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<a href="DetectabilitySimulation_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>
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<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>
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<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">// $Maintainer: Stephan Aiche$</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Stephan Aiche, Chris Bielow$</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;<span class="preprocessor">#ifndef OPENMS_SIMULATION_DETECTABILITYSIMULATION_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_SIMULATION_DETECTABILITYSIMULATION_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SimTypes_8h.html">OpenMS/SIMULATION/SimTypes.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;{</div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DetectabilitySimulation.html">   53</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1DetectabilitySimulation.html">DetectabilitySimulation</a> :</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</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;</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <a class="code" href="classOpenMS_1_1DetectabilitySimulation.html">DetectabilitySimulation</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_1DetectabilitySimulation.html">DetectabilitySimulation</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DetectabilitySimulation.html">DetectabilitySimulation</a> &amp; source);</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;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1DetectabilitySimulation.html">DetectabilitySimulation</a>();</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    <a class="code" href="classOpenMS_1_1DetectabilitySimulation.html">DetectabilitySimulation</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DetectabilitySimulation.html">DetectabilitySimulation</a> &amp; source);</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="keywordtype">void</span> filterDetectability(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapSim</a> &amp; features);</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;    <span class="keywordtype">void</span> predictDetectabilities(std::vector&lt;String&gt; &amp; peptides_vector, std::vector&lt;DoubleReal&gt; &amp; labels,</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;                                std::vector&lt;DoubleReal&gt; &amp; detectabilities);</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    <span class="keywordtype">void</span> setDefaultParams_();</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;    <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DetectabilitySimulation.html#a4e877fb7eb5cd2d9471205a169c223dc">   95</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1DetectabilitySimulation.html#a4e877fb7eb5cd2d9471205a169c223dc">min_detect_</a>;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DetectabilitySimulation.html#ae867a950ff117c82ed0fd9e2fbb9b1a7">   98</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">OpenMS::String</a> <a class="code" href="classOpenMS_1_1DetectabilitySimulation.html#ae867a950ff117c82ed0fd9e2fbb9b1a7">dt_model_file_</a>;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    <span class="keywordtype">void</span> svmFilter_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapSim</a> &amp;);</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="keywordtype">void</span> noFilter_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapSim</a> &amp;);</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;  };</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;}</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="preprocessor">#endif</span></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_1DetectabilitySimulation_html"><div class="ttname"><a href="classOpenMS_1_1DetectabilitySimulation.html">OpenMS::DetectabilitySimulation</a></div><div class="ttdoc">Simulates peptide detectability. </div><div class="ttdef"><b>Definition:</b> DetectabilitySimulation.h:53</div></div>
<div class="ttc" id="SimTypes_8h_html"><div class="ttname"><a href="SimTypes_8h.html">SimTypes.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap</a></div><div class="ttdoc">A container for features. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:111</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DetectabilitySimulation_html_ae867a950ff117c82ed0fd9e2fbb9b1a7"><div class="ttname"><a href="classOpenMS_1_1DetectabilitySimulation.html#ae867a950ff117c82ed0fd9e2fbb9b1a7">OpenMS::DetectabilitySimulation::dt_model_file_</a></div><div class="ttdeci">OpenMS::String dt_model_file_</div><div class="ttdoc">Name of the svm model file. </div><div class="ttdef"><b>Definition:</b> DetectabilitySimulation.h:98</div></div>
<div class="ttc" id="classOpenMS_1_1DetectabilitySimulation_html_a4e877fb7eb5cd2d9471205a169c223dc"><div class="ttname"><a href="classOpenMS_1_1DetectabilitySimulation.html#a4e877fb7eb5cd2d9471205a169c223dc">OpenMS::DetectabilitySimulation::min_detect_</a></div><div class="ttdeci">DoubleReal min_detect_</div><div class="ttdoc">Minimum allowed detectability likelihood of a peptide. </div><div class="ttdef"><b>Definition:</b> DetectabilitySimulation.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
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