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<a href="HiddenMarkovModel_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Andreas Bertsch $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;</div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor">#ifndef OPENMS_ANALYSIS_ID_HIDDENMARKOVMODEL_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_ID_HIDDENMARKOVMODEL_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;set&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Map_8h.html">OpenMS/DATASTRUCTURES/Map.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Types_8h.html">OpenMS/CONCEPT/Types.h</a>&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="StringList_8h.html">OpenMS/DATASTRUCTURES/StringList.h</a>&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;utility&gt;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;{</div>
<div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HMMState.html">   54</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;  {</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a>();</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> &amp; state);</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name, <span class="keywordtype">bool</span> hidden = <span class="keyword">true</span>);</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a>();</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> &amp;);</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    <span class="keywordtype">void</span> setName(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name);</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getName() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;    <span class="keywordtype">void</span> setHidden(<span class="keywordtype">bool</span> hidden);</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;    <span class="keywordtype">bool</span> isHidden() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;    <span class="keywordtype">void</span> addPredecessorState(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * state);</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    <span class="keywordtype">void</span> deletePredecessorState(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * state);</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    <span class="keywordtype">void</span> addSuccessorState(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * state);</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    <span class="keywordtype">void</span> deleteSuccessorState(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * state);</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;    <span class="keyword">const</span> std::set&lt;HMMState *&gt; &amp; getPredecessorStates() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;    <span class="keyword">const</span> std::set&lt;HMMState *&gt; &amp; getSuccessorStates() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div>
<div class="line"><a name="l00114"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HMMState.html#acaa04a44b52496c9e782a403c2fb93a3">  114</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1HMMState.html#acaa04a44b52496c9e782a403c2fb93a3">hidden_</a>;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;</div>
<div class="line"><a name="l00117"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HMMState.html#a46d25a1d56b8ab56e84b8bd0c7581e8f">  117</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1HMMState.html#a46d25a1d56b8ab56e84b8bd0c7581e8f">name_</a>;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HMMState.html#a90e2c638fb49ac754accefd0017872bf">  120</a></span>&#160;    std::set&lt;HMMState *&gt; <a class="code" href="classOpenMS_1_1HMMState.html#a90e2c638fb49ac754accefd0017872bf">pre_states_</a>;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;</div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HMMState.html#a0748be8113a06c4578eeb1677b936fe9">  123</a></span>&#160;    std::set&lt;HMMState *&gt; <a class="code" href="classOpenMS_1_1HMMState.html#a0748be8113a06c4578eeb1677b936fe9">succ_states_</a>;</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;  };</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;</div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html">  134</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a></div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;  {</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;    <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a>();</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;    <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a> &amp; hmm_new);</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a>();</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;    <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a> &amp;);</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;    <span class="keywordtype">void</span> writeGraphMLFile(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename);</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;    <span class="keywordtype">void</span> write(std::ostream &amp; out) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> getTransitionProbability(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; s1, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; s2) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;    <span class="keywordtype">void</span> setTransitionProbability(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; s1, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; s2, <a class="code" href="classdouble.html">DoubleReal</a> prob);</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getNumberOfStates() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;    <span class="keywordtype">void</span> addNewState(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * state);</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;    <span class="keywordtype">void</span> addNewState(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name);</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;    <span class="keywordtype">void</span> addSynonymTransition(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name1, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name2, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; synonym1, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; synonym2);</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;    <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">evaluate</a>();</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    <span class="keywordtype">void</span> train();</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;    <span class="keywordtype">void</span> setInitialTransitionProbability(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; state, <a class="code" href="classdouble.html">DoubleReal</a> prob);</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;    <span class="keywordtype">void</span> clearInitialTransitionProbabilities();</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;    <span class="keywordtype">void</span> setTrainingEmissionProbability(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; state, <a class="code" href="classdouble.html">DoubleReal</a> prob);</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;    <span class="keywordtype">void</span> clearTrainingEmissionProbabilities();</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;    <span class="keywordtype">void</span> enableTransition(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; s1, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; s2);</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;    <span class="keywordtype">void</span> disableTransition(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; s1, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; s2);</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;    <span class="keywordtype">void</span> disableTransitions();</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;    <span class="keywordtype">void</span> calculateEmissionProbabilities(<a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, DoubleReal&gt;</a> &amp; emission_probs);</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;    <span class="keywordtype">void</span> dump();</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;    <span class="keywordtype">void</span> forwardDump();</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;    <span class="comment">//void buildSynonyms();</span></div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;    <span class="keywordtype">void</span> estimateUntrainedTransitions();</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;    <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * getState(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name);</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * getState(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;    <span class="keywordtype">void</span> clear();</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;    <span class="keywordtype">void</span> setPseudoCounts(<a class="code" href="classdouble.html">DoubleReal</a> pseudo_counts);</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> getPseudoCounts() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;    <span class="keywordtype">void</span> setVariableModifications(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> &amp; modifications);</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;    <span class="keywordtype">void</span> disableTransition_(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * s1, <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * s2);</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;    <span class="keywordtype">void</span> enableTransition_(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * s1, <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * s2);</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;    <span class="keywordtype">void</span> setTrainingEmissionProbability_(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * state, <a class="code" href="classdouble.html">DoubleReal</a> prob);</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;    <span class="keywordtype">void</span> setTransitionProbability_(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * s1, <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * s2, <a class="code" href="classdouble.html">DoubleReal</a> prob);</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> getTransitionProbability_(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * s1, <a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> * s2) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;</div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;</div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;    <span class="keywordtype">void</span> calculateForwardPart_();</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;    <span class="keywordtype">void</span> calculateBackwardPart_();</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> getForwardVariable_(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> *);</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> getBackwardVariable_(<a class="code" href="classOpenMS_1_1HMMState.html">HMMState</a> *);</div>
<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;</div>
<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;    <span class="comment">// transition probs</span></div>
<div class="line"><a name="l00278"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#a167f2afb12749c3b8e5fb56731c87541">  278</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, Map&lt;HMMState *, DoubleReal&gt;</a> &gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#a167f2afb12749c3b8e5fb56731c87541">trans_</a>;</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;    <span class="comment">// transition prob counts</span></div>
<div class="line"><a name="l00281"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#a7cab49069c7deaae1e2306eb8b13934a">  281</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, Map&lt;HMMState *, DoubleReal&gt;</a> &gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#a7cab49069c7deaae1e2306eb8b13934a">count_trans_</a>;</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;</div>
<div class="line"><a name="l00283"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#a4221705db64ccb957b6cc25c453f4d1f">  283</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, Map&lt;HMMState *, std::vector&lt;DoubleReal&gt;</a> &gt; &gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#a4221705db64ccb957b6cc25c453f4d1f">count_trans_all_</a>;</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;</div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;    <span class="comment">// all transition probs of all training steps (for model checking)</span></div>
<div class="line"><a name="l00286"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#ade70e6b1e50e14bb3e346109b3bcce05">  286</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, Map&lt;HMMState *, std::vector&lt;DoubleReal&gt;</a> &gt; &gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#ade70e6b1e50e14bb3e346109b3bcce05">train_count_trans_all_</a>;</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;    <span class="comment">// number of training steps of the transitions</span></div>
<div class="line"><a name="l00289"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#ab907b97329259a275d3b8ce40cde9011">  289</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, Map&lt;HMMState *, Size&gt;</a> &gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#ab907b97329259a275d3b8ce40cde9011">training_steps_count_</a>;</div>
<div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;    <span class="comment">// forward variables</span></div>
<div class="line"><a name="l00292"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#a22c63302de3fd5eea869da629b1b99d4">  292</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, DoubleReal&gt;</a> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#a22c63302de3fd5eea869da629b1b99d4">forward_</a>;</div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;    <span class="comment">// backward variables</span></div>
<div class="line"><a name="l00295"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#ad714e1e8f08abce647d613b77dd0a472">  295</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, DoubleReal&gt;</a> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#ad714e1e8f08abce647d613b77dd0a472">backward_</a>;</div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;    <span class="comment">// name to state Mapping</span></div>
<div class="line"><a name="l00298"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#aa387783acf2c4d98d5a008a3e7696be2">  298</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, HMMState *&gt;</a> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#aa387783acf2c4d98d5a008a3e7696be2">name_to_state_</a>;</div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;</div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;    <span class="comment">// emission probabilities</span></div>
<div class="line"><a name="l00301"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#a644dcdf896b4537a06499262f268ae1d">  301</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, DoubleReal&gt;</a> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#a644dcdf896b4537a06499262f268ae1d">train_emission_prob_</a>;</div>
<div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;</div>
<div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;    <span class="comment">// initial transition probabilities</span></div>
<div class="line"><a name="l00304"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#aa614cc86dc45afcf94297a043b123eb0">  304</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, DoubleReal&gt;</a> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#aa614cc86dc45afcf94297a043b123eb0">init_prob_</a>;</div>
<div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;</div>
<div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;    <span class="comment">// all states of the HMM</span></div>
<div class="line"><a name="l00307"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#ac28909dc24c1560deec13aad6e593454">  307</a></span>&#160;    std::set&lt;HMMState *&gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#ac28909dc24c1560deec13aad6e593454">states_</a>;</div>
<div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;</div>
<div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;    <span class="comment">// trained transitions</span></div>
<div class="line"><a name="l00310"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#a56962bf56def2e162fec62711b6479b5">  310</a></span>&#160;    std::set&lt;std::pair&lt;HMMState *, HMMState *&gt; &gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#a56962bf56def2e162fec62711b6479b5">trained_trans_</a>;</div>
<div class="line"><a name="l00311"></a><span class="lineno">  311</span>&#160;</div>
<div class="line"><a name="l00312"></a><span class="lineno">  312</span>&#160;    <span class="comment">// synonym transitions Mapping</span></div>
<div class="line"><a name="l00313"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#ab4c74fe10ac349c28452a40fd05a6c5b">  313</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, Map&lt;String, std::pair&lt;String, String&gt;</a> &gt; &gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#ab4c74fe10ac349c28452a40fd05a6c5b">synonym_trans_names_</a>;</div>
<div class="line"><a name="l00314"></a><span class="lineno">  314</span>&#160;</div>
<div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;    <span class="comment">// synonym transitions</span></div>
<div class="line"><a name="l00316"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#a88afae9a099bb9cc930b4edd9c451086">  316</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, Map&lt;HMMState *, std::pair&lt;HMMState *, HMMState *&gt;</a> &gt; &gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#a88afae9a099bb9cc930b4edd9c451086">synonym_trans_</a>;</div>
<div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;</div>
<div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;    <span class="comment">// transitions which are enabled</span></div>
<div class="line"><a name="l00319"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#ad5beff60d29d5e41bdbd52b82983d28a">  319</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;HMMState *, std::set&lt;HMMState *&gt;</a> &gt; <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#ad5beff60d29d5e41bdbd52b82983d28a">enabled_trans_</a>;</div>
<div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;</div>
<div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;    <span class="comment">// pseudocounts used in this instance</span></div>
<div class="line"><a name="l00322"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#a65610d019ea6929ae1ccb1e08e21a15f">  322</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#a65610d019ea6929ae1ccb1e08e21a15f">pseudo_counts_</a>;</div>
<div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;</div>
<div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;    <span class="comment">// copy all the stuff from one HMM to this</span></div>
<div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;    <span class="keywordtype">void</span> copy_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a> &amp; source);</div>
<div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;</div>
<div class="line"><a name="l00327"></a><span class="lineno"><a class="line" href="classOpenMS_1_1HiddenMarkovModel.html#a31e1aad211f7b162ab3e7f786fe70798">  327</a></span>&#160;    <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html#a31e1aad211f7b162ab3e7f786fe70798">var_modifications_</a>;</div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;  };</div>
<div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;}</div>
<div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_a31e1aad211f7b162ab3e7f786fe70798"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#a31e1aad211f7b162ab3e7f786fe70798">OpenMS::HiddenMarkovModel::var_modifications_</a></div><div class="ttdeci">StringList var_modifications_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:327</div></div>
<div class="ttc" id="Types_8h_html"><div class="ttname"><a href="Types_8h.html">Types.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1HMMState_html_acaa04a44b52496c9e782a403c2fb93a3"><div class="ttname"><a href="classOpenMS_1_1HMMState.html#acaa04a44b52496c9e782a403c2fb93a3">OpenMS::HMMState::hidden_</a></div><div class="ttdeci">bool hidden_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1HMMState_html_a0748be8113a06c4578eeb1677b936fe9"><div class="ttname"><a href="classOpenMS_1_1HMMState.html#a0748be8113a06c4578eeb1677b936fe9">OpenMS::HMMState::succ_states_</a></div><div class="ttdeci">std::set&lt; HMMState * &gt; succ_states_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1HMMState_html_a90e2c638fb49ac754accefd0017872bf"><div class="ttname"><a href="classOpenMS_1_1HMMState.html#a90e2c638fb49ac754accefd0017872bf">OpenMS::HMMState::pre_states_</a></div><div class="ttdeci">std::set&lt; HMMState * &gt; pre_states_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:120</div></div>
<div class="ttc" id="StringList_8h_html"><div class="ttname"><a href="StringList_8h.html">StringList.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_a88afae9a099bb9cc930b4edd9c451086"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#a88afae9a099bb9cc930b4edd9c451086">OpenMS::HiddenMarkovModel::synonym_trans_</a></div><div class="ttdeci">Map&lt; HMMState *, Map&lt; HMMState *, std::pair&lt; HMMState *, HMMState * &gt; &gt; &gt; synonym_trans_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:316</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_ac28909dc24c1560deec13aad6e593454"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#ac28909dc24c1560deec13aad6e593454">OpenMS::HiddenMarkovModel::states_</a></div><div class="ttdeci">std::set&lt; HMMState * &gt; states_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:307</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_ade70e6b1e50e14bb3e346109b3bcce05"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#ade70e6b1e50e14bb3e346109b3bcce05">OpenMS::HiddenMarkovModel::train_count_trans_all_</a></div><div class="ttdeci">Map&lt; HMMState *, Map&lt; HMMState *, std::vector&lt; DoubleReal &gt; &gt; &gt; train_count_trans_all_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:286</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_aa614cc86dc45afcf94297a043b123eb0"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#aa614cc86dc45afcf94297a043b123eb0">OpenMS::HiddenMarkovModel::init_prob_</a></div><div class="ttdeci">Map&lt; HMMState *, DoubleReal &gt; init_prob_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:304</div></div>
<div class="ttc" id="Map_8h_html"><div class="ttname"><a href="Map_8h.html">Map.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_a167f2afb12749c3b8e5fb56731c87541"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#a167f2afb12749c3b8e5fb56731c87541">OpenMS::HiddenMarkovModel::trans_</a></div><div class="ttdeci">Map&lt; HMMState *, Map&lt; HMMState *, DoubleReal &gt; &gt; trans_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:278</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_ab4c74fe10ac349c28452a40fd05a6c5b"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#ab4c74fe10ac349c28452a40fd05a6c5b">OpenMS::HiddenMarkovModel::synonym_trans_names_</a></div><div class="ttdeci">Map&lt; String, Map&lt; String, std::pair&lt; String, String &gt; &gt; &gt; synonym_trans_names_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:313</div></div>
<div class="ttc" id="classOpenMS_1_1HMMState_html_a46d25a1d56b8ab56e84b8bd0c7581e8f"><div class="ttname"><a href="classOpenMS_1_1HMMState.html#a46d25a1d56b8ab56e84b8bd0c7581e8f">OpenMS::HMMState::name_</a></div><div class="ttdeci">String name_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_a56962bf56def2e162fec62711b6479b5"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#a56962bf56def2e162fec62711b6479b5">OpenMS::HiddenMarkovModel::trained_trans_</a></div><div class="ttdeci">std::set&lt; std::pair&lt; HMMState *, HMMState * &gt; &gt; trained_trans_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:310</div></div>
<div class="ttc" id="classOpenMS_1_1HMMState_html"><div class="ttname"><a href="classOpenMS_1_1HMMState.html">OpenMS::HMMState</a></div><div class="ttdoc">Hidden Markov Model State class for the Hidden Markov Model. </div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_aa387783acf2c4d98d5a008a3e7696be2"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#aa387783acf2c4d98d5a008a3e7696be2">OpenMS::HiddenMarkovModel::name_to_state_</a></div><div class="ttdeci">Map&lt; String, HMMState * &gt; name_to_state_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:298</div></div>
<div class="ttc" id="namespaceOpenMS_1_1OptimizationFunctions_html_aacf12ce6c8657d87174c792d19c318bf"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">OpenMS::OptimizationFunctions::evaluate</a></div><div class="ttdeci">int evaluate(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)</div><div class="ttdoc">Driver function for the evaluation of function and jacobian. </div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_a7cab49069c7deaae1e2306eb8b13934a"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#a7cab49069c7deaae1e2306eb8b13934a">OpenMS::HiddenMarkovModel::count_trans_</a></div><div class="ttdeci">Map&lt; HMMState *, Map&lt; HMMState *, DoubleReal &gt; &gt; count_trans_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:281</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_a22c63302de3fd5eea869da629b1b99d4"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#a22c63302de3fd5eea869da629b1b99d4">OpenMS::HiddenMarkovModel::forward_</a></div><div class="ttdeci">Map&lt; HMMState *, DoubleReal &gt; forward_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:292</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_ad5beff60d29d5e41bdbd52b82983d28a"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#ad5beff60d29d5e41bdbd52b82983d28a">OpenMS::HiddenMarkovModel::enabled_trans_</a></div><div class="ttdeci">Map&lt; HMMState *, std::set&lt; HMMState * &gt; &gt; enabled_trans_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:319</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html"><div class="ttname"><a href="classOpenMS_1_1StringList.html">OpenMS::StringList</a></div><div class="ttdoc">String list. </div><div class="ttdef"><b>Definition:</b> StringList.h:56</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_a65610d019ea6929ae1ccb1e08e21a15f"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#a65610d019ea6929ae1ccb1e08e21a15f">OpenMS::HiddenMarkovModel::pseudo_counts_</a></div><div class="ttdeci">DoubleReal pseudo_counts_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:322</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_ad714e1e8f08abce647d613b77dd0a472"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#ad714e1e8f08abce647d613b77dd0a472">OpenMS::HiddenMarkovModel::backward_</a></div><div class="ttdeci">Map&lt; HMMState *, DoubleReal &gt; backward_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:295</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html">OpenMS::HiddenMarkovModel</a></div><div class="ttdoc">Hidden Markov Model implementation of PILIS. </div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:134</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_a644dcdf896b4537a06499262f268ae1d"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#a644dcdf896b4537a06499262f268ae1d">OpenMS::HiddenMarkovModel::train_emission_prob_</a></div><div class="ttdeci">Map&lt; HMMState *, DoubleReal &gt; train_emission_prob_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:301</div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_ab907b97329259a275d3b8ce40cde9011"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#ab907b97329259a275d3b8ce40cde9011">OpenMS::HiddenMarkovModel::training_steps_count_</a></div><div class="ttdeci">Map&lt; HMMState *, Map&lt; HMMState *, Size &gt; &gt; training_steps_count_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:289</div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html_a4221705db64ccb957b6cc25c453f4d1f"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html#a4221705db64ccb957b6cc25c453f4d1f">OpenMS::HiddenMarkovModel::count_trans_all_</a></div><div class="ttdeci">Map&lt; HMMState *, Map&lt; HMMState *, std::vector&lt; DoubleReal &gt; &gt; &gt; count_trans_all_</div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:283</div></div>
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