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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.HMM-module.html">Package&nbsp;HMM</a> ::
        Module&nbsp;DynamicProgramming
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<h1 class="epydoc">Source Code for <a href="Bio.HMM.DynamicProgramming-module.html">Module Bio.HMM.DynamicProgramming</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">"""Dynamic Programming algorithms for general usage.</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">This module contains classes which implement Dynamic Programming</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">algorithms that can be used generally.</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"> </tt>
<a name="AbstractDPAlgorithms"></a><div id="AbstractDPAlgorithms-def"><a name="L7"></a><tt class="py-lineno">  7</tt> <a class="py-toggle" href="#" id="AbstractDPAlgorithms-toggle" onclick="return toggle('AbstractDPAlgorithms');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html">AbstractDPAlgorithms</a><tt class="py-op">:</tt> </tt>
</div><div id="AbstractDPAlgorithms-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AbstractDPAlgorithms-expanded"><a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line">    <tt class="py-docstring">"""An abstract class to calculate forward and backward probabiliies.</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-docstring">    This class should not be instantiated directly, but should be used</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring">    through a derived class which implements proper scaling of variables.</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring">    This class is just meant to encapsulate the basic foward and backward</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring">    algorithms, and allow derived classes to deal with the problems of</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring">    multiplying probabilities.</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring">    Derived class of this must implement:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring">    o _forward_recursion -- Calculate the forward values in the recursion</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">    using some kind of technique for preventing underflow errors.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">    o _backward_recursion -- Calculate the backward values in the recursion</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring">    step using some technique to prevent underflow errors.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="AbstractDPAlgorithms.__init__"></a><div id="AbstractDPAlgorithms.__init__-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="AbstractDPAlgorithms.__init__-toggle" onclick="return toggle('AbstractDPAlgorithms.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-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">markov_model</tt><tt class="py-op">,</tt> <tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractDPAlgorithms.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractDPAlgorithms.__init__-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">        <tt class="py-docstring">"""Initialize to calculate foward and backward probabilities.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring">        Arguments:</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring">        o markov_model -- The current Markov model we are working with.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-docstring">        o sequence -- A training sequence containing a set of emissions.</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt> <tt class="py-op">=</tt> <tt class="py-name">markov_model</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt> <tt class="py-op">=</tt> <tt id="link-0" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-0', 'sequence', 'link-0');">sequence</a></tt> </tt>
</div><a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"> </tt>
<a name="AbstractDPAlgorithms._foward_recursion"></a><div id="AbstractDPAlgorithms._foward_recursion-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="AbstractDPAlgorithms._foward_recursion-toggle" onclick="return toggle('AbstractDPAlgorithms._foward_recursion');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#_foward_recursion">_foward_recursion</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cur_state</tt><tt class="py-op">,</tt> <tt class="py-param">sequence_pos</tt><tt class="py-op">,</tt> <tt class="py-param">forward_vars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractDPAlgorithms._foward_recursion-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractDPAlgorithms._foward_recursion-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">        <tt class="py-docstring">"""Calculate the forward recursion value.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"Subclasses must implement"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"> </tt>
<a name="AbstractDPAlgorithms.forward_algorithm"></a><div id="AbstractDPAlgorithms.forward_algorithm-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="AbstractDPAlgorithms.forward_algorithm-toggle" onclick="return toggle('AbstractDPAlgorithms.forward_algorithm');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#forward_algorithm">forward_algorithm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractDPAlgorithms.forward_algorithm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractDPAlgorithms.forward_algorithm-expanded"><a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">        <tt class="py-docstring">"""Calculate sequence probability using the forward algorithm.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">        This implements the foward algorithm, as described on p57-58 of</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">        Durbin et al.</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">        Returns:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-docstring">        o A dictionary containing the foward variables. This has keys of the</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">        form (state letter, position in the training sequence), and values</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring">        containing the calculated forward variable.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-docstring">        o The calculated probability of the sequence.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">        <tt class="py-comment"># all of the different letters that the state path can be in</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">state_letters</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt><tt class="py-op">.</tt><tt class="py-name">states</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-1', 'alphabet', 'link-1');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Variable Bio.Alphabet.Alphabet.letters=Bio.Alphabet.Alphabet-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters=Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters=Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACProtein.letters=Bio.Alphabet.IUPAC.IUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html#letters,Variable Bio.Alphabet.Reduced.HPModel.letters=Bio.Alphabet.Reduced.HPModel-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy10.letters=Bio.Alphabet.Reduced.Murphy10-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy15.letters=Bio.Alphabet.Reduced.Murphy15-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy4.letters=Bio.Alphabet.Reduced.Murphy4-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy8.letters=Bio.Alphabet.Reduced.Murphy8-class.html#letters,Variable Bio.Alphabet.Reduced.PC5.letters=Bio.Alphabet.Reduced.PC5-class.html#letters,Variable Bio.Alphabet.SecondaryStructure.letters=Bio.Alphabet.SecondaryStructure-class.html#letters,Variable Bio.Alphabet.SingleLetterAlphabet.letters=Bio.Alphabet.SingleLetterAlphabet-class.html#letters,Variable Bio.Alphabet.ThreeLetterProtein.letters=Bio.Alphabet.ThreeLetterProtein-class.html#letters,Variable Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters=Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html#letters,Variable Bio.SeqUtils.ProteinX.letters=Bio.SeqUtils.ProteinX-class.html#letters"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-2', 'letters', 'link-2');">letters</a></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">         </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">        <tt class="py-comment"># -- initialize the algorithm</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># NOTE: My index numbers are one less than what is given in Durbin</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># et al, since we are indexing the sequence going from 0 to</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># (Length - 1) not 1 to Length, like in Durbin et al.</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">forward_var</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">        <tt class="py-comment"># f_{0}(0) = 1 </tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">forward_var</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">state_letters</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-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-comment"># f_{k}(0) = 0, for k &gt; 0</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt class="py-name">k</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">len</tt><tt class="py-op">(</tt><tt class="py-name">state_letters</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">            <tt class="py-name">forward_var</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">state_letters</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">        <tt class="py-comment"># -- now do the recursion step</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># loop over the training sequence</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># Recursion step: (i = 1 .. L)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt id="link-3" 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-3', 'i', 'link-3');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt><tt class="py-op">.</tt><tt class="py-name">emissions</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">            <tt class="py-comment"># now loop over the letters in the state path</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">for</tt> <tt class="py-name">main_state</tt> <tt class="py-keyword">in</tt> <tt class="py-name">state_letters</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">                <tt class="py-comment"># calculate the forward value using the appropriate</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"># method to prevent underflow errors</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-name">forward_value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.HMM.DynamicProgramming.ScaledDPAlgorithms._forward_recursion()=Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#_forward_recursion"><a title="Bio.HMM.DynamicProgramming.ScaledDPAlgorithms._forward_recursion" class="py-name" href="#" onclick="return doclink('link-4', '_forward_recursion', 'link-4');">_forward_recursion</a></tt><tt class="py-op">(</tt><tt class="py-name">main_state</tt><tt class="py-op">,</tt> <tt id="link-5" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-5', 'i', 'link-3');">i</a></tt><tt class="py-op">,</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">                                                        <tt class="py-name">forward_var</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">forward_value</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">                    <tt class="py-name">forward_var</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">main_state</tt><tt class="py-op">,</tt> <tt id="link-6" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-6', 'i', 'link-3');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">forward_value</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">                 </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-comment"># -- termination step - calculate the probability of the sequence</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">first_state</tt> <tt class="py-op">=</tt> <tt class="py-name">state_letters</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt class="py-name">seq_prob</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">state_item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">state_letters</tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">            <tt class="py-comment"># f_{k}(L)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">forward_value</tt> <tt class="py-op">=</tt> <tt class="py-name">forward_var</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">state_item</tt><tt class="py-op">,</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">                                         <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">_seq</tt><tt class="py-op">.</tt><tt class="py-name">emissions</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">            <tt class="py-comment"># a_{k0}</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">transition_value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt class="py-name">transition_prob</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">state_item</tt><tt class="py-op">,</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">                                                         <tt class="py-name">first_state</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">            <tt class="py-name">seq_prob</tt> <tt class="py-op">+=</tt> <tt class="py-name">forward_value</tt> <tt class="py-op">*</tt> <tt class="py-name">transition_value</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">return</tt> <tt class="py-name">forward_var</tt><tt class="py-op">,</tt> <tt class="py-name">seq_prob</tt> </tt>
</div><a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"> </tt>
<a name="AbstractDPAlgorithms._backward_recursion"></a><div id="AbstractDPAlgorithms._backward_recursion-def"><a name="L102"></a><tt class="py-lineno">102</tt> <a class="py-toggle" href="#" id="AbstractDPAlgorithms._backward_recursion-toggle" onclick="return toggle('AbstractDPAlgorithms._backward_recursion');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#_backward_recursion">_backward_recursion</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cur_state</tt><tt class="py-op">,</tt> <tt class="py-param">sequence_pos</tt><tt class="py-op">,</tt> <tt class="py-param">forward_vars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractDPAlgorithms._backward_recursion-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractDPAlgorithms._backward_recursion-expanded"><a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-docstring">"""Calculate the backward recursion value.</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"Subclasses must implement"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"> </tt>
<a name="AbstractDPAlgorithms.backward_algorithm"></a><div id="AbstractDPAlgorithms.backward_algorithm-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="AbstractDPAlgorithms.backward_algorithm-toggle" onclick="return toggle('AbstractDPAlgorithms.backward_algorithm');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#backward_algorithm">backward_algorithm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractDPAlgorithms.backward_algorithm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractDPAlgorithms.backward_algorithm-expanded"><a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-docstring">"""Calculate sequence probability using the backward algorithm.</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"><tt class="py-docstring">        This implements the backward algorithm, as described on p58-59 of</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"><tt class="py-docstring">        Durbin et al.</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">        Returns:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line"><tt class="py-docstring">        o A dictionary containing the backwards variables. This has keys</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line"><tt class="py-docstring">        of the form (state letter, position in the training sequence),</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"><tt class="py-docstring">        and values containing the calculated backward variable.</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">        <tt class="py-comment"># all of the different letters that the state path can be in</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">state_letters</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt><tt class="py-op">.</tt><tt class="py-name">states</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-7', 'alphabet', 'link-1');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-8', 'letters', 'link-2');">letters</a></tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">         </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">        <tt class="py-comment"># -- initialize the algorithm</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># NOTE: My index numbers are one less than what is given in Durbin</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># et al, since we are indexing the sequence going from 0 to</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># (Length - 1) not 1 to Length, like in Durbin et al.</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#</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">backward_var</tt> <tt class="py-op">=</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>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">        <tt class="py-name">first_letter</tt> <tt class="py-op">=</tt> <tt class="py-name">state_letters</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">        <tt class="py-comment"># b_{k}(L) = a_{k0} for all k</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt class="py-name">state</tt> <tt class="py-keyword">in</tt> <tt class="py-name">state_letters</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">            <tt class="py-name">backward_var</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">state</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">_seq</tt><tt class="py-op">.</tt><tt class="py-name">emissions</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">              <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt class="py-name">transition_prob</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">state</tt><tt class="py-op">,</tt> <tt class="py-name">state_letters</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="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-comment"># -- recursion</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># first loop over the training sequence backwards</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># Recursion step: (i = L - 1 ... 1)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">all_indexes</tt> <tt class="py-op">=</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt><tt class="py-op">.</tt><tt class="py-name">emissions</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="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">        <tt class="py-name">all_indexes</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.GFF.easy.Location.reverse()=Bio.GFF.easy.Location-class.html#reverse,Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse,Function Bio.SeqUtils.reverse()=Bio.SeqUtils-module.html#reverse"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-9', 'reverse', 'link-9');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-10" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-10', 'i', 'link-3');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">all_indexes</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">            <tt class="py-comment"># now loop over the letters in the state path</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">for</tt> <tt class="py-name">main_state</tt> <tt class="py-keyword">in</tt> <tt class="py-name">state_letters</tt><tt class="py-op">:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">                <tt class="py-comment"># calculate the backward value using the appropriate</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment"># method to prevent underflow errors</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-name">backward_value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.HMM.DynamicProgramming.AbstractDPAlgorithms._backward_recursion()=Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#_backward_recursion,Method Bio.HMM.DynamicProgramming.ScaledDPAlgorithms._backward_recursion()=Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#_backward_recursion"><a title="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms._backward_recursion
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms._backward_recursion" class="py-name" href="#" onclick="return doclink('link-11', '_backward_recursion', 'link-11');">_backward_recursion</a></tt><tt class="py-op">(</tt><tt class="py-name">main_state</tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-12', 'i', 'link-3');">i</a></tt><tt class="py-op">,</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">                                                          <tt class="py-name">backward_var</tt><tt class="py-op">)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line"> </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">backward_value</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">                    <tt class="py-name">backward_var</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">main_state</tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-13', 'i', 'link-3');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">backward_value</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line"> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">        <tt class="py-comment"># skip the termination step to avoid recalculations -- you should</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># get sequence probabilities using the forward algorithm</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">backward_var</tt> </tt>
</div></div><a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">         </tt>
<a name="ScaledDPAlgorithms"></a><div id="ScaledDPAlgorithms-def"><a name="L157"></a><tt class="py-lineno">157</tt> <a class="py-toggle" href="#" id="ScaledDPAlgorithms-toggle" onclick="return toggle('ScaledDPAlgorithms');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html">ScaledDPAlgorithms</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractDPAlgorithms</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ScaledDPAlgorithms-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ScaledDPAlgorithms-expanded"><a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">    <tt class="py-docstring">"""Implement forward and backward algorithms using a rescaling approach.</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line"><tt class="py-docstring">    This scales the f and b variables, so that they remain within a</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line"><tt class="py-docstring">    manageable numerical interval during calculations. This approach is</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line"><tt class="py-docstring">    described in Durbin et al. on p 78.</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line"><tt class="py-docstring">    This approach is a little more straightfoward then log transformation</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line"><tt class="py-docstring">    but may still give underflow errors for some types of models. In these</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"><tt class="py-docstring">    cases, the LogDPAlgorithms class should be used.</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="ScaledDPAlgorithms.__init__"></a><div id="ScaledDPAlgorithms.__init__-def"><a name="L168"></a><tt class="py-lineno">168</tt> <a class="py-toggle" href="#" id="ScaledDPAlgorithms.__init__-toggle" onclick="return toggle('ScaledDPAlgorithms.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-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">markov_model</tt><tt class="py-op">,</tt> <tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ScaledDPAlgorithms.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ScaledDPAlgorithms.__init__-expanded"><a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">        <tt class="py-docstring">"""Initialize the scaled approach to calculating probabilities.</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"><tt class="py-docstring">        Arguments:</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-docstring">        o markov_model -- The current Markov model we are working with.</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-docstring">        o sequence -- A TrainingSequence object that must have a</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line"><tt class="py-docstring">        set of emissions to work with.</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
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Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-15', '__init__', 'link-15');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">markov_model</tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
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Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-16', 'sequence', 'link-0');">sequence</a></tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_s_values</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line"> </tt>
<a name="ScaledDPAlgorithms._calculate_s_value"></a><div id="ScaledDPAlgorithms._calculate_s_value-def"><a name="L181"></a><tt class="py-lineno">181</tt> <a class="py-toggle" href="#" id="ScaledDPAlgorithms._calculate_s_value-toggle" onclick="return toggle('ScaledDPAlgorithms._calculate_s_value');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#_calculate_s_value">_calculate_s_value</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq_pos</tt><tt class="py-op">,</tt> <tt class="py-param">previous_vars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ScaledDPAlgorithms._calculate_s_value-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ScaledDPAlgorithms._calculate_s_value-expanded"><a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">        <tt class="py-docstring">"""Calculate the next scaling variable for a sequence position.</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"><tt class="py-docstring">        This utilizes the approach of choosing s values such that the</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"><tt class="py-docstring">        sum of all of the scaled f values is equal to 1.</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line"><tt class="py-docstring">        Arguments:</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"><tt class="py-docstring">        o seq_pos -- The current position we are at in the sequence.</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"><tt class="py-docstring">        o previous_vars -- All of the forward or backward variables</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"><tt class="py-docstring">        calculated so far.</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line"><tt class="py-docstring">        Returns:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line"><tt class="py-docstring">        o The calculated scaling variable for the sequence item.</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">        <tt class="py-comment"># all of the different letters the state can have</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">state_letters</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt><tt class="py-op">.</tt><tt class="py-name">states</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-17', 'alphabet', 'link-1');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-18', 'letters', 'link-2');">letters</a></tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">        <tt class="py-comment"># loop over all of the possible states</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">s_value</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">main_state</tt> <tt class="py-keyword">in</tt> <tt class="py-name">state_letters</tt><tt class="py-op">:</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">            <tt class="py-name">emission</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt class="py-name">emission_prob</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">main_state</tt><tt class="py-op">,</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">                                               <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt><tt class="py-op">.</tt><tt class="py-name">emissions</tt><tt class="py-op">[</tt><tt class="py-name">seq_pos</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line"> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">            <tt class="py-comment"># now sum over all of the previous vars and transitions</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">trans_and_var_sum</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">second_state</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.HMM.MarkovModel.HiddenMarkovModel.transitions_from()=Bio.HMM.MarkovModel.HiddenMarkovModel-class.html#transitions_from"><a title="Bio.HMM.MarkovModel.HiddenMarkovModel.transitions_from" class="py-name" href="#" onclick="return doclink('link-19', 'transitions_from', 'link-19');">transitions_from</a></tt><tt class="py-op">(</tt><tt class="py-name">main_state</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">                <tt class="py-comment"># the value of the previous f or b value</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-name">var_value</tt> <tt class="py-op">=</tt> <tt class="py-name">previous_vars</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">second_state</tt><tt class="py-op">,</tt> <tt class="py-name">seq_pos</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="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">                <tt class="py-comment"># the transition probability</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-name">trans_value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt class="py-name">transition_prob</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">second_state</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">main_state</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line"> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">                <tt class="py-name">trans_and_var_sum</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-name">var_value</tt> <tt class="py-op">*</tt> <tt class="py-name">trans_value</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line"> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">            <tt class="py-name">s_value</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-name">emission</tt> <tt class="py-op">*</tt> <tt class="py-name">trans_and_var_sum</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line"> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">s_value</tt> </tt>
</div><a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"> </tt>
<a name="ScaledDPAlgorithms._forward_recursion"></a><div id="ScaledDPAlgorithms._forward_recursion-def"><a name="L223"></a><tt class="py-lineno">223</tt> <a class="py-toggle" href="#" id="ScaledDPAlgorithms._forward_recursion-toggle" onclick="return toggle('ScaledDPAlgorithms._forward_recursion');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#_forward_recursion">_forward_recursion</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cur_state</tt><tt class="py-op">,</tt> <tt class="py-param">sequence_pos</tt><tt class="py-op">,</tt> <tt class="py-param">forward_vars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ScaledDPAlgorithms._forward_recursion-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ScaledDPAlgorithms._forward_recursion-expanded"><a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">        <tt class="py-docstring">"""Calculate the value of the forward recursion.</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"><tt class="py-docstring">        Arguments:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"><tt class="py-docstring">        o cur_state -- The letter of the state we are calculating the</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"><tt class="py-docstring">        forward variable for.</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"><tt class="py-docstring">        o sequence_pos -- The position we are at in the training seq.</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line"><tt class="py-docstring">        o forward_vars -- The current set of forward variables</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">        <tt class="py-comment"># calculate the s value, if we haven't done so already (ie. during</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># a previous forward or backward recursion)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</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-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_s_values</tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'has_key', 'link-20');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">sequence_pos</tt><tt class="py-op">)</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_s_values</tt><tt class="py-op">[</tt><tt class="py-name">sequence_pos</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-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.HMM.DynamicProgramming.ScaledDPAlgorithms._calculate_s_value()=Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#_calculate_s_value"><a title="Bio.HMM.DynamicProgramming.ScaledDPAlgorithms._calculate_s_value" class="py-name" href="#" onclick="return doclink('link-21', '_calculate_s_value', 'link-21');">_calculate_s_value</a></tt><tt class="py-op">(</tt><tt class="py-name">sequence_pos</tt><tt class="py-op">,</tt> <tt class="py-name">forward_vars</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line"> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">        <tt class="py-comment"># e_{l}(x_{i})</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">seq_letter</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt><tt class="py-op">.</tt><tt class="py-name">emissions</tt><tt class="py-op">[</tt><tt class="py-name">sequence_pos</tt><tt class="py-op">]</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">        <tt class="py-name">cur_emission_prob</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt class="py-name">emission_prob</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">cur_state</tt><tt class="py-op">,</tt> <tt class="py-name">seq_letter</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">        <tt class="py-comment"># divide by the scaling value</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">scale_emission_prob</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">cur_emission_prob</tt><tt class="py-op">)</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">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_s_values</tt><tt class="py-op">[</tt><tt class="py-name">sequence_pos</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">         </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">        <tt class="py-comment"># loop over all of the possible states at the position</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">state_pos_sum</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">        <tt class="py-name">have_transition</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">second_state</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.HMM.MarkovModel.HiddenMarkovModel.transitions_from" class="py-name" href="#" onclick="return doclink('link-22', 'transitions_from', 'link-19');">transitions_from</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_state</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">            <tt class="py-name">have_transition</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">             </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">            <tt class="py-comment"># get the previous forward_var values</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment"># f_{k}(i - 1)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">prev_forward</tt> <tt class="py-op">=</tt> <tt class="py-name">forward_vars</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">second_state</tt><tt class="py-op">,</tt> <tt class="py-name">sequence_pos</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="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">            <tt class="py-comment"># a_{kl}</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">cur_trans_prob</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt class="py-name">transition_prob</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">second_state</tt><tt class="py-op">,</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">                                                       <tt class="py-name">cur_state</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">            <tt class="py-name">state_pos_sum</tt> <tt class="py-op">+=</tt> <tt class="py-name">prev_forward</tt> <tt class="py-op">*</tt> <tt class="py-name">cur_trans_prob</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line"> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">        <tt class="py-comment"># if we have the possiblity of having a transition</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># return the recursion value</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">have_transition</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">scale_emission_prob</tt> <tt class="py-op">*</tt> <tt class="py-name">state_pos_sum</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line"> </tt>
<a name="ScaledDPAlgorithms._backward_recursion"></a><div id="ScaledDPAlgorithms._backward_recursion-def"><a name="L270"></a><tt class="py-lineno">270</tt> <a class="py-toggle" href="#" id="ScaledDPAlgorithms._backward_recursion-toggle" onclick="return toggle('ScaledDPAlgorithms._backward_recursion');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#_backward_recursion">_backward_recursion</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cur_state</tt><tt class="py-op">,</tt> <tt class="py-param">sequence_pos</tt><tt class="py-op">,</tt> <tt class="py-param">backward_vars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ScaledDPAlgorithms._backward_recursion-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ScaledDPAlgorithms._backward_recursion-expanded"><a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">        <tt class="py-docstring">"""Calculate the value of the backward recursion</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line"><tt class="py-docstring">        Arguments:</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line"><tt class="py-docstring">        o cur_state -- The letter of the state we are calculating the</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line"><tt class="py-docstring">        forward variable for.</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"><tt class="py-docstring">        o sequence_pos -- The position we are at in the training seq.</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line"><tt class="py-docstring">        o backward_vars -- The current set of backward variables</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">        <tt class="py-comment"># calculate the s value, if we haven't done so already (ie. during</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># a previous forward or backward recursion)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</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-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_s_values</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-23', 'has_key', 'link-20');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">sequence_pos</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_s_values</tt><tt class="py-op">[</tt><tt class="py-name">sequence_pos</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">              <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.HMM.DynamicProgramming.ScaledDPAlgorithms._calculate_s_value" class="py-name" href="#" onclick="return doclink('link-24', '_calculate_s_value', 'link-21');">_calculate_s_value</a></tt><tt class="py-op">(</tt><tt class="py-name">sequence_pos</tt><tt class="py-op">,</tt> <tt class="py-name">backward_vars</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line"> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">        <tt class="py-comment"># loop over all of the possible states at the position</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">state_pos_sum</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line">        <tt class="py-name">have_transition</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">second_state</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.HMM.MarkovModel.HiddenMarkovModel.transitions_from" class="py-name" href="#" onclick="return doclink('link-25', 'transitions_from', 'link-19');">transitions_from</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_state</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">            <tt class="py-name">have_transition</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">            <tt class="py-comment"># e_{l}(x_{i + 1})</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">seq_letter</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt><tt class="py-op">.</tt><tt class="py-name">emissions</tt><tt class="py-op">[</tt><tt class="py-name">sequence_pos</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">            <tt class="py-name">cur_emission_prob</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt class="py-name">emission_prob</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">cur_state</tt><tt class="py-op">,</tt> <tt class="py-name">seq_letter</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line"> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">            <tt class="py-comment"># get the previous backward_var value</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment"># b_{l}(i + 1)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">prev_backward</tt> <tt class="py-op">=</tt> <tt class="py-name">backward_vars</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">second_state</tt><tt class="py-op">,</tt> <tt class="py-name">sequence_pos</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="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line"> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">            <tt class="py-comment"># the transition probability -- a_{kl}</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">cur_transition_prob</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mm</tt><tt class="py-op">.</tt><tt class="py-name">transition_prob</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">cur_state</tt><tt class="py-op">,</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">                                                            <tt class="py-name">second_state</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line"> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">            <tt class="py-name">state_pos_sum</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-name">cur_emission_prob</tt> <tt class="py-op">*</tt> <tt class="py-name">prev_backward</tt> <tt class="py-op">*</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">                              <tt class="py-name">cur_transition_prob</tt><tt class="py-op">)</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line"> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">        <tt class="py-comment"># if we have a probability for a transition, return it</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">have_transition</tt><tt class="py-op">:</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">state_pos_sum</tt> <tt class="py-op">/</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_s_values</tt><tt class="py-op">[</tt><tt class="py-name">sequence_pos</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">        <tt class="py-comment"># otherwise we have no probability (ie. we can't do this transition)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># and return None</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div></div><a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">             </tt>
<a name="LogDPAlgorithms"></a><div id="LogDPAlgorithms-def"><a name="L316"></a><tt class="py-lineno">316</tt> <a class="py-toggle" href="#" id="LogDPAlgorithms-toggle" onclick="return toggle('LogDPAlgorithms');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.LogDPAlgorithms-class.html">LogDPAlgorithms</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractDPAlgorithms</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LogDPAlgorithms-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="LogDPAlgorithms-expanded"><a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">    <tt class="py-docstring">"""Implement forward and backward algorithms using a log approach.</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line"><tt class="py-docstring">    This uses the approach of calculating the sum of log probabilities</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line"><tt class="py-docstring">    using a lookup table for common values.</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line"><tt class="py-docstring">    XXX This is not implemented yet!</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="LogDPAlgorithms.__init__"></a><div id="LogDPAlgorithms.__init__-def"><a name="L324"></a><tt class="py-lineno">324</tt> <a class="py-toggle" href="#" id="LogDPAlgorithms.__init__-toggle" onclick="return toggle('LogDPAlgorithms.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.DynamicProgramming.LogDPAlgorithms-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">markov_model</tt><tt class="py-op">,</tt> <tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LogDPAlgorithms.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LogDPAlgorithms.__init__-expanded"><a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"Haven't coded this yet..."</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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