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<a href="PSLPFormulation_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>
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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: Alexandra Zerck $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: $</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_ANALYSIS_TARGETED_PSLPFORMULATION_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_ANALYSIS_TARGETED_PSLPFORMULATION_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#include &lt;<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>&gt;</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="LPWrapper_8h.html">OpenMS/DATASTRUCTURES/LPWrapper.h</a>&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="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;{</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;  <span class="keyword">class </span>PrecursorIonSelectionPreprocessing;</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;  <span class="keyword">class </span>PSProteinInference;</div>
<div class="line"><a name="l00051"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PSLPFormulation.html">   51</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a> :</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;  {</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;</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="l00058"></a><span class="lineno">   58</span>&#160;</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;    <a class="code" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a>();</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a>();</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;</div>
<div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">   66</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">IndexTriple</a></div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    {</div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a2b11212b5257b0c9f05b5d36f266dd67">   68</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a2b11212b5257b0c9f05b5d36f266dd67">feature</a>;</div>
<div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a70e4788ce6e5dd2fb7780bc492db20d5">   69</a></span>&#160;      <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a70e4788ce6e5dd2fb7780bc492db20d5">scan</a>;</div>
<div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#ac8ce2b86c4cf3b7dc5e9961155e21f92">   70</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#ac8ce2b86c4cf3b7dc5e9961155e21f92">variable</a>;</div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#ad00b56bf94e188184c11c6fd0af6f914">   71</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#ad00b56bf94e188184c11c6fd0af6f914">rt_probability</a>;</div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#aa48c6b11534b7ebe74ec08ec7b70aecb">   72</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#aa48c6b11534b7ebe74ec08ec7b70aecb">signal_weight</a>;</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a24b2e6838da320481d4725b945c06e1f">   73</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a24b2e6838da320481d4725b945c06e1f">prot_acc</a>;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    };</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> InputPeakType&gt;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    <span class="keywordtype">void</span> createAndSolveILPForKnownLCMSMapFeatureBased(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features,</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;                                                      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;InputPeakType&gt;</a> &amp; experiment,</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;                                                      std::vector&lt;IndexTriple&gt; &amp; variable_indices,</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;                                                      std::vector&lt;std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &gt; &amp; mass_ranges,</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;                                                      std::set&lt;Int&gt; &amp; charges_set, <a class="code" href="classunsigned_01int.html">UInt</a> ms2_spectra_per_rt_bin,</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;                                                      std::vector&lt;int&gt; &amp; solution_indices);</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    <span class="keywordtype">void</span> createAndSolveILPForInclusionListCreation(<a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp; preprocessing,</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;                                                   <a class="code" href="classunsigned_01int.html">UInt</a> ms2_spectra_per_rt_bin, <a class="code" href="classunsigned_01int.html">UInt</a> max_list_size,</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;                                                   <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; precursors,</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;                                                   <span class="keywordtype">bool</span> solve_ILP = <span class="keyword">true</span>);</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> InputPeakType&gt;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    <span class="keywordtype">void</span> createAndSolveCombinedLPForKnownLCMSMapFeatureBased(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features,</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;                                                             <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;InputPeakType&gt;</a> &amp; experiment,</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;                                                             std::vector&lt;IndexTriple&gt; &amp; variable_indices,</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;                                                             std::vector&lt;int&gt; &amp; solution_indices,</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;                                                             std::vector&lt;std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &gt; &amp; mass_ranges,</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;                                                             std::set&lt;Int&gt; &amp; charges_set, <a class="code" href="classunsigned_01int.html">UInt</a> ms2_spectra_per_rt_bin,</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;                                                             <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> step_size = 0, <span class="keywordtype">bool</span> sequential_order = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;    <span class="keywordtype">void</span> updateStepSizeConstraint(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> iteration, <a class="code" href="classunsigned_01int.html">UInt</a> step_size);</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;    <span class="keywordtype">void</span> updateFeatureILPVariables(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; new_features, std::vector&lt;IndexTriple&gt; &amp; variable_indices, std::map&lt;<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::vector&lt;String&gt; &gt; &amp; feature_constraints_map);</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;    <span class="keywordtype">void</span> updateRTConstraintsForSequentialILP(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp; rt_index, <a class="code" href="classunsigned_01int.html">UInt</a> ms2_spectra_per_rt_bin, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_rt_index);</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;    <span class="keywordtype">void</span> updateCombinedILP(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features, <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp; preprocessed_db, std::vector&lt;IndexTriple&gt; &amp; variable_indices,</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;                           std::vector&lt;String&gt; &amp; new_protein_accs, std::vector&lt;String&gt; &amp; protein_accs, <a class="code" href="classOpenMS_1_1PSProteinInference.html">PSProteinInference</a> &amp; prot_inference, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp; variable_counter,</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;                           std::map&lt;<a class="code" href="classOpenMS_1_1String.html">String</a>, std::vector&lt;Size&gt; &gt; &amp; protein_feature_map, <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> &amp; new_feature, std::map&lt;String, Size&gt; &amp; protein_variable_index_map,</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;                           std::map&lt;<a class="code" href="classOpenMS_1_1String.html">String</a>, std::set&lt;String&gt; &gt; &amp; prot_id_counter);</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;    <span class="keywordtype">void</span> solveILP(std::vector&lt;int&gt; &amp; solution_indices);</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;</div>
<div class="line"><a name="l00128"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PSLPFormulation.html#a2b206fdbe8649b90b854129f37fc594a">  128</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a2b206fdbe8649b90b854129f37fc594a">setLPSolver</a>(<a class="code" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> solver)</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;    {</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;      solver_ = solver;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;    }</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;</div>
<div class="line"><a name="l00133"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PSLPFormulation.html#ac945a0966726a3a644d194b81c28d960">  133</a></span>&#160;    <a class="code" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> <a class="code" href="classOpenMS_1_1PSLPFormulation.html#ac945a0966726a3a644d194b81c28d960">getLPSolver</a>()</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;    {</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;      <span class="keywordflow">return</span> solver_;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;    }</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1IndexLess.html">  138</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexLess.html">IndexLess</a> :</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;      std::binary_function&lt;IndexTriple, IndexTriple, bool&gt;</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;    {</div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1IndexLess.html#a9f04da0abc6e3d5ce7402d0018e8d150">  141</a></span>&#160;      <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexLess.html#a9f04da0abc6e3d5ce7402d0018e8d150">operator()</a>(<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">IndexTriple</a>  <span class="keyword">const</span> &amp; left,</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;                             <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">IndexTriple</a> <span class="keyword">const</span> &amp; right)<span class="keyword"> const</span></div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;        <span class="keywordflow">return</span> left.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a2b11212b5257b0c9f05b5d36f266dd67">feature</a> &lt; right.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a2b11212b5257b0c9f05b5d36f266dd67">feature</a>;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;      }</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;    };</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;</div>
<div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1ScanLess.html">  150</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PSLPFormulation_1_1ScanLess.html">ScanLess</a> :</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;      std::binary_function&lt;IndexTriple, IndexTriple, bool&gt;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;    {</div>
<div class="line"><a name="l00153"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1ScanLess.html#a9f04da0abc6e3d5ce7402d0018e8d150">  153</a></span>&#160;      <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1ScanLess.html#a9f04da0abc6e3d5ce7402d0018e8d150">operator()</a>(<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">IndexTriple</a>  <span class="keyword">const</span> &amp; left,</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;                             <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">IndexTriple</a>  <span class="keyword">const</span> &amp; right)<span class="keyword"> const</span></div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;        <span class="keywordflow">return</span> left.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a70e4788ce6e5dd2fb7780bc492db20d5">scan</a> &lt; right.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a70e4788ce6e5dd2fb7780bc492db20d5">scan</a>;</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;      }</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;    };</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div>
<div class="line"><a name="l00161"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1VariableIndexLess.html">  161</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PSLPFormulation_1_1VariableIndexLess.html">VariableIndexLess</a> :</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;      std::binary_function&lt;IndexTriple, IndexTriple, bool&gt;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;    {</div>
<div class="line"><a name="l00164"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PSLPFormulation_1_1VariableIndexLess.html#a9f04da0abc6e3d5ce7402d0018e8d150">  164</a></span>&#160;      <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1VariableIndexLess.html#a9f04da0abc6e3d5ce7402d0018e8d150">operator()</a>(<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">IndexTriple</a>  <span class="keyword">const</span> &amp; left,</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;                             <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">IndexTriple</a>  <span class="keyword">const</span> &amp; right)<span class="keyword"> const</span></div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;        <span class="keywordflow">return</span> left.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#ac8ce2b86c4cf3b7dc5e9961155e21f92">variable</a> &lt; right.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#ac8ce2b86c4cf3b7dc5e9961155e21f92">variable</a>;</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;      }</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;    };</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> InputPeakType&gt;</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;    <span class="keywordtype">void</span> getXIC_(<span class="keyword">const</span> std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &amp; end_points,</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;                 std::vector&lt;DoubleReal&gt; &amp; weights,</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;                 <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;InputPeakType&gt;</a> &amp; experiment,</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;                 <span class="keyword">const</span> <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">normalize</a>);</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> InputPeakType&gt;</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;    <span class="keywordtype">void</span> calculateXICs_(std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; &amp; xics,</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;                        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features,</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;                        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;InputPeakType&gt;</a> &amp; experiment,</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;                        <span class="keyword">const</span> std::vector&lt;std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &gt; &amp; mass_ranges,</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">normalize</a>);</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;    <span class="keywordtype">void</span> createAndSolveILP_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features, std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; &amp; intensity_weights,</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;                            std::set&lt;Int&gt; &amp; charges_set, std::vector&lt;std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &gt; &amp; mass_ranges,</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;                            std::vector&lt;IndexTriple&gt; &amp; variable_indices, std::vector&lt;int&gt; &amp; solution_indices,</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;                            <a class="code" href="classunsigned_01int.html">UInt</a> ms2_spectra_per_rt_bin, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_scans);</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;    <span class="keywordtype">void</span> createAndSolveCombinedLPFeatureBased_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features, std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; &amp; intensity_weights,</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;                                               std::set&lt;Int&gt; &amp; charges_set, std::vector&lt;std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &gt; &amp; mass_ranges,</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;                                               std::vector&lt;IndexTriple&gt; &amp; variable_indices, std::vector&lt;Int&gt; &amp; solution_indices,</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;                                               <a class="code" href="classunsigned_01int.html">UInt</a> ms2_spectra_per_rt_bin, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_scans, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> step_size = 0, <span class="keywordtype">bool</span> sequential_order = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;    <span class="keywordtype">void</span> addProteinToILP_(<a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp; preprocessing,</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;                          std::map&lt;<a class="code" href="classOpenMS_1_1String.html">String</a>, std::vector&lt;DoubleReal&gt; &gt;::const_iterator map_iter,</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;                          <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp; counter, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp; pep_counter, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp; feature_counter,</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;                          std::vector&lt;IndexTriple&gt; &amp; variable_indices,</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;                          std::map&lt;String, Size&gt; &amp; protein_penalty_index_map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; precursors);</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;    <span class="keywordtype">void</span> addPrecursorAcquisitionNumberConstraint_(std::vector&lt;IndexTriple&gt; &amp; variable_indices, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_features, <a class="code" href="classunsigned_01int.html">UInt</a> number_of_msms_per_precursor);</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;    <span class="keywordtype">void</span> addMaxInclusionListSizeConstraints_(std::vector&lt;IndexTriple&gt; &amp; variable_indices, <span class="comment">/*Size number_of_features,*/</span> <a class="code" href="classunsigned_01int.html">UInt</a> max_list_size);</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;    <span class="keywordtype">void</span> addRTBinCapacityConstraint_(std::vector&lt;IndexTriple&gt; &amp; variable_indices,</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;                                     <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_rt_index, <a class="code" href="classunsigned_01int.html">UInt</a> ms2_spectra_per_rt_bin, <span class="keywordtype">bool</span> sequential_order = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;    <span class="keywordtype">void</span> addProteinCoverageConstraint_(std::vector&lt;IndexTriple&gt; &amp; variable_indices,</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;                                       <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp; preprocessing,</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;                                       std::map&lt;String, Size&gt; protein_variable_index_map);</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;    <span class="keywordtype">void</span> addStepSizeConstraint_(std::vector&lt;IndexTriple&gt; &amp; variable_indices, <a class="code" href="classunsigned_01int.html">UInt</a> step_size);</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;    <span class="keywordtype">void</span> assembleInclusionListForProteinBasedLP_(std::vector&lt;IndexTriple&gt; &amp; variable_indices, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; precursors, std::vector&lt;int&gt; &amp; solution_indices, <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp; preprocessing);</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;    <span class="keywordtype">void</span> updateObjFunction_(<a class="code" href="classOpenMS_1_1String.html">String</a> acc, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features, <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp; preprocessed_db, std::vector&lt;IndexTriple&gt; &amp; variable_indices);</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;    <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> getNumberOfPrecsInSpectrum_(<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> constr_idx);</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;</div>
<div class="line"><a name="l00230"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PSLPFormulation.html#a3fde56a178e0bdc00cd84a011415ee41">  230</a></span>&#160;    <a class="code" href="classOpenMS_1_1LPWrapper.html">LPWrapper</a> * <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a3fde56a178e0bdc00cd84a011415ee41">model_</a>;</div>
<div class="line"><a name="l00231"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PSLPFormulation.html#afb8f1202d548f01394d85fbeb51f9adf">  231</a></span>&#160;    <a class="code" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> <a class="code" href="classOpenMS_1_1PSLPFormulation.html#afb8f1202d548f01394d85fbeb51f9adf">solver_</a>;</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;  };</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">typename</span> InputPeakType&gt;</div>
<div class="line"><a name="l00235"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PSLPFormulation.html#a350a55d7f8d02185064c3682c0a4d7f8">  235</a></span>&#160;  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a350a55d7f8d02185064c3682c0a4d7f8">PSLPFormulation::getXIC_</a>(<span class="keyword">const</span> std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &amp; end_points,</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;                                std::vector&lt;DoubleReal&gt; &amp; weights,</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;                                <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;InputPeakType&gt;</a> &amp; experiment,</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">normalize</a>)</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;  {</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> max_weight = 0.;</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;    weights.clear();</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;    <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; end_points.size(); i += 2)</div>
<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;    {</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> weight = 0.;</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = end_points[i].second; j &lt;= end_points[i + 1].second; ++j)</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;      {</div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;        weight += experiment[end_points[i].first][j].getIntensity();</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;        <span class="comment">// std::cout &lt;&lt; &quot; add &quot;&lt;&lt;experiment[end_points[i].first][j].getIntensity()&lt;&lt;std::endl;</span></div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;      }</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;      <span class="keywordflow">if</span> (weight &gt; max_weight)</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;        max_weight = weight;</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;</div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;      weights.push_back(weight);</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;    }</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;    <span class="keywordflow">if</span> (normalize)</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;    {</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;      <span class="comment">// normalize weights</span></div>
<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; weights.size(); ++i)</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;      {</div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;<span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;<span class="preprocessor"></span>        <span class="keywordflow">if</span> (end_points.size() &gt;= i)</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;        {</div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;          std::cout &lt;&lt; <span class="stringliteral">&quot;scan &quot;</span> &lt;&lt; end_points[i].first &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; weights[i] &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; max_weight</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;                    &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; weights[i] / max_weight &lt;&lt; std::endl;</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;        }</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;<span class="preprocessor"></span>        weights[i] /= max_weight;</div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;      }</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;    }</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;  }</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">typename</span> InputPeakType&gt;</div>
<div class="line"><a name="l00274"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PSLPFormulation.html#a8a38d766081c104c51a498b4d836a456">  274</a></span>&#160;  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a8a38d766081c104c51a498b4d836a456">PSLPFormulation::calculateXICs_</a>(std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; &amp; xics,</div>
<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;                                       <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features,</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;                                       <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;InputPeakType&gt;</a> &amp; experiment,</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;                                       <span class="keyword">const</span> std::vector&lt;std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &gt; &amp; mass_ranges,</div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;                                       <span class="keyword">const</span> <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">normalize</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;    xics.clear();</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;    xics.resize(features.size());</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;    <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; features.size(); ++i)</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;    {</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;      <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a350a55d7f8d02185064c3682c0a4d7f8">getXIC_</a>(mass_ranges[i], xics[i], experiment, normalize);</div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;    }</div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;  }</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="keyword">template</span> &lt;<span class="keyword">typename</span> InputPeakType&gt;</div>
<div class="line"><a name="l00289"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PSLPFormulation.html#a2a93e2928cdbb7704c7d49a33f13b091">  289</a></span>&#160;  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a2a93e2928cdbb7704c7d49a33f13b091">PSLPFormulation::createAndSolveILPForKnownLCMSMapFeatureBased</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features,</div>
<div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;                                                                     <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;InputPeakType&gt;</a> &amp; experiment,</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;                                                                     std::vector&lt;IndexTriple&gt; &amp; variable_indices,</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;                                                                     std::vector&lt;std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &gt; &amp; mass_ranges,</div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;                                                                     std::set&lt;Int&gt; &amp; charges_set, <a class="code" href="classunsigned_01int.html">UInt</a> ms2_spectra_per_rt_bin,</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;                                                                     std::vector&lt;int&gt; &amp; solution_indices)</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;  {</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;    std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; intensity_weights;</div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;    <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a8a38d766081c104c51a498b4d836a456">calculateXICs_</a>(intensity_weights, features, experiment, mass_ranges, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;<span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;<span class="preprocessor"></span>    std::cout &lt;&lt; <span class="stringliteral">&quot;got xics&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;    <a class="code" href="classOpenMS_1_1PSLPFormulation.html#abf5924afa9c5296213f21da56c7727c5">createAndSolveILP_</a>(features, intensity_weights, charges_set, mass_ranges, variable_indices, solution_indices,</div>
<div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;                       ms2_spectra_per_rt_bin, experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</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;</div>
<div class="line"><a name="l00307"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#a24b1a9c3ebd7c67a0a0a1c4b9a17559f">  307</a></span>&#160;  <span class="keyword">inline</span> OPENMS_DLLAPI std::ostream &amp; <a class="code" href="namespaceOpenMS.html#a74df8b74439d1f76961c8d987fb074fd">operator&lt;&lt;</a>(std::ostream &amp; os, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">PSLPFormulation::IndexTriple</a> &amp; triple)</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;    os &lt;&lt; <span class="stringliteral">&quot;feature: &quot;</span> &lt;&lt; triple.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a2b11212b5257b0c9f05b5d36f266dd67">feature</a> &lt;&lt; <span class="stringliteral">&quot; scan: &quot;</span> &lt;&lt; triple.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a70e4788ce6e5dd2fb7780bc492db20d5">scan</a> &lt;&lt; <span class="stringliteral">&quot; variable: &quot;</span> &lt;&lt; triple.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#ac8ce2b86c4cf3b7dc5e9961155e21f92">variable</a> &lt;&lt; <span class="stringliteral">&quot; prot_acc: &quot;</span> &lt;&lt; triple.<a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a24b2e6838da320481d4725b945c06e1f">prot_acc</a>;</div>
<div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160;    <span class="keywordflow">return</span> os;</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;</div>
<div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">typename</span> InputPeakType&gt;</div>
<div class="line"><a name="l00314"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PSLPFormulation.html#a79f7295c0f12730a06e4e2c871f6a322">  314</a></span>&#160;  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a79f7295c0f12730a06e4e2c871f6a322">PSLPFormulation::createAndSolveCombinedLPForKnownLCMSMapFeatureBased</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features,</div>
<div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;                                                                            <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;InputPeakType&gt;</a> &amp; experiment,</div>
<div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;                                                                            std::vector&lt;IndexTriple&gt; &amp; variable_indices,</div>
<div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;                                                                            std::vector&lt;Int&gt; &amp; solution_indices,</div>
<div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;                                                                            std::vector&lt;std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &gt; &amp; mass_ranges,</div>
<div class="line"><a name="l00319"></a><span class="lineno">  319</span>&#160;                                                                            std::set&lt;Int&gt; &amp; charges_set, <a class="code" href="classunsigned_01int.html">UInt</a> ms2_spectra_per_rt_bin,</div>
<div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;                                                                            <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> step_size, <span class="keywordtype">bool</span> sequential_order)</div>
<div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;  {</div>
<div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;</div>
<div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;    std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; intensity_weights;</div>
<div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;    <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a8a38d766081c104c51a498b4d836a456">calculateXICs_</a>(intensity_weights, features, experiment, mass_ranges, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;<span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;<span class="preprocessor"></span>    std::cout &lt;&lt; <span class="stringliteral">&quot;got xics&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;    <a class="code" href="classOpenMS_1_1PSLPFormulation.html#a1086e2f906cf141a7bd2b42da33126b2">createAndSolveCombinedLPFeatureBased_</a>(features, intensity_weights, charges_set, mass_ranges, variable_indices, solution_indices, ms2_spectra_per_rt_bin,</div>
<div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;                                          experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), step_size, sequential_order);</div>
<div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;  }</div>
<div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;</div>
<div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;} <span class="comment">// namespace</span></div>
<div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;</div>
<div class="line"><a name="l00335"></a><span class="lineno">  335</span>&#160;<span class="preprocessor">#endif // OPENMS_ANALYSIS_ID_PSLPFORMULATION_H</span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1IndexTriple_html_aa48c6b11534b7ebe74ec08ec7b70aecb"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#aa48c6b11534b7ebe74ec08ec7b70aecb">OpenMS::PSLPFormulation::IndexTriple::signal_weight</a></div><div class="ttdeci">DoubleReal signal_weight</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:72</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_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1LPWrapper_html_ab659f8690ca779b8c3d73fe524a39a00"><div class="ttname"><a href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">OpenMS::LPWrapper::SOLVER</a></div><div class="ttdeci">SOLVER</div><div class="ttdef"><b>Definition:</b> LPWrapper.h:124</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1IndexLess_html_a9f04da0abc6e3d5ce7402d0018e8d150"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1IndexLess.html#a9f04da0abc6e3d5ce7402d0018e8d150">OpenMS::PSLPFormulation::IndexLess::operator()</a></div><div class="ttdeci">bool operator()(IndexTriple const &amp;left, IndexTriple const &amp;right) const </div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:141</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1IndexLess_html"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1IndexLess.html">OpenMS::PSLPFormulation::IndexLess</a></div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:138</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap&lt;&gt;</a></div></div>
<div class="ttc" id="namespaceOpenMS_html_a74df8b74439d1f76961c8d987fb074fd"><div class="ttname"><a href="namespaceOpenMS.html#a74df8b74439d1f76961c8d987fb074fd">OpenMS::operator&lt;&lt;</a></div><div class="ttdeci">std::ostream &amp; operator&lt;&lt;(std::ostream &amp;os, const ItraqQuantifier::ItraqQuantifierStats &amp;stats)</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1IndexTriple_html"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">OpenMS::PSLPFormulation::IndexTriple</a></div><div class="ttdoc">Struct that holds the indices of the precursors in the feature map and the ilp formulation. </div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:66</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_1PSLPFormulation_html_a79f7295c0f12730a06e4e2c871f6a322"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#a79f7295c0f12730a06e4e2c871f6a322">OpenMS::PSLPFormulation::createAndSolveCombinedLPForKnownLCMSMapFeatureBased</a></div><div class="ttdeci">void createAndSolveCombinedLPForKnownLCMSMapFeatureBased(const FeatureMap&lt;&gt; &amp;features, const MSExperiment&lt; InputPeakType &gt; &amp;experiment, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::vector&lt; int &gt; &amp;solution_indices, std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, std::set&lt; Int &gt; &amp;charges_set, UInt ms2_spectra_per_rt_bin, Size step_size=0, bool sequential_order=false)</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:314</div></div>
<div class="ttc" id="classOpenMS_1_1LPWrapper_html"><div class="ttname"><a href="classOpenMS_1_1LPWrapper.html">OpenMS::LPWrapper</a></div><div class="ttdef"><b>Definition:</b> LPWrapper.h:61</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a546b9a9117f4207e3cfc9ef2ea4aad3d"><div class="ttname"><a href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">OpenSwath::normalize</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI void normalize(const std::vector&lt; double &gt; &amp;intensities, double normalization_factor, std::vector&lt; double &gt; &amp;normalized_intensities)</div><div class="ttdoc">Normalize intensities in vector by normalization_factor. </div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1VariableIndexLess_html"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1VariableIndexLess.html">OpenMS::PSLPFormulation::VariableIndexLess</a></div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:161</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1ScanLess_html"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1ScanLess.html">OpenMS::PSLPFormulation::ScanLess</a></div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:150</div></div>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html_a1086e2f906cf141a7bd2b42da33126b2"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#a1086e2f906cf141a7bd2b42da33126b2">OpenMS::PSLPFormulation::createAndSolveCombinedLPFeatureBased_</a></div><div class="ttdeci">void createAndSolveCombinedLPFeatureBased_(const FeatureMap&lt;&gt; &amp;features, std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; &amp;intensity_weights, std::set&lt; Int &gt; &amp;charges_set, std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::vector&lt; Int &gt; &amp;solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans, Size step_size=0, bool sequential_order=false)</div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="LPWrapper_8h_html"><div class="ttname"><a href="LPWrapper_8h.html">LPWrapper.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html_afb8f1202d548f01394d85fbeb51f9adf"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#afb8f1202d548f01394d85fbeb51f9adf">OpenMS::PSLPFormulation::solver_</a></div><div class="ttdeci">LPWrapper::SOLVER solver_</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:231</div></div>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html_a2b206fdbe8649b90b854129f37fc594a"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#a2b206fdbe8649b90b854129f37fc594a">OpenMS::PSLPFormulation::setLPSolver</a></div><div class="ttdeci">void setLPSolver(LPWrapper::SOLVER solver)</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:128</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelectionPreprocessing_html"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">OpenMS::PrecursorIonSelectionPreprocessing</a></div><div class="ttdoc">This class implements the database preprocessing needing for precursor ion selection. </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelectionPreprocessing.h:56</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1IndexTriple_html_a2b11212b5257b0c9f05b5d36f266dd67"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a2b11212b5257b0c9f05b5d36f266dd67">OpenMS::PSLPFormulation::IndexTriple::feature</a></div><div class="ttdeci">Size feature</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:68</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1IndexTriple_html_ac8ce2b86c4cf3b7dc5e9961155e21f92"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#ac8ce2b86c4cf3b7dc5e9961155e21f92">OpenMS::PSLPFormulation::IndexTriple::variable</a></div><div class="ttdeci">Size variable</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:70</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1ScanLess_html_a9f04da0abc6e3d5ce7402d0018e8d150"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1ScanLess.html#a9f04da0abc6e3d5ce7402d0018e8d150">OpenMS::PSLPFormulation::ScanLess::operator()</a></div><div class="ttdeci">bool operator()(IndexTriple const &amp;left, IndexTriple const &amp;right) const </div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:153</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1VariableIndexLess_html_a9f04da0abc6e3d5ce7402d0018e8d150"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1VariableIndexLess.html#a9f04da0abc6e3d5ce7402d0018e8d150">OpenMS::PSLPFormulation::VariableIndexLess::operator()</a></div><div class="ttdeci">bool operator()(IndexTriple const &amp;left, IndexTriple const &amp;right) const </div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:164</div></div>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html_ac945a0966726a3a644d194b81c28d960"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#ac945a0966726a3a644d194b81c28d960">OpenMS::PSLPFormulation::getLPSolver</a></div><div class="ttdeci">LPWrapper::SOLVER getLPSolver()</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:133</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1PSProteinInference_html"><div class="ttname"><a href="classOpenMS_1_1PSProteinInference.html">OpenMS::PSProteinInference</a></div><div class="ttdoc">This class implements protein inference for the precursor ion selection strategies. </div><div class="ttdef"><b>Definition:</b> PSProteinInference.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html_abf5924afa9c5296213f21da56c7727c5"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#abf5924afa9c5296213f21da56c7727c5">OpenMS::PSLPFormulation::createAndSolveILP_</a></div><div class="ttdeci">void createAndSolveILP_(const FeatureMap&lt;&gt; &amp;features, std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; &amp;intensity_weights, std::set&lt; Int &gt; &amp;charges_set, std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::vector&lt; int &gt; &amp;solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans)</div><div class="ttdoc">Creates and solves the ILP. </div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1IndexTriple_html_ad00b56bf94e188184c11c6fd0af6f914"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#ad00b56bf94e188184c11c6fd0af6f914">OpenMS::PSLPFormulation::IndexTriple::rt_probability</a></div><div class="ttdeci">DoubleReal rt_probability</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html_a2a93e2928cdbb7704c7d49a33f13b091"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#a2a93e2928cdbb7704c7d49a33f13b091">OpenMS::PSLPFormulation::createAndSolveILPForKnownLCMSMapFeatureBased</a></div><div class="ttdeci">void createAndSolveILPForKnownLCMSMapFeatureBased(const FeatureMap&lt;&gt; &amp;features, const MSExperiment&lt; InputPeakType &gt; &amp;experiment, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, std::set&lt; Int &gt; &amp;charges_set, UInt ms2_spectra_per_rt_bin, std::vector&lt; int &gt; &amp;solution_indices)</div><div class="ttdoc">Encode ILP formulation for a given LC-MS map, but unknown protein sample. </div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:289</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_1PSLPFormulation_html_a350a55d7f8d02185064c3682c0a4d7f8"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#a350a55d7f8d02185064c3682c0a4d7f8">OpenMS::PSLPFormulation::getXIC_</a></div><div class="ttdeci">void getXIC_(const std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &amp;end_points, std::vector&lt; DoubleReal &gt; &amp;weights, const MSExperiment&lt; InputPeakType &gt; &amp;experiment, const bool normalize)</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:235</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1IndexTriple_html_a24b2e6838da320481d4725b945c06e1f"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a24b2e6838da320481d4725b945c06e1f">OpenMS::PSLPFormulation::IndexTriple::prot_acc</a></div><div class="ttdeci">String prot_acc</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:73</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>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html_a8a38d766081c104c51a498b4d836a456"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#a8a38d766081c104c51a498b4d836a456">OpenMS::PSLPFormulation::calculateXICs_</a></div><div class="ttdeci">void calculateXICs_(std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; &amp;xics, const FeatureMap&lt;&gt; &amp;features, const MSExperiment&lt; InputPeakType &gt; &amp;experiment, const std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, const bool normalize)</div><div class="ttdoc">Calculates the XICs for all features. </div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:274</div></div>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html_a3fde56a178e0bdc00cd84a011415ee41"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html#a3fde56a178e0bdc00cd84a011415ee41">OpenMS::PSLPFormulation::model_</a></div><div class="ttdeci">LPWrapper * model_</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:230</div></div>
<div class="ttc" id="structOpenMS_1_1PSLPFormulation_1_1IndexTriple_html_a70e4788ce6e5dd2fb7780bc492db20d5"><div class="ttname"><a href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html#a70e4788ce6e5dd2fb7780bc492db20d5">OpenMS::PSLPFormulation::IndexTriple::scan</a></div><div class="ttdeci">Int scan</div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:69</div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html">OpenMS::PSLPFormulation</a></div><div class="ttdoc">Implements ILP formulation of precursor selection problems. </div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:51</div></div>
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