comment"># Check the score that would occur if there were a gap in</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequence A.</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">col</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-name">row_score</tt> <tt class="py-op">=</tt> <tt class="py-name">row_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-name">row_score</tt> <tt class="py-op">=</tt> <tt class="py-name">nogap_score</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> <tt class="py-comment"># Make sure it's not the best.</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-comment"># Check the score that would occur if there were a gap in</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequence B. </tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">row</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-name">col_score</tt> <tt class="py-op">=</tt> <tt class="py-name">col_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-name">col_score</tt> <tt class="py-op">=</tt> <tt class="py-name">nogap_score</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-name">best_score</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">nogap_score</tt><tt class="py-op">,</tt> <tt class="py-name">row_score</tt><tt class="py-op">,</tt> <tt class="py-name">col_score</tt><tt class="py-op">)</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-name">best_score_rint</tt> <tt class="py-op">=</tt> <tt id="link-174" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-174', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">best_score</tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-name">best_index</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">best_score_rint</tt> <tt class="py-op">==</tt> <tt id="link-175" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-175', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">nogap_score</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-name">best_index</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-176', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">best_score_rint</tt> <tt class="py-op">==</tt> <tt id="link-177" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-177', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">row_score</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-name">best_index</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-178', 'extend', 'link-13');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">row_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">best_score_rint</tt> <tt class="py-op">==</tt> <tt id="link-179" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-179', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">col_score</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-name">best_index</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-180', 'extend', 'link-13');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">col_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-comment"># Set the score and traceback matrices.</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-181" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-181', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">best_score</tt> <tt class="py-op">+</tt> <tt class="py-name">match_fn</tt><tt class="py-op">(</tt><tt class="py-name">sequenceA</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">align_globally</tt> <tt class="py-keyword">and</tt> <tt id="link-182" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-182', 'score', 'link-90');">score</a></tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-183" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-183', 'score', 'link-90');">score</a></tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt class="py-name">trace_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">best_index</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-comment"># Update the cached column scores. The best score for</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># this can come from either extending the gap in the</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># previous cached score, or opening a new gap from the</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># most previously seen character. Compare the two scores</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># and keep the best one.</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">open_score</tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">first_B_gap</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-name">extend_score</tt> <tt class="py-op">=</tt> <tt class="py-name">col_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">extend_B</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-name">open_score_rint</tt><tt class="py-op">,</tt> <tt class="py-name">extend_score_rint</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt id="link-184" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-184', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">open_score</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-185" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-185', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">extend_score</tt><tt class="py-op">)</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">open_score_rint</tt> <tt class="py-op">></tt> <tt class="py-name">extend_score_rint</tt><tt class="py-op">:</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-name">col_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">open_score</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-name">col_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">extend_score_rint</tt> <tt class="py-op">></tt> <tt class="py-name">open_score_rint</tt><tt class="py-op">:</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-name">col_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">extend_score</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> <tt class="py-name">col_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">open_score</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">col_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-name">col_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">col_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-comment"># Update the cached row scores.</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">open_score</tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">first_A_gap</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-name">extend_score</tt> <tt class="py-op">=</tt> <tt class="py-name">row_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">extend_A</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-name">open_score_rint</tt><tt class="py-op">,</tt> <tt class="py-name">extend_score_rint</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt id="link-186" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-186', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">open_score</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-187" class="py-name"><a title="Bio.pairwise2.rint" class="py-name" href="#" onclick="return doclink('link-187', 'rint', 'link-92');">rint</a></tt><tt class="py-op">(</tt><tt class="py-name">extend_score</tt><tt class="py-op">)</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">open_score_rint</tt> <tt class="py-op">></tt> <tt class="py-name">extend_score_rint</tt><tt class="py-op">:</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-name">row_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">open_score</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-name">row_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">extend_score_rint</tt> <tt class="py-op">></tt> <tt class="py-name">open_score_rint</tt><tt class="py-op">:</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-name">row_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">extend_score</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt class="py-name">row_cache_score</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">open_score</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">row_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-name">row_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">row_cache_index</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-name">trace_matrix</tt> </tt>
</div><a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> </tt>
<a name="_recover_alignments"></a><div id="_recover_alignments-def"><a name="L534"></a><tt class="py-lineno">534</tt> <a class="py-toggle" href="#" id="_recover_alignments-toggle" onclick="return toggle('_recover_alignments');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_recover_alignments">_recover_alignments</a><tt class="py-op">(</tt><tt class="py-param">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-param">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-param">starts</tt><tt class="py-op">,</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-param">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-param">trace_matrix</tt><tt class="py-op">,</tt> <tt class="py-param">align_globally</tt><tt class="py-op">,</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-param">penalize_end_gaps</tt><tt class="py-op">,</tt> <tt class="py-param">gap_char</tt><tt class="py-op">,</tt> <tt class="py-param">one_alignment_only</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_recover_alignments-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_recover_alignments-expanded"><a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-comment"># Recover the alignments by following the traceback matrix. This</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># is a recursive procedure, but it's implemented here iteratively</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># with a stack.</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">lenA</tt><tt class="py-op">,</tt> <tt class="py-name">lenB</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sequenceA</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">sequenceB</tt><tt class="py-op">)</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-name">tracebacks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># list of (seq1, seq2, score, begin, end)</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-name">in_process</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># list of ([same as tracebacks], prev_pos, next_pos)</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-comment"># sequenceA and sequenceB may be sequences, including strings,</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># lists, or list-like objects. In order to preserve the type of</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the object, we need to use slices on the sequences instead of</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># indexes. For example, sequenceA[row] may return a type that's</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># not compatible with sequenceA, e.g. if sequenceA is a list and</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequenceA[row] is a string. Thus, avoid using indexes and use</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># slices, e.g. sequenceA[row:row+1]. Assume that client-defined</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequence classes preserve these semantics.</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-comment"># Initialize the in_process stack</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-188" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-188', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">starts</tt><tt class="py-op">:</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">align_globally</tt><tt class="py-op">:</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> <tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt id="link-189" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-189', 'end', 'link-189');">end</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>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt id="link-190" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-190', 'end', 'link-189');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">lenA</tt><tt class="py-op">-</tt><tt class="py-name">row</tt><tt class="py-op">,</tt> <tt class="py-name">lenB</tt><tt class="py-op">-</tt><tt class="py-name">col</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-191" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-191', 'end', 'link-189');">end</a></tt><tt class="py-op">:</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> <tt id="link-192" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-192', 'end', 'link-189');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> <tt class="py-comment"># Initialize the in_process list with empty sequences of the</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># same type as sequenceA. To do this, take empty slices of</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the sequences.</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">in_process</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-193', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">sequenceA</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-194" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-194', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt id="link-195" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-195', 'end', 'link-189');">end</a></tt><tt class="py-op">,</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">lenA</tt><tt class="py-op">,</tt> <tt class="py-name">lenB</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">one_alignment_only</tt><tt class="py-op">:</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">in_process</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tracebacks</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt id="link-196" class="py-name"><a title="Bio.pairwise2.MAX_ALIGNMENTS" class="py-name" href="#" onclick="return doclink('link-196', 'MAX_ALIGNMENTS', 'link-2');">MAX_ALIGNMENTS</a></tt><tt class="py-op">:</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> <tt class="py-name">seqA</tt><tt class="py-op">,</tt> <tt class="py-name">seqB</tt><tt class="py-op">,</tt> <tt id="link-197" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-197', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt id="link-198" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-198', 'end', 'link-189');">end</a></tt><tt class="py-op">,</tt> <tt class="py-name">prev_pos</tt><tt class="py-op">,</tt> <tt class="py-name">next_pos</tt> <tt class="py-op">=</tt> <tt class="py-name">in_process</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name" targets="Method Bio.Seq.MutableSeq.pop()=Bio.Seq.MutableSeq-class.html#pop"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-199', 'pop', 'link-199');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"> <tt class="py-name">prevA</tt><tt class="py-op">,</tt> <tt class="py-name">prevB</tt> <tt class="py-op">=</tt> <tt class="py-name">prev_pos</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">next_pos</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> <tt class="py-name">prevlen</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqA</tt><tt class="py-op">)</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> <tt class="py-comment"># add the rest of the sequences</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">seqA</tt> <tt class="py-op">=</tt> <tt class="py-name">sequenceA</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">prevA</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">seqA</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-name">seqB</tt> <tt class="py-op">=</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">prevB</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">seqB</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-comment"># add the rest of the gaps</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">seqA</tt><tt class="py-op">,</tt> <tt class="py-name">seqB</tt> <tt class="py-op">=</tt> <tt id="link-200" class="py-name" targets="Function Bio.pairwise2._lpad_until_equal()=Bio.pairwise2-module.html#_lpad_until_equal"><a title="Bio.pairwise2._lpad_until_equal" class="py-name" href="#" onclick="return doclink('link-200', '_lpad_until_equal', 'link-200');">_lpad_until_equal</a></tt><tt class="py-op">(</tt><tt class="py-name">seqA</tt><tt class="py-op">,</tt> <tt class="py-name">seqB</tt><tt class="py-op">,</tt> <tt class="py-name">gap_char</tt><tt class="py-op">)</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> <tt class="py-comment"># Now make sure begin is set.</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">begin</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">align_globally</tt><tt class="py-op">:</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-name">begin</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> <tt class="py-name">begin</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqA</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">prevlen</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-name">tracebacks</tt><tt class="py-op">.</tt><tt id="link-201" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-201', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">seqA</tt><tt class="py-op">,</tt> <tt class="py-name">seqB</tt><tt class="py-op">,</tt> <tt id="link-202" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-202', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt id="link-203" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-203', 'end', 'link-189');">end</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-name">nextA</tt><tt class="py-op">,</tt> <tt class="py-name">nextB</tt> <tt class="py-op">=</tt> <tt class="py-name">next_pos</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt class="py-name">nseqA</tt><tt class="py-op">,</tt> <tt class="py-name">nseqB</tt> <tt class="py-op">=</tt> <tt class="py-name">prevA</tt><tt class="py-op">-</tt><tt class="py-name">nextA</tt><tt class="py-op">,</tt> <tt class="py-name">prevB</tt><tt class="py-op">-</tt><tt class="py-name">nextB</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt class="py-name">maxseq</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">nseqA</tt><tt class="py-op">,</tt> <tt class="py-name">nseqB</tt><tt class="py-op">)</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-name">ngapA</tt><tt class="py-op">,</tt> <tt class="py-name">ngapB</tt> <tt class="py-op">=</tt> <tt class="py-name">maxseq</tt><tt class="py-op">-</tt><tt class="py-name">nseqA</tt><tt class="py-op">,</tt> <tt class="py-name">maxseq</tt><tt class="py-op">-</tt><tt class="py-name">nseqB</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt class="py-name">seqA</tt> <tt class="py-op">=</tt> <tt class="py-name">sequenceA</tt><tt class="py-op">[</tt><tt class="py-name">nextA</tt><tt class="py-op">:</tt><tt class="py-name">nextA</tt><tt class="py-op">+</tt><tt class="py-name">nseqA</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">gap_char</tt><tt class="py-op">*</tt><tt class="py-name">ngapA</tt> <tt class="py-op">+</tt> <tt class="py-name">seqA</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-name">seqB</tt> <tt class="py-op">=</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">[</tt><tt class="py-name">nextB</tt><tt class="py-op">:</tt><tt class="py-name">nextB</tt><tt class="py-op">+</tt><tt class="py-name">nseqB</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">gap_char</tt><tt class="py-op">*</tt><tt class="py-name">ngapB</tt> <tt class="py-op">+</tt> <tt class="py-name">seqB</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt class="py-name">prev_pos</tt> <tt class="py-op">=</tt> <tt class="py-name">next_pos</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-comment"># local alignment stops early if score falls < 0</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">align_globally</tt> <tt class="py-keyword">and</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">nextA</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">nextB</tt><tt class="py-op">]</tt> <tt class="py-op"><=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> <tt class="py-name">begin</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">prevA</tt><tt class="py-op">,</tt> <tt class="py-name">prevB</tt><tt class="py-op">)</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-name">in_process</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-204', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">seqA</tt><tt class="py-op">,</tt> <tt class="py-name">seqB</tt><tt class="py-op">,</tt> <tt id="link-205" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-205', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt id="link-206" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-206', 'end', 'link-189');">end</a></tt><tt class="py-op">,</tt> <tt class="py-name">prev_pos</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">next_pos</tt> <tt class="py-keyword">in</tt> <tt class="py-name">trace_matrix</tt><tt class="py-op">[</tt><tt class="py-name">nextA</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">nextB</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-name">in_process</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-207', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">seqA</tt><tt class="py-op">,</tt> <tt class="py-name">seqB</tt><tt class="py-op">,</tt> <tt id="link-208" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-208', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt id="link-209" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-209', 'end', 'link-189');">end</a></tt><tt class="py-op">,</tt> <tt class="py-name">prev_pos</tt><tt class="py-op">,</tt> <tt class="py-name">next_pos</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">one_alignment_only</tt><tt class="py-op">:</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-210" class="py-name" targets="Function Bio.pairwise2._clean_alignments()=Bio.pairwise2-module.html#_clean_alignments"><a title="Bio.pairwise2._clean_alignments" class="py-name" href="#" onclick="return doclink('link-210', '_clean_alignments', 'link-210');">_clean_alignments</a></tt><tt class="py-op">(</tt><tt class="py-name">tracebacks</tt><tt class="py-op">)</tt> </tt>
</div><a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> </tt>
<a name="_find_start"></a><div id="_find_start-def"><a name="L609"></a><tt class="py-lineno">609</tt> <a class="py-toggle" href="#" id="_find_start-toggle" onclick="return toggle('_find_start');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_find_start">_find_start</a><tt class="py-op">(</tt><tt class="py-param">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-param">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-param">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-param">gap_A_fn</tt><tt class="py-op">,</tt> <tt class="py-param">gap_B_fn</tt><tt class="py-op">,</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> <tt class="py-param">penalize_end_gaps</tt><tt class="py-op">,</tt> <tt class="py-param">align_globally</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_find_start-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_find_start-expanded"><a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-comment"># Return a list of (score, (row, col)) indicating every possible</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># place to start the tracebacks.</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">align_globally</tt><tt class="py-op">:</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">:</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-name">starts</tt> <tt class="py-op">=</tt> <tt id="link-211" class="py-name" targets="Function Bio.pairwise2._find_global_start()=Bio.pairwise2-module.html#_find_global_start"><a title="Bio.pairwise2._find_global_start" class="py-name" href="#" onclick="return doclink('link-211', '_find_global_start', 'link-211');">_find_global_start</a></tt><tt class="py-op">(</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-name">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-name">gap_A_fn</tt><tt class="py-op">,</tt> <tt class="py-name">gap_B_fn</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-name">starts</tt> <tt class="py-op">=</tt> <tt id="link-212" class="py-name"><a title="Bio.pairwise2._find_global_start" class="py-name" href="#" onclick="return doclink('link-212', '_find_global_start', 'link-211');">_find_global_start</a></tt><tt class="py-op">(</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> <tt class="py-name">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-name">sequenceB</tt><tt class="py-op">,</tt> <tt class="py-name">score_matrix</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 class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt class="py-name">starts</tt> <tt class="py-op">=</tt> <tt id="link-213" class="py-name" targets="Function Bio.pairwise2._find_local_start()=Bio.pairwise2-module.html#_find_local_start"><a title="Bio.pairwise2._find_local_start" class="py-name" href="#" onclick="return doclink('link-213', '_find_local_start', 'link-213');">_find_local_start</a></tt><tt class="py-op">(</tt><tt class="py-name">score_matrix</tt><tt class="py-op">)</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">starts</tt> </tt>
</div><a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> </tt>
<a name="_find_global_start"></a><div id="_find_global_start-def"><a name="L624"></a><tt class="py-lineno">624</tt> <a class="py-toggle" href="#" id="_find_global_start-toggle" onclick="return toggle('_find_global_start');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_find_global_start">_find_global_start</a><tt class="py-op">(</tt><tt class="py-param">sequenceA</tt><tt class="py-op">,</tt> <tt class="py-param">sequenceB</tt><tt class="py-op">,</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> <tt class="py-param">score_matrix</tt><tt class="py-op">,</tt> <tt class="py-param">gap_A_fn</tt><tt class="py-op">,</tt> <tt class="py-param">gap_B_fn</tt><tt class="py-op">,</tt> <tt class="py-param">penalize_end_gaps</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_find_global_start-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_find_global_start-expanded"><a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"> <tt class="py-comment"># The whole sequence should be aligned, so return the positions at</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the end of either one of the sequences.</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-214" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.nrows()=Bio.Affy.CelFile.CelRecord-class.html#nrows"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-214', 'nrows', 'link-214');">nrows</a></tt><tt class="py-op">,</tt> <tt id="link-215" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.ncols()=Bio.Affy.CelFile.CelRecord-class.html#ncols"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-215', 'ncols', 'link-215');">ncols</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">score_matrix</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">score_matrix</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="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-comment"># Search all rows in the last column.</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">row</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt id="link-216" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-216', 'nrows', 'link-214');">nrows</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-comment"># Find the score, penalizing end gaps if necessary.</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-217" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-217', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-218" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-218', 'ncols', 'link-215');">ncols</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">:</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> <tt id="link-219" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-219', 'score', 'link-90');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">gap_B_fn</tt><tt class="py-op">(</tt><tt id="link-220" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-220', 'ncols', 'link-215');">ncols</a></tt><tt class="py-op">,</tt> <tt id="link-221" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-221', 'nrows', 'link-214');">nrows</a></tt><tt class="py-op">-</tt><tt class="py-name">row</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-name">positions</tt><tt class="py-op">.</tt><tt id="link-222" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-222', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-223" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-223', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">,</tt> <tt id="link-224" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-224', 'ncols', 'link-215');">ncols</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt class="py-comment"># Search all columns in the last row.</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">col</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt id="link-225" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-225', 'ncols', 'link-215');">ncols</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt id="link-226" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-226', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt id="link-227" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-227', 'nrows', 'link-214');">nrows</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">penalize_end_gaps</tt><tt class="py-op">:</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt id="link-228" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-228', 'score', 'link-90');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">gap_A_fn</tt><tt class="py-op">(</tt><tt id="link-229" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-229', 'nrows', 'link-214');">nrows</a></tt><tt class="py-op">,</tt> <tt id="link-230" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-230', 'ncols', 'link-215');">ncols</a></tt><tt class="py-op">-</tt><tt class="py-name">col</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt class="py-name">positions</tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-231', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-232" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-232', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-233" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-233', 'nrows', 'link-214');">nrows</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">positions</tt> </tt>
</div><a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> </tt>
<a name="_find_local_start"></a><div id="_find_local_start-def"><a name="L645"></a><tt class="py-lineno">645</tt> <a class="py-toggle" href="#" id="_find_local_start-toggle" onclick="return toggle('_find_local_start');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_find_local_start">_find_local_start</a><tt class="py-op">(</tt><tt class="py-param">score_matrix</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_find_local_start-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_find_local_start-expanded"><a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt class="py-comment"># Return every position in the matrix.</tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt id="link-234" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-234', 'nrows', 'link-214');">nrows</a></tt><tt class="py-op">,</tt> <tt id="link-235" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-235', 'ncols', 'link-215');">ncols</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">score_matrix</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">score_matrix</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="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">row</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt id="link-236" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-236', 'nrows', 'link-214');">nrows</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">col</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt id="link-237" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-237', 'ncols', 'link-215');">ncols</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> <tt id="link-238" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-238', 'score', 'link-90');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">score_matrix</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> <tt class="py-name">positions</tt><tt class="py-op">.</tt><tt id="link-239" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-239', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-240" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-240', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">row</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">positions</tt> </tt>
</div><a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> </tt>
<a name="_clean_alignments"></a><div id="_clean_alignments-def"><a name="L655"></a><tt class="py-lineno">655</tt> <a class="py-toggle" href="#" id="_clean_alignments-toggle" onclick="return toggle('_clean_alignments');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_clean_alignments">_clean_alignments</a><tt class="py-op">(</tt><tt class="py-param">alignments</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_clean_alignments-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_clean_alignments-expanded"><a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt class="py-comment"># Take a list of alignments and return a cleaned version. Remove</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># duplicates, make sure begin and end are set correctly, remove</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># empty alignments.</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">alignments</tt> <tt class="py-op">=</tt> <tt id="link-241" class="py-name"><a title="Bio.listfns" class="py-name" href="#" onclick="return doclink('link-241', 'listfns', 'link-1');">listfns</a></tt><tt class="py-op">.</tt><tt id="link-242" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-242', 'items', 'link-242');">items</a></tt><tt class="py-op">(</tt><tt class="py-name">alignments</tt><tt class="py-op">)</tt> <tt class="py-comment"># Get rid of duplicates</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt id="link-243" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-243', 'i', 'link-18');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-244" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-244', 'i', 'link-18');">i</a></tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alignments</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt class="py-name">seqA</tt><tt class="py-op">,</tt> <tt class="py-name">seqB</tt><tt class="py-op">,</tt> <tt id="link-245" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-245', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt id="link-246" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-246', 'end', 'link-189');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">alignments</tt><tt class="py-op">[</tt><tt id="link-247" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-247', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt class="py-comment"># Make sure end is set reasonably.</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-248" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-248', 'end', 'link-189');">end</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-comment"># global alignment</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> <tt id="link-249" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-249', 'end', 'link-189');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqA</tt><tt class="py-op">)</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-250" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-250', 'end', 'link-189');">end</a></tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt id="link-251" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-251', 'end', 'link-189');">end</a></tt> <tt class="py-op">=</tt> <tt id="link-252" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-252', 'end', 'link-189');">end</a></tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqA</tt><tt class="py-op">)</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-comment"># If there's no alignment here, get rid of it.</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">begin</tt> <tt class="py-op">>=</tt> <tt id="link-253" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-253', 'end', 'link-189');">end</a></tt><tt class="py-op">:</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">alignments</tt><tt class="py-op">[</tt><tt id="link-254" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-254', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> <tt class="py-name">alignments</tt><tt class="py-op">[</tt><tt id="link-255" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-255', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">seqA</tt><tt class="py-op">,</tt> <tt class="py-name">seqB</tt><tt class="py-op">,</tt> <tt id="link-256" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-256', 'score', 'link-90');">score</a></tt><tt class="py-op">,</tt> <tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt id="link-257" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-257', 'end', 'link-189');">end</a></tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> <tt id="link-258" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-258', 'i', 'link-18');">i</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">alignments</tt> </tt>
</div><a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> </tt>
<a name="_pad_until_equal"></a><div id="_pad_until_equal-def"><a name="L676"></a><tt class="py-lineno">676</tt> <a class="py-toggle" href="#" id="_pad_until_equal-toggle" onclick="return toggle('_pad_until_equal');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_pad_until_equal">_pad_until_equal</a><tt class="py-op">(</tt><tt class="py-param">s1</tt><tt class="py-op">,</tt> <tt class="py-param">s2</tt><tt class="py-op">,</tt> <tt class="py-param">char</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_pad_until_equal-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_pad_until_equal-expanded"><a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"> <tt class="py-comment"># Add char to the end of s1 or s2 until they are equal length.</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ls1</tt><tt class="py-op">,</tt> <tt class="py-name">ls2</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-259" class="py-name" targets="Variable Martel.test.test_swissprot38.s1=Martel.test.test_swissprot38-module.html#s1"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-259', 's1', 'link-259');">s1</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-260" class="py-name" targets="Variable Martel.test.test_swissprot38.s2=Martel.test.test_swissprot38-module.html#s2"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-260', 's2', 'link-260');">s2</a></tt><tt class="py-op">)</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ls1</tt> <tt class="py-op"><</tt> <tt class="py-name">ls2</tt><tt class="py-op">:</tt> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"> <tt id="link-261" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-261', 's1', 'link-259');">s1</a></tt> <tt class="py-op">=</tt> <tt id="link-262" class="py-name" targets="Function Bio.pairwise2._pad()=Bio.pairwise2-module.html#_pad"><a title="Bio.pairwise2._pad" class="py-name" href="#" onclick="return doclink('link-262', '_pad', 'link-262');">_pad</a></tt><tt class="py-op">(</tt><tt id="link-263" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-263', 's1', 'link-259');">s1</a></tt><tt class="py-op">,</tt> <tt class="py-name">char</tt><tt class="py-op">,</tt> <tt class="py-name">ls2</tt><tt class="py-op">-</tt><tt class="py-name">ls1</tt><tt class="py-op">)</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">ls2</tt> <tt class="py-op"><</tt> <tt class="py-name">ls1</tt><tt class="py-op">:</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"> <tt id="link-264" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-264', 's2', 'link-260');">s2</a></tt> <tt class="py-op">=</tt> <tt id="link-265" class="py-name"><a title="Bio.pairwise2._pad" class="py-name" href="#" onclick="return doclink('link-265', '_pad', 'link-262');">_pad</a></tt><tt class="py-op">(</tt><tt id="link-266" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-266', 's2', 'link-260');">s2</a></tt><tt class="py-op">,</tt> <tt class="py-name">char</tt><tt class="py-op">,</tt> <tt class="py-name">ls1</tt><tt class="py-op">-</tt><tt class="py-name">ls2</tt><tt class="py-op">)</tt> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-267" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-267', 's1', 'link-259');">s1</a></tt><tt class="py-op">,</tt> <tt id="link-268" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-268', 's2', 'link-260');">s2</a></tt> </tt>
</div><a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"> </tt>
<a name="_lpad_until_equal"></a><div id="_lpad_until_equal-def"><a name="L685"></a><tt class="py-lineno">685</tt> <a class="py-toggle" href="#" id="_lpad_until_equal-toggle" onclick="return toggle('_lpad_until_equal');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_lpad_until_equal">_lpad_until_equal</a><tt class="py-op">(</tt><tt class="py-param">s1</tt><tt class="py-op">,</tt> <tt class="py-param">s2</tt><tt class="py-op">,</tt> <tt class="py-param">char</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_lpad_until_equal-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_lpad_until_equal-expanded"><a name="L686"></a><tt class="py-lineno">686</tt> <tt class="py-line"> <tt class="py-comment"># Add char to the beginning of s1 or s2 until they are equal</tt> </tt>
<a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># length.</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ls1</tt><tt class="py-op">,</tt> <tt class="py-name">ls2</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-269" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-269', 's1', 'link-259');">s1</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-270" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-270', 's2', 'link-260');">s2</a></tt><tt class="py-op">)</tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ls1</tt> <tt class="py-op"><</tt> <tt class="py-name">ls2</tt><tt class="py-op">:</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"> <tt id="link-271" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-271', 's1', 'link-259');">s1</a></tt> <tt class="py-op">=</tt> <tt id="link-272" class="py-name" targets="Function Bio.pairwise2._lpad()=Bio.pairwise2-module.html#_lpad"><a title="Bio.pairwise2._lpad" class="py-name" href="#" onclick="return doclink('link-272', '_lpad', 'link-272');">_lpad</a></tt><tt class="py-op">(</tt><tt id="link-273" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-273', 's1', 'link-259');">s1</a></tt><tt class="py-op">,</tt> <tt class="py-name">char</tt><tt class="py-op">,</tt> <tt class="py-name">ls2</tt><tt class="py-op">-</tt><tt class="py-name">ls1</tt><tt class="py-op">)</tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">ls2</tt> <tt class="py-op"><</tt> <tt class="py-name">ls1</tt><tt class="py-op">:</tt> </tt>
<a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"> <tt id="link-274" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-274', 's2', 'link-260');">s2</a></tt> <tt class="py-op">=</tt> <tt id="link-275" class="py-name"><a title="Bio.pairwise2._lpad" class="py-name" href="#" onclick="return doclink('link-275', '_lpad', 'link-272');">_lpad</a></tt><tt class="py-op">(</tt><tt id="link-276" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-276', 's2', 'link-260');">s2</a></tt><tt class="py-op">,</tt> <tt class="py-name">char</tt><tt class="py-op">,</tt> <tt class="py-name">ls1</tt><tt class="py-op">-</tt><tt class="py-name">ls2</tt><tt class="py-op">)</tt> </tt>
<a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-277" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-277', 's1', 'link-259');">s1</a></tt><tt class="py-op">,</tt> <tt id="link-278" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-278', 's2', 'link-260');">s2</a></tt> </tt>
</div><a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"> </tt>
<a name="_pad"></a><div id="_pad-def"><a name="L695"></a><tt class="py-lineno">695</tt> <a class="py-toggle" href="#" id="_pad-toggle" onclick="return toggle('_pad');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_pad">_pad</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">char</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_pad-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_pad-expanded"><a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"> <tt class="py-comment"># Append n chars to the end of s.</tt> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-279" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-279', 's', 'link-279');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-name">char</tt><tt class="py-op">*</tt><tt class="py-name">n</tt> </tt>
</div><a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"> </tt>
<a name="_lpad"></a><div id="_lpad-def"><a name="L699"></a><tt class="py-lineno">699</tt> <a class="py-toggle" href="#" id="_lpad-toggle" onclick="return toggle('_lpad');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#_lpad">_lpad</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">char</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_lpad-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_lpad-expanded"><a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"> <tt class="py-comment"># Prepend n chars to the beginning of s.</tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">char</tt><tt class="py-op">*</tt><tt class="py-name">n</tt> <tt class="py-op">+</tt> <tt id="link-280" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-280', 's', 'link-279');">s</a></tt> </tt>
</div><a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"><tt id="link-281" class="py-name" targets="Variable Bio.pairwise2._PRECISION=Bio.pairwise2-module.html#_PRECISION"><a title="Bio.pairwise2._PRECISION" class="py-name" href="#" onclick="return doclink('link-281', '_PRECISION', 'link-281');">_PRECISION</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1000</tt> </tt>
<a name="rint"></a><div id="rint-def"><a name="L704"></a><tt class="py-lineno">704</tt> <a class="py-toggle" href="#" id="rint-toggle" onclick="return toggle('rint');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#rint">rint</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">precision</tt><tt class="py-op">=</tt><tt id="link-282" class="py-name"><a title="Bio.pairwise2._PRECISION" class="py-name" href="#" onclick="return doclink('link-282', '_PRECISION', 'link-281');">_PRECISION</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="rint-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="rint-expanded"><a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-283" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-283', 'x', 'link-11');">x</a></tt> <tt class="py-op">*</tt> <tt class="py-name">precision</tt> <tt class="py-op">+</tt> <tt class="py-number">0.5</tt><tt class="py-op">)</tt> </tt>
</div><a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> </tt>
<a name="identity_match"></a><div id="identity_match-def"><a name="L707"></a><tt class="py-lineno">707</tt> <a class="py-toggle" href="#" id="identity_match-toggle" onclick="return toggle('identity_match');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.pairwise2.identity_match-class.html">identity_match</a><tt class="py-op">:</tt> </tt>
</div><div id="identity_match-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="identity_match-expanded"><a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"> <tt class="py-docstring">"""identity_match([match][, mismatch]) -> match_fn</tt> </tt>
<a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"><tt class="py-docstring"> Create a match function for use in an alignment. match and</tt> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"><tt class="py-docstring"> mismatch are the scores to give when two residues are equal or</tt> </tt>
<a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"><tt class="py-docstring"> unequal. By default, match is 1 and mismatch is 0.</tt> </tt>
<a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="identity_match.__init__"></a><div id="identity_match.__init__-def"><a name="L715"></a><tt class="py-lineno">715</tt> <a class="py-toggle" href="#" id="identity_match.__init__-toggle" onclick="return toggle('identity_match.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.identity_match-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">match</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">mismatch</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="identity_match.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="identity_match.__init__-expanded"><a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-284" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-284', 'match', 'link-26');">match</a></tt> <tt class="py-op">=</tt> <tt id="link-285" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-285', 'match', 'link-26');">match</a></tt> </tt>
<a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mismatch</tt> <tt class="py-op">=</tt> <tt class="py-name">mismatch</tt> </tt>
</div><a name="identity_match.__call__"></a><div id="identity_match.__call__-def"><a name="L718"></a><tt class="py-lineno">718</tt> <a class="py-toggle" href="#" id="identity_match.__call__-toggle" onclick="return toggle('identity_match.__call__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.identity_match-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">charA</tt><tt class="py-op">,</tt> <tt class="py-param">charB</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="identity_match.__call__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="identity_match.__call__-expanded"><a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">charA</tt> <tt class="py-op">==</tt> <tt class="py-name">charB</tt><tt class="py-op">:</tt> </tt>
<a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-286" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-286', 'match', 'link-26');">match</a></tt> </tt>
<a name="L721"></a><tt class="py-lineno">721</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">mismatch</tt> </tt>
</div></div><a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"> </tt>
<a name="dictionary_match"></a><div id="dictionary_match-def"><a name="L723"></a><tt class="py-lineno">723</tt> <a class="py-toggle" href="#" id="dictionary_match-toggle" onclick="return toggle('dictionary_match');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.pairwise2.dictionary_match-class.html">dictionary_match</a><tt class="py-op">:</tt> </tt>
</div><div id="dictionary_match-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="dictionary_match-expanded"><a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> <tt class="py-docstring">"""dictionary_match(score_dict[, symmetric]) -> match_fn</tt> </tt>
<a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"><tt class="py-docstring"> Create a match function for use in an alignment. score_dict is a</tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"><tt class="py-docstring"> dictionary where the keys are tuples (residue 1, residue 2) and</tt> </tt>
<a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"><tt class="py-docstring"> the values are the match scores between those residues. symmetric</tt> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"><tt class="py-docstring"> is a flag that indicates whether the scores are symmetric. If</tt> </tt>
<a name="L730"></a><tt class="py-lineno">730</tt> <tt class="py-line"><tt class="py-docstring"> true, then if (res 1, res 2) doesn't exist, I will use the score</tt> </tt>
<a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"><tt class="py-docstring"> at (res 2, res 1).</tt> </tt>
<a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="dictionary_match.__init__"></a><div id="dictionary_match.__init__-def"><a name="L734"></a><tt class="py-lineno">734</tt> <a class="py-toggle" href="#" id="dictionary_match.__init__-toggle" onclick="return toggle('dictionary_match.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.dictionary_match-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">score_dict</tt><tt class="py-op">,</tt> <tt class="py-param">symmetric</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="dictionary_match.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="dictionary_match.__init__-expanded"><a name="L735"></a><tt class="py-lineno">735</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">score_dict</tt> <tt class="py-op">=</tt> <tt class="py-name">score_dict</tt> </tt>
<a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">symmetric</tt> <tt class="py-op">=</tt> <tt class="py-name">symmetric</tt> </tt>
</div><a name="dictionary_match.__call__"></a><div id="dictionary_match.__call__-def"><a name="L737"></a><tt class="py-lineno">737</tt> <a class="py-toggle" href="#" id="dictionary_match.__call__-toggle" onclick="return toggle('dictionary_match.__call__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.dictionary_match-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">charA</tt><tt class="py-op">,</tt> <tt class="py-param">charB</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="dictionary_match.__call__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="dictionary_match.__call__-expanded"><a name="L738"></a><tt class="py-lineno">738</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">symmetric</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">score_dict</tt><tt class="py-op">.</tt><tt id="link-287" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-287', 'has_key', 'link-287');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">charA</tt><tt class="py-op">,</tt> <tt class="py-name">charB</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"> <tt class="py-comment"># If the score dictionary is symmetric, then look up the</tt> </tt>
<a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># score both ways.</tt> </tt>
<a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">charB</tt><tt class="py-op">,</tt> <tt class="py-name">charA</tt> <tt class="py-op">=</tt> <tt class="py-name">charA</tt><tt class="py-op">,</tt> <tt class="py-name">charB</tt> </tt>
<a name="L742"></a><tt class="py-lineno">742</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">score_dict</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">charA</tt><tt class="py-op">,</tt> <tt class="py-name">charB</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L743"></a><tt class="py-lineno">743</tt> <tt class="py-line"> </tt>
<a name="affine_penalty"></a><div id="affine_penalty-def"><a name="L744"></a><tt class="py-lineno">744</tt> <a class="py-toggle" href="#" id="affine_penalty-toggle" onclick="return toggle('affine_penalty');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.pairwise2.affine_penalty-class.html">affine_penalty</a><tt class="py-op">:</tt> </tt>
</div><div id="affine_penalty-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="affine_penalty-expanded"><a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"> <tt class="py-docstring">"""affine_penalty(open, extend[, penalize_extend_when_opening]) -> gap_fn</tt> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"><tt class="py-docstring"> Create a gap function for use in an alignment.</tt> </tt>
<a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="affine_penalty.__init__"></a><div id="affine_penalty.__init__-def"><a name="L750"></a><tt class="py-lineno">750</tt> <a class="py-toggle" href="#" id="affine_penalty.__init__-toggle" onclick="return toggle('affine_penalty.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.affine_penalty-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">open</tt><tt class="py-op">,</tt> <tt class="py-param">extend</tt><tt class="py-op">,</tt> <tt class="py-param">penalize_extend_when_opening</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="affine_penalty.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="affine_penalty.__init__-expanded"><a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-288" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-288', 'open', 'link-38');">open</a></tt> <tt class="py-op">></tt> <tt class="py-number">0</tt> <tt class="py-keyword">or</tt> <tt id="link-289" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-289', 'extend', 'link-13');">extend</a></tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Gap penalties should be non-positive."</tt> </tt>
<a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-290" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-290', 'open', 'link-38');">open</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-291', 'extend', 'link-13');">extend</a></tt> <tt class="py-op">=</tt> <tt id="link-292" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-292', 'open', 'link-38');">open</a></tt><tt class="py-op">,</tt> <tt id="link-293" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-293', 'extend', 'link-13');">extend</a></tt> </tt>
<a name="L754"></a><tt class="py-lineno">754</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">penalize_extend_when_opening</tt> <tt class="py-op">=</tt> <tt class="py-name">penalize_extend_when_opening</tt> </tt>
</div><a name="affine_penalty.__call__"></a><div id="affine_penalty.__call__-def"><a name="L755"></a><tt class="py-lineno">755</tt> <a class="py-toggle" href="#" id="affine_penalty.__call__-toggle" onclick="return toggle('affine_penalty.__call__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2.affine_penalty-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="affine_penalty.__call__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="affine_penalty.__call__-expanded"><a name="L756"></a><tt class="py-lineno">756</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-294" class="py-name"><a title="Bio.pairwise2.calc_affine_penalty" class="py-name" href="#" onclick="return doclink('link-294', 'calc_affine_penalty', 'link-143');">calc_affine_penalty</a></tt><tt class="py-op">(</tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</tt> <tt class="py-line"> <tt id="link-295" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-295', 'length', 'link-295');">length</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-296" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-296', 'open', 'link-38');">open</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-297" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-297', 'extend', 'link-13');">extend</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">penalize_extend_when_opening</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"> </tt>
<a name="calc_affine_penalty"></a><div id="calc_affine_penalty-def"><a name="L759"></a><tt class="py-lineno">759</tt> <a class="py-toggle" href="#" id="calc_affine_penalty-toggle" onclick="return toggle('calc_affine_penalty');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#calc_affine_penalty">calc_affine_penalty</a><tt class="py-op">(</tt><tt class="py-param">length</tt><tt class="py-op">,</tt> <tt class="py-param">open</tt><tt class="py-op">,</tt> <tt class="py-param">extend</tt><tt class="py-op">,</tt> <tt class="py-param">penalize_extend_when_opening</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="calc_affine_penalty-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="calc_affine_penalty-expanded"><a name="L760"></a><tt class="py-lineno">760</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-298" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-298', 'length', 'link-295');">length</a></tt> <tt class="py-op"><=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L761"></a><tt class="py-lineno">761</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"> <tt class="py-name">penalty</tt> <tt class="py-op">=</tt> <tt id="link-299" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-299', 'open', 'link-38');">open</a></tt> <tt class="py-op">+</tt> <tt id="link-300" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-300', 'extend', 'link-13');">extend</a></tt> <tt class="py-op">*</tt> <tt id="link-301" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-301', 'length', 'link-295');">length</a></tt> </tt>
<a name="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">penalize_extend_when_opening</tt><tt class="py-op">:</tt> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"> <tt class="py-name">penalty</tt> <tt class="py-op">-=</tt> <tt id="link-302" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-302', 'extend', 'link-13');">extend</a></tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">penalty</tt> </tt>
</div><a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"> </tt>
<a name="print_matrix"></a><div id="print_matrix-def"><a name="L767"></a><tt class="py-lineno">767</tt> <a class="py-toggle" href="#" id="print_matrix-toggle" onclick="return toggle('print_matrix');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#print_matrix">print_matrix</a><tt class="py-op">(</tt><tt class="py-param">matrix</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="print_matrix-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="print_matrix-expanded"><a name="L768"></a><tt class="py-lineno">768</tt> <tt class="py-line"> <tt class="py-docstring">"""print_matrix(matrix)</tt> </tt>
<a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"><tt class="py-docstring"> Print out a matrix. For debugging purposes.</tt> </tt>
<a name="L771"></a><tt class="py-lineno">771</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"> <tt class="py-comment"># Transpose the matrix and get the length of the values in each column.</tt> </tt>
<a name="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">matrixT</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-303" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-303', 'x', 'link-11');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-304" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.matrix()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#matrix,Variable Bio.MetaTool.metatool_format.matrix=Bio.MetaTool.metatool_format-module.html#matrix,Method Bio.Prosite._RecordConsumer.matrix()=Bio.Prosite._RecordConsumer-class.html#matrix"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-304', 'matrix', 'link-304');">matrix</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-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-305" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-305', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-306" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-306', 'matrix', 'link-304');">matrix</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L776"></a><tt class="py-lineno">776</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-307" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-307', 'matrix', 'link-304');">matrix</a></tt><tt class="py-op">[</tt><tt id="link-308" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-308', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"> <tt class="py-name">matrixT</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-309" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-309', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-310" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-310', 'matrix', 'link-304');">matrix</a></tt><tt class="py-op">[</tt><tt id="link-311" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-311', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"> <tt class="py-name">ndigits</tt> <tt class="py-op">=</tt> <tt id="link-312" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-312', 'map', 'link-312');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">,</tt> <tt class="py-name">matrixT</tt><tt class="py-op">)</tt> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-313" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-313', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-314" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-314', 'matrix', 'link-304');">matrix</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-315" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-315', 'matrix', 'link-304');">matrix</a></tt><tt class="py-op">[</tt><tt id="link-316" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-316', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">ndigits</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%*s "</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt> <tt id="link-317" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-317', 'matrix', 'link-304');">matrix</a></tt><tt class="py-op">[</tt><tt id="link-318" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-318', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
</div><a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> </tt>
<a name="format_alignment"></a><div id="format_alignment-def"><a name="L785"></a><tt class="py-lineno">785</tt> <a class="py-toggle" href="#" id="format_alignment-toggle" onclick="return toggle('format_alignment');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.pairwise2-module.html#format_alignment">format_alignment</a><tt class="py-op">(</tt><tt class="py-param">align1</tt><tt class="py-op">,</tt> <tt class="py-param">align2</tt><tt class="py-op">,</tt> <tt class="py-param">score</tt><tt class="py-op">,</tt> <tt class="py-param">begin</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="format_alignment-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="format_alignment-expanded"><a name="L786"></a><tt class="py-lineno">786</tt> <tt class="py-line"> <tt class="py-docstring">"""format_alignment(align1, align2, score, begin, end) -> string</tt> </tt>
<a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"><tt class="py-docstring"> Format the alignment prettily into a string.</tt> </tt>
<a name="L789"></a><tt class="py-lineno">789</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L791"></a><tt class="py-lineno">791</tt> <tt class="py-line"> <tt id="link-319" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-319', 's', 'link-279');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"> <tt id="link-320" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-320', 's', 'link-279');">s</a></tt><tt class="py-op">.</tt><tt id="link-321" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-321', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">align1</tt><tt class="py-op">)</tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"> <tt id="link-322" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-322', 's', 'link-279');">s</a></tt><tt class="py-op">.</tt><tt id="link-323" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-323', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">*</tt><tt class="py-name">begin</tt><tt class="py-op">,</tt> <tt class="py-string">"|"</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt id="link-324" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-324', 'end', 'link-189');">end</a></tt><tt class="py-op">-</tt><tt class="py-name">begin</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"> <tt id="link-325" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-325', 's', 'link-279');">s</a></tt><tt class="py-op">.</tt><tt id="link-326" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-326', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">align2</tt><tt class="py-op">)</tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"> <tt id="link-327" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-327', 's', 'link-279');">s</a></tt><tt class="py-op">.</tt><tt id="link-328" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-328', 'append', 'link-102');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">" Score=%g\n"</tt> <tt class="py-op">%</tt> <tt id="link-329" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-329', 'score', 'link-90');">score</a></tt><tt class="py-op">)</tt> </tt>
<a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-330" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-330', 's', 'link-279');">s</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L797"></a><tt class="py-lineno">797</tt> <tt class="py-line"> </tt>
<a name="L798"></a><tt class="py-lineno">798</tt> <tt class="py-line"> </tt>
<a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"><tt class="py-comment"># Try and load C implementations of functions. If I can't,</tt> </tt>
<a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># then just ignore and use the pure python implementations.</tt> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L802"></a><tt class="py-lineno">802</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">cpairwise2</tt> </tt>
<a name="L803"></a><tt class="py-lineno">803</tt> <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L804"></a><tt class="py-lineno">804</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L805"></a><tt class="py-lineno">805</tt> <tt class="py-line"><tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L806"></a><tt class="py-lineno">806</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L807"></a><tt class="py-lineno">807</tt> <tt class="py-line"> <tt id="link-331" class="py-name" targets="Variable Bio.MarkovModel.this_module=Bio.MarkovModel-module.html#this_module,Variable Bio.pairwise2.this_module=Bio.pairwise2-module.html#this_module"><a title="Bio.MarkovModel.this_module
Bio.pairwise2.this_module" class="py-name" href="#" onclick="return doclink('link-331', 'this_module', 'link-331');">this_module</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">modules</tt><tt class="py-op">[</tt><tt class="py-name">__name__</tt><tt class="py-op">]</tt> </tt>
<a name="L808"></a><tt class="py-lineno">808</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-332" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-332', 'name', 'link-3');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">cpairwise2</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">.</tt><tt id="link-333" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-333', 'keys', 'link-333');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L809"></a><tt class="py-lineno">809</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-334" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-334', 'name', 'link-3');">name</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"__"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L810"></a><tt class="py-lineno">810</tt> <tt class="py-line"> <tt id="link-335" class="py-name"><a title="Bio.MarkovModel.this_module
Bio.pairwise2.this_module" class="py-name" href="#" onclick="return doclink('link-335', 'this_module', 'link-331');">this_module</a></tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">[</tt><tt id="link-336" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-336', 'name', 'link-3');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">cpairwise2</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">[</tt><tt id="link-337" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-337', 'name', 'link-3');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L811"></a><tt class="py-lineno">811</tt> <tt class="py-line"> </tt><script type="text/javascript">
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