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<a href="OfflinePrecursorIonSelection_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> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <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> <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> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <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> <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> <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> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
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<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Alexandra Zerck $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Alexandra Zerck $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_ANALYSIS_TARGETED_OFFLINEPRECURSORIONSELECTION_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_TARGETED_OFFLINEPRECURSORIONSELECTION_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="IDMapper_8h.html">OpenMS/ANALYSIS/ID/IDMapper.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="FeatureXMLFile_8h.html">OpenMS/FORMAT/FeatureXMLFile.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="PSLPFormulation_8h.html">OpenMS/ANALYSIS/TARGETED/PSLPFormulation.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> {</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keyword">class </span>PeptideIdentification;</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keyword">class </span>ProteinIdentification;</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keyword">class </span>String;</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html"> 61</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html">OfflinePrecursorIonSelection</a> :</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  {</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#aff2cbb90bd3ebac2208d25616c0ecf7f"> 65</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">PSLPFormulation::IndexTriple</a> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#aff2cbb90bd3ebac2208d25616c0ecf7f">IndexTriple</a>;</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html">OfflinePrecursorIonSelection</a>();</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html">OfflinePrecursorIonSelection</a>();</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordtype">void</span> makePrecursorSelectionForKnownLCMSMap(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a>& features,</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& experiment,</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& ms2,</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  std::set<Int>& charges_set,</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keywordtype">bool</span> feature_based);</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordtype">void</span> getMassRanges(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a>& features,</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& experiment,</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  std::vector<std::vector<std::pair<Size, Size> > >& indices);</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keywordtype">void</span> createProteinSequenceBasedLPInclusionList(<a class="code" href="classOpenMS_1_1String.html">String</a> include, <a class="code" href="classOpenMS_1_1String.html">String</a> rt_model_file, <a class="code" href="classOpenMS_1_1String.html">String</a> pt_model_file, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a>& precursors);</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#a2b206fdbe8649b90b854129f37fc594a"> 100</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#a2b206fdbe8649b90b854129f37fc594a">setLPSolver</a>(<a class="code" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> solver)</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  {</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  solver_ = solver;</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  std::cout << <span class="stringliteral">" LPSolver set to "</span> << solver_ << std::endl;</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  }</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ac945a0966726a3a644d194b81c28d960"> 106</a></span>  <a class="code" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ac945a0966726a3a644d194b81c28d960">getLPSolver</a>()</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  {</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="keywordflow">return</span> solver_;</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  }</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keywordtype">void</span> calculateXICs_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a>& features,</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keyword">const</span> std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& experiment,</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keyword">const</span> std::set<Int>& charges_set,</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  std::vector<std::vector<std::pair<Size, DoubleReal> > >& xics);</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordtype">void</span> checkMassRanges_(std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& experiment);</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> T></div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordtype">void</span> updateExclusionList_(std::vector<std::pair<T, Size> >& exclusion_list);</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordtype">void</span> updateExclusionList_(std::map<std::pair<DoubleReal, DoubleReal>, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="code" href="structOpenMS_1_1PairComparatorSecondElement.html">PairComparatorSecondElement</a><std::pair<DoubleReal, DoubleReal> > >& exclusion_list);</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#afb8f1202d548f01394d85fbeb51f9adf"> 134</a></span>  <a class="code" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#afb8f1202d548f01394d85fbeb51f9adf">solver_</a>;</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  };</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#aa36b2ed6c06f4252dec15cd4f6d72635"> 138</a></span>  <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenMS.html#aa36b2ed6c06f4252dec15cd4f6d72635">enclosesBoundingBox</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Feature.html">Feature</a>& f, <span class="keyword">typename</span> <a class="code" href="classdouble.html">MSExperiment<InputPeakType>::CoordinateType</a> rt, <span class="keyword">typename</span> <a class="code" href="classdouble.html">MSExperiment<InputPeakType>::CoordinateType</a> mz)</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  {</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordtype">bool</span> enclose_hit = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keyword">const</span> std::vector<ConvexHull2D>& hulls = f.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>();</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < hulls.size(); ++i)</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  {</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordflow">if</span> (hulls[i].getBoundingBox().encloses(rt, mz))</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  {</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  enclose_hit = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordflow">return</span> enclose_hit;</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  }</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  }</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordflow">return</span> enclose_hit;</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  }</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00154"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ae895e8f290c7f5869249e59a7b53c417"> 154</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ae895e8f290c7f5869249e59a7b53c417">OfflinePrecursorIonSelection::getMassRanges</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a>& features,</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& experiment,</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  std::vector<std::vector<std::pair<Size, Size> > >& indices)</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  {</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordflow">if</span> (experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">empty</a>())</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1InvalidSize.html">Exception::InvalidSize</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, 0);</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> f = 0; f < features.size(); ++f)</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  {</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  std::vector<std::pair<Size, Size> > vec;</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> rt = 0; rt < experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++rt)</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  {</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="comment">// is scan relevant?</span></div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordflow">if</span> (!enclosesBoundingBox<InputPeakType>(features[f], experiment[rt].getRT(), features[f].getMZ()))</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span> </div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  std::pair<Size, Size> start;</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  std::pair<Size, Size> end;</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordtype">bool</span> start_found = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordtype">bool</span> end_found = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">MSSpectrum<InputPeakType>::ConstIterator</a> mz_iter = experiment[rt].MZBegin(features[f].getMZ());</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">MSSpectrum<InputPeakType>::ConstIterator</a> mz_end = mz_iter;</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="keywordflow">if</span> (mz_iter == experiment[rt].end())</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="comment">// check to the left</span></div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordflow">while</span> (enclosesBoundingBox<InputPeakType>(features[f], experiment[rt].getRT(), mz_iter->getMZ()))</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  {</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  start_found = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  start.first = rt;</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  start.second = distance(experiment[rt].begin(), mz_iter);</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordflow">if</span> (mz_iter == experiment[rt].begin())</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  --mz_iter;</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  end_found = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  end.first = rt;</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  end.second = start.second;</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  }</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="comment">// and now to the right</span></div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="keywordflow">while</span> (mz_end != experiment[rt].end() && enclosesBoundingBox<InputPeakType>(features[f], experiment[rt].getRT(), mz_end->getMZ()))</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  {</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  end_found = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  end.first = rt;</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  end.second = distance(experiment[rt].begin(), mz_end);</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  ++mz_end;</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  }</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="keywordflow">if</span> (start_found && end_found)</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  {</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  vec.push_back(start);</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  vec.push_back(end);</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  }</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span> <span class="preprocessor"></span> <span class="keywordflow">else</span> <span class="keywordflow">if</span> (start_found || end_found)</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  {</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  std::cout << <span class="stringliteral">"start "</span> << start_found << <span class="stringliteral">" end "</span> << end_found << std::endl;</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  std::cout << <span class="stringliteral">"feature: "</span> << f << <span class="stringliteral">" rt: "</span> << rt << std::endl;</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  }</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span> <span class="preprocessor"></span> }</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span> <span class="preprocessor"></span> <span class="keywordflow">if</span> (vec.size() > 0)</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  {</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  std::cout << vec.size() << <span class="stringliteral">" / 2 scans"</span> << std::endl;</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < vec.size(); i += 2)</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  {</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  std::cout << <span class="stringliteral">"Feature "</span> << f << <span class="stringliteral">" RT : "</span> << vec[i].first</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  << <span class="stringliteral">" MZ : "</span> << experiment[vec[i].first][vec[i].second].getMZ() << <span class="stringliteral">" "</span></div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  << experiment[vec[i + 1].first][vec[i + 1].second].getMZ() << std::endl;</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  }</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  }</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span> <span class="preprocessor"></span> <span class="keywordflow">if</span> (vec.empty())</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  {</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"According to the convex hulls no mass traces found for this feature->estimate!"</span></div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  << features[f].getRT() << <span class="stringliteral">" "</span> << features[f].getMZ() << <span class="stringliteral">" "</span> << features[f].getCharge() << std::endl;</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> <span class="preprocessor"></span> <span class="comment">// we estimate the convex hull</span></div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">MSExperiment<InputPeakType>::ConstIterator</a> spec_iter = experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">RTBegin</a>(features[f].getRT());</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keywordflow">if</span> (spec_iter == experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>())</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  --spec_iter;</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <a class="code" href="classdouble.html">DoubleReal</a> dist1 = fabs(spec_iter->getRT() - features[f].getRT());</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <a class="code" href="classdouble.html">DoubleReal</a> dist2 = std::numeric_limits<DoubleReal>::max();</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <a class="code" href="classdouble.html">DoubleReal</a> dist3 = std::numeric_limits<DoubleReal>::max();</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keywordflow">if</span> ((spec_iter + 1) != experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>())</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  {</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  dist2 = fabs((spec_iter + 1)->getRT() - features[f].getRT());</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  }</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keywordflow">if</span> (spec_iter != experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>())</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  {</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  dist3 = fabs((spec_iter - 1)->getRT() - features[f].getRT());</div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  }</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keywordflow">if</span> (dist3 <= dist1 && dist3 <= dist2)</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  {</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  --spec_iter;</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  }</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (dist2 <= dist3 && dist2 <= dist1)</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  {</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  ++spec_iter;</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  }</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  std::pair<Size, Size> start;</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  std::pair<Size, Size> end;</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  start.first = distance(experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>(), spec_iter);</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  end.first = start.first;</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span> </div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">MSSpectrum<InputPeakType>::ConstIterator</a> mz_iter = spec_iter->MZBegin(features[f].getMZ());</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <span class="keywordflow">if</span> (spec_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>() == spec_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>())</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  {</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  indices.push_back(vec);</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  }</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="keywordflow">if</span> (mz_iter == spec_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>() || (mz_iter->getMZ() > features[f].getMZ() && mz_iter != spec_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>()))</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  --mz_iter;</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordflow">while</span> (mz_iter != spec_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>())</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  {</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="keywordflow">if</span> (fabs((mz_iter - 1)->getMZ() - features[f].getMZ()) < 0.5)</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  --mz_iter;</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  }</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  start.second = distance(spec_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>(), mz_iter);</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">MSSpectrum<InputPeakType>::ConstIterator</a> mz_end = mz_iter;</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span> <span class="preprocessor"></span> std::cout << features[f].getMZ() << <span class="stringliteral">" Start: "</span> << experiment[start.first].getRT() << <span class="stringliteral">" "</span> << experiment[start.first][start.second].getMZ();</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span> <span class="preprocessor"></span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge = features[f].getCharge();</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <span class="keywordflow">if</span> (charge == 0)</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  charge = 1;</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keywordflow">while</span> (mz_end + 1 != spec_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>())</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  {</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="keywordflow">if</span> (fabs((mz_end + 1)->getMZ() - features[f].getMZ()) < 3.0 / (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)charge)</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  ++mz_end;</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  }</div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  end.second = distance(spec_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>(), mz_end);</div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"\tEnd: "</span> << experiment[end.first].getRT() << <span class="stringliteral">" "</span> << experiment[end.first][end.second].getMZ() << std::endl;</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span> <span class="preprocessor"></span> vec.push_back(start);</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  vec.push_back(end);</div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  }</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span> </div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  indices.push_back(vec);</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  }</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <span class="comment">// eliminate nearby peaks</span></div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"exclude_overlapping_peaks"</span>) == <span class="stringliteral">"true"</span>)</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#acca2e18b840cc4b903f2958efca7aa1a">checkMassRanges_</a>(indices, experiment);</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  }</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span> </div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00305"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#a09cf655b910fa7166cd8b27d17e02453"> 305</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#a09cf655b910fa7166cd8b27d17e02453">OfflinePrecursorIonSelection::calculateXICs_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a>& features,</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <span class="keyword">const</span> std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& experiment,</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keyword">const</span> std::set<Int>& charges_set,</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  std::vector<std::vector<std::pair<Size, DoubleReal> > >& xics)</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  {</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  xics.clear();</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  xics.resize(experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <span class="comment">// for each feature</span></div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> f = 0; f < mass_ranges.size(); ++f)</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  {</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="comment">// is charge valid</span></div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  <span class="keywordflow">if</span> (charges_set.count(features[f].getCharge()) < 1)</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  {</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  }</div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="comment">// go through all scans where the feature occurs</span></div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s < mass_ranges[f].size(); s += 2)</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  {</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="comment">// sum intensity over all raw datapoints belonging to the feature in the current scan</span></div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <a class="code" href="classdouble.html">DoubleReal</a> weight = 0.;</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = mass_ranges[f][s].second; j <= mass_ranges[f][s + 1].second; ++j)</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  {</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  weight += experiment[mass_ranges[f][s].first][j].getIntensity();</div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  }</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="comment">// enter xic in the vector for scan</span></div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  xics[mass_ranges[f][s].first].push_back(std::make_pair(f, weight));</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  }</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  }</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span> </div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s < xics.size(); ++s)</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  {</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  sort(xics[s].begin(), xics[s].end(), <a class="code" href="structOpenMS_1_1PairComparatorSecondElement.html">PairComparatorSecondElement</a><std::pair<Size, DoubleReal> >());</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  }</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  }</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span> </div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00342"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#afc3ec85793adf0cdaacc5803e59f6c17"> 342</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#afc3ec85793adf0cdaacc5803e59f6c17">OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a>& features,</div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& experiment,</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& ms2,</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  std::set<Int>& charges_set,</div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordtype">bool</span> feature_based)</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  {</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span> </div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> window = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"selection_window"</span>);</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> excl_window = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"min_peak_distance"</span>);</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span> </div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  <span class="comment">// get the mass ranges for each features for each scan it occurs in</span></div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  std::vector<std::vector<std::pair<Size, Size> > > indices;</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ae895e8f290c7f5869249e59a7b53c417">getMassRanges</a>(features, experiment, indices);</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  <a class="code" href="classdouble.html">DoubleReal</a> rt_dist = 0.;</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  <span class="keywordflow">if</span> (experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() > 1)</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  {</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  rt_dist = experiment[1].getRT() - experiment[0].getRT();</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  }</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span> </div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  <span class="comment">// feature based selection (e.g. with LC-MALDI)</span></div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  <span class="keywordflow">if</span> (feature_based)</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  {</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  <span class="comment">// create ILP</span></div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  <a class="code" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a> ilp_wrapper;</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> </div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  std::vector<IndexTriple> variable_indices;</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  std::vector<int> solution_indices;</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  ilp_wrapper.<a class="code" href="classOpenMS_1_1PSLPFormulation.html#a2a93e2928cdbb7704c7d49a33f13b091">createAndSolveILPForKnownLCMSMapFeatureBased</a>(features, experiment, variable_indices,</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  indices, charges_set,</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"ms2_spectra_per_rt_bin"</span>),</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  solution_indices);</div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span> </div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  sort(variable_indices.begin(), variable_indices.end(), <a class="code" href="structOpenMS_1_1PSLPFormulation_1_1IndexLess.html">PSLPFormulation::IndexLess</a>());</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"best_solution "</span> << std::endl;</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span> <span class="preprocessor"></span> <span class="comment">// print best solution</span></div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="comment">// create inclusion list</span></div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < solution_indices.size(); ++i)</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  {</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> feature_index = variable_indices[solution_indices[i]].feature;</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> feature_scan_idx = variable_indices[solution_indices[i]].scan;</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">MSExperiment<InputPeakType>::ConstIterator</a> scan = experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>() + feature_scan_idx;</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSExperiment<InputPeakType>::SpectrumType</a> ms2_spec;</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a> p;</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  std::vector<Precursor> pcs;</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  p.<a class="code" href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(features[feature_index].getIntensity());</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  p.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(features[feature_index].getMZ());</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  p.<a class="code" href="classOpenMS_1_1Precursor.html#aca40a4630f5f8a0568899b74a62dcd4b">setCharge</a>(features[feature_index].getCharge());</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  pcs.push_back(p);</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  ms2_spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ad85e4e6fe1ec77097d9108f38a8e57ae">setPrecursors</a>(pcs);</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  ms2_spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">setRT</a>(scan->getRT() + rt_dist / 2.0);</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  ms2_spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a24f081fe74bbbf773533ad19e96d8358">setMSLevel</a>(2);</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  <span class="comment">// link ms2 spectrum with features overlapping its precursor</span></div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  <span class="comment">// Warning: this depends on the current order of features in the map</span></div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  <span class="comment">// Attention: make sure to name ALL features that overlap, not only one!</span></div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  ms2_spec.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"parent_feature_ids"</span>, <a class="code" href="classOpenMS_1_1IntList.html#ac244d9a257aab1a24c1a622ccacab745">IntList::create</a>(<a class="code" href="classOpenMS_1_1String.html">String</a>(feature_index)));</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  ms2.<a class="code" href="classOpenMS_1_1MSExperiment.html#ae9dafbb74a1a4c430ceef03e25ab8e10">addSpectrum</a>(ms2_spec);</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  std::cout << <span class="stringliteral">" MS2 spectra generated at: "</span> << scan->getRT() << <span class="stringliteral">" x "</span> << p.<a class="code" href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() << <span class="stringliteral">"\n"</span>;</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span> </div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  }</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span> <span class="preprocessor"></span> std::cout << solution_indices.size() << <span class="stringliteral">" out of "</span> << features.size()</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  << <span class="stringliteral">" precursors are in best solution.\n"</span>;</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span> <span class="preprocessor"></span> }</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  <span class="keywordflow">else</span> <span class="comment">// scan based selection (take the x highest signals for each spectrum)</span></div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  {</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"scan based precursor selection"</span> << std::endl;</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span> <span class="preprocessor"></span> <span class="comment">// if the highest signals for each scan shall be selected we don't need an ILP formulation</span></div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span> </div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  <span class="comment">//cache the values for each feature</span></div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  std::vector<DoubleList> feature_elution_bounds;</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  std::vector<DoubleList> elution_profile_intensities;</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  std::vector<DoubleList> isotope_intensities;</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span> </div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="keywordtype">bool</span> meta_values_present = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span> </div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="keywordflow">if</span> (!features.empty() &&</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  features[0].metaValueExists(<span class="stringliteral">"elution_profile_bounds"</span>) &&</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  features[0].metaValueExists(<span class="stringliteral">"elution_profile_intensities"</span>) &&</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  features[0].metaValueExists(<span class="stringliteral">"isotope_intensities"</span>))</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  {</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> feat = 0; feat < features.size(); ++feat)</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  {</div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  feature_elution_bounds.push_back(features[feat].getMetaValue(<span class="stringliteral">"elution_profile_bounds"</span>));</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  elution_profile_intensities.push_back(features[feat].getMetaValue(<span class="stringliteral">"elution_profile_intensities"</span>));</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  isotope_intensities.push_back(features[feat].getMetaValue(<span class="stringliteral">"isotope_intensities"</span>));</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  }</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  meta_values_present = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  }</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span> </div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  <span class="comment">//for each feature cache for which scans it has to be considered</span></div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  std::vector<std::vector<Size> > scan_features(experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span> </div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> feat = 0; feat < features.size(); ++feat)</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  {</div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <span class="keywordflow">if</span> (charges_set.count(features[feat].getCharge()))</div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  {</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> lower_rt = features[feat].getConvexHull().getBoundingBox().minX();</div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> upper_rt = features[feat].getConvexHull().getBoundingBox().maxX();</div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">MSExperiment<InputPeakType>::ConstIterator</a> it;</div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  <span class="keywordflow">for</span> (it = experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">RTBegin</a>(lower_rt); it != experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#aecc2b466c4b527df363f5b1287a5e646">RTEnd</a>(upper_rt); ++it)</div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  {</div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  scan_features[it - experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>()].push_back(feat);</div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  }</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  }</div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  }</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span> </div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keywordtype">bool</span> dynamic_exclusion = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"Exclusion:use_dynamic_exclusion"</span>) == <span class="stringliteral">"true"</span> ? <span class="keyword">true</span> : <span class="keyword">false</span>;</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  <span class="keyword">typedef</span> std::map<std::pair<DoubleReal, DoubleReal>, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="code" href="structOpenMS_1_1PairComparatorSecondElement.html">PairComparatorSecondElement<std::pair<DoubleReal, DoubleReal></a> > > ExclusionListType;</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  ExclusionListType exclusion_list;</div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  Size exclusion_specs = (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>)(floor((<a class="code" href="classdouble.html">DoubleReal</a>)<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"Exclusion:exclusion_time"</span>) / (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>) rt_dist));</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  <span class="keywordflow">if</span> (!dynamic_exclusion)</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  {</div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  <span class="comment">//if the dynamic exclusion if not active we use the eclusion list to guarantee no two peaks within min_peak_distance are selected for single scan</span></div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  exclusion_specs = 0;</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  }</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span> </div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  <span class="comment">//cache bounding boxes of features and mass traces (mass trace bb are also widened for effective discovery of enclosing peaks in intervalls)</span></div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  std::map<Size, typename OpenMS::DBoundingBox<2> > bounding_boxes_f;</div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  std::map<std::pair<Size, Size>, <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1DBoundingBox.html">OpenMS::DBoundingBox<2></a> > bounding_boxes;</div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <span class="keywordflow">for</span> (Size feature_num = 0; feature_num < features.size(); ++feature_num)</div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  {</div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  <span class="keywordflow">if</span> (charges_set.count(features[feature_num].getCharge()))</div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  {</div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  bounding_boxes_f.insert(std::make_pair(feature_num, features[feature_num].getConvexHull().getBoundingBox()));</div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  <span class="keyword">const</span> std::vector<ConvexHull2D> mass_traces = features[feature_num].getConvexHulls();</div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  <span class="keywordflow">for</span> (Size mass_trace_num = 0; mass_trace_num < mass_traces.size(); ++mass_trace_num)</div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  {</div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1DBoundingBox.html">OpenMS::DBoundingBox<2></a> tmp_bbox = mass_traces[mass_trace_num].getBoundingBox();</div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  tmp_bbox.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a3faa28974e310e9743446f1c184496a6">setMinY</a>(tmp_bbox.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ad7c0ea2d4aceb7723ebcf33ae386634f">minY</a>() - window);</div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  tmp_bbox.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a71b4e57973d9ad60975b774f4eeaef06">setMaxY</a>(tmp_bbox.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a1e8f4d69eddc6bd53fb8b1101e24f765">maxY</a>() + window);</div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  bounding_boxes.insert(std::make_pair(std::make_pair(feature_num, mass_trace_num), tmp_bbox));</div>
<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  }</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  }</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  }</div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span> </div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  Size max_spec = (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>)<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"ms2_spectra_per_rt_bin"</span>);</div>
<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  <span class="comment">// get best x signals for each scan</span></div>
<div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  <span class="keywordflow">for</span> (Size i = 0; i < experiment.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++i)</div>
<div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  {</div>
<div class="line"><a name="l00486"></a><span class="lineno"> 486</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00487"></a><span class="lineno"> 487</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"scan "</span> << experiment[i].getRT() << <span class="stringliteral">":"</span>;</div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ac76fec6f118131b8d46e5e2885ad7d50">updateExclusionList_</a>(exclusion_list);</div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<InputPeakType></a> scan = experiment[i];</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  scan.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a93f1c9f620403aec160d98e83e125502">sortByIntensity</a>(<span class="keyword">true</span>);</div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  Size selected_peaks = 0, j = 0;</div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span> </div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  <span class="keywordflow">while</span> (selected_peaks < max_spec && j < scan.size())</div>
<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  {</div>
<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  <a class="code" href="classdouble.html">DoubleReal</a> peak_mz = scan[j].getMZ();</div>
<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  <a class="code" href="classdouble.html">DoubleReal</a> peak_rt = scan.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>();</div>
<div class="line"><a name="l00499"></a><span class="lineno"> 499</span> </div>
<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  ExclusionListType::iterator it_low = exclusion_list.lower_bound(std::make_pair(peak_mz, peak_mz));</div>
<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  <span class="keywordflow">if</span> (it_low != exclusion_list.end() && it_low->first.first <= peak_mz)</div>
<div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  {</div>
<div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  ++j;</div>
<div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00505"></a><span class="lineno"> 505</span>  }</div>
<div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  ++selected_peaks;</div>
<div class="line"><a name="l00507"></a><span class="lineno"> 507</span> </div>
<div class="line"><a name="l00508"></a><span class="lineno"> 508</span>  <span class="comment">//find all features (mass traces that are in the window around peak_mz)</span></div>
<div class="line"><a name="l00509"></a><span class="lineno"> 509</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSExperiment<InputPeakType>::SpectrumType</a> ms2_spec;</div>
<div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  std::vector<Precursor> pcs;</div>
<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  std::set<std::pair<Size, Size> > selected_mt;</div>
<div class="line"><a name="l00512"></a><span class="lineno"> 512</span>  <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> parent_feature_ids;</div>
<div class="line"><a name="l00513"></a><span class="lineno"> 513</span> </div>
<div class="line"><a name="l00514"></a><span class="lineno"> 514</span>  <a class="code" href="classdouble.html">DoubleReal</a> local_mz = peak_mz;</div>
<div class="line"><a name="l00515"></a><span class="lineno"> 515</span>  <span class="comment">//std::cerr<<"MZ pos: "<<local_mz<<std::endl;</span></div>
<div class="line"><a name="l00516"></a><span class="lineno"> 516</span>  <span class="keywordflow">for</span> (Size scan_feat_id = 0; scan_feat_id < scan_features[i].size(); ++scan_feat_id)</div>
<div class="line"><a name="l00517"></a><span class="lineno"> 517</span>  {</div>
<div class="line"><a name="l00518"></a><span class="lineno"> 518</span>  Size feature_num = scan_features[i][scan_feat_id];</div>
<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  <span class="keywordflow">if</span> (bounding_boxes_f[feature_num].encloses(peak_rt, local_mz))</div>
<div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  {</div>
<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  <span class="comment">//find a mass trace enclosing the point</span></div>
<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  <a class="code" href="classdouble.html">DoubleReal</a> feature_intensity = 0;</div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  <span class="keywordflow">for</span> (Size mass_trace_num = 0; mass_trace_num < features[feature_num].getConvexHulls().size(); ++mass_trace_num)</div>
<div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  {</div>
<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  <span class="keywordflow">if</span> (bounding_boxes[std::make_pair(feature_num, mass_trace_num)].encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(peak_rt, local_mz)))</div>
<div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  {</div>
<div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  <a class="code" href="classdouble.html">DoubleReal</a> elu_factor = 1.0, iso_factor = 1.0;</div>
<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  <span class="comment">//get the intensity factor for the position in the elution profile</span></div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  <span class="keywordflow">if</span> (meta_values_present)</div>
<div class="line"><a name="l00530"></a><span class="lineno"> 530</span>  {</div>
<div class="line"><a name="l00531"></a><span class="lineno"> 531</span>  <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a> xxx = elution_profile_intensities[feature_num];</div>
<div class="line"><a name="l00532"></a><span class="lineno"> 532</span>  <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a> yyy = feature_elution_bounds[feature_num];</div>
<div class="line"><a name="l00533"></a><span class="lineno"> 533</span> <span class="comment">// std::cout << "PEAKRT: " << peak_rt << std::endl;</span></div>
<div class="line"><a name="l00534"></a><span class="lineno"> 534</span> <span class="comment">// std::cout << "Max: " << yyy[3] << " vs. " << bounding_boxes_f[feature_num].maxX() << std::endl;</span></div>
<div class="line"><a name="l00535"></a><span class="lineno"> 535</span> <span class="comment">// std::cout << "Min: " << yyy[1] << " vs. " << bounding_boxes_f[feature_num].minX() << std::endl;</span></div>
<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(i - yyy[0] < xxx.size(), <span class="stringliteral">"Tried to access invalid index for elution factor"</span>);</div>
<div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  elu_factor = xxx[i - yyy[0]]; <span class="comment">// segfault here: "i-yyy[0]" yields invalid index</span></div>
<div class="line"><a name="l00538"></a><span class="lineno"> 538</span>  iso_factor = isotope_intensities[feature_num][mass_trace_num];</div>
<div class="line"><a name="l00539"></a><span class="lineno"> 539</span>  }</div>
<div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  feature_intensity += features[feature_num].getIntensity() * iso_factor * elu_factor;</div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  }</div>
<div class="line"><a name="l00542"></a><span class="lineno"> 542</span>  }</div>
<div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a> p;</div>
<div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  p.<a class="code" href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(feature_intensity);</div>
<div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  p.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(features[feature_num].getMZ());</div>
<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  p.<a class="code" href="classOpenMS_1_1Precursor.html#aca40a4630f5f8a0568899b74a62dcd4b">setCharge</a>(features[feature_num].getCharge());</div>
<div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  pcs.push_back(p);</div>
<div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  parent_feature_ids.push_back((<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>)feature_num);</div>
<div class="line"><a name="l00549"></a><span class="lineno"> 549</span>  }</div>
<div class="line"><a name="l00550"></a><span class="lineno"> 550</span>  }</div>
<div class="line"><a name="l00551"></a><span class="lineno"> 551</span> </div>
<div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  <span class="keywordflow">if</span> (!pcs.empty())</div>
<div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  {</div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span>  <span class="comment">//std::cerr<<"scan "<<i<<" added spectrum for features: "<<parent_feature_ids<<std::endl;</span></div>
<div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  ms2_spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ad85e4e6fe1ec77097d9108f38a8e57ae">setPrecursors</a>(pcs);</div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  ms2_spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a24f081fe74bbbf773533ad19e96d8358">setMSLevel</a>(2);</div>
<div class="line"><a name="l00557"></a><span class="lineno"> 557</span>  ms2_spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">setRT</a>(experiment[i].getRT() + rt_dist / 2.0); <span class="comment">//(selected_peaks+1)*rt_dist/(max_spec+1) );</span></div>
<div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  ms2_spec.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"parent_feature_ids"</span>, parent_feature_ids);</div>
<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  ms2.<a class="code" href="classOpenMS_1_1MSExperiment.html#ae9dafbb74a1a4c430ceef03e25ab8e10">addSpectrum</a>(ms2_spec);</div>
<div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  }</div>
<div class="line"><a name="l00561"></a><span class="lineno"> 561</span> </div>
<div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  <span class="comment">//add m/z window to exclusion list</span></div>
<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  exclusion_list.insert(std::make_pair(std::make_pair(peak_mz - excl_window, peak_mz + excl_window), exclusion_specs + 1));</div>
<div class="line"><a name="l00564"></a><span class="lineno"> 564</span> </div>
<div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  ++j;</div>
<div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  }</div>
<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  }</div>
<div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  }</div>
<div class="line"><a name="l00569"></a><span class="lineno"> 569</span>  }</div>
<div class="line"><a name="l00570"></a><span class="lineno"> 570</span> </div>
<div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00572"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#acca2e18b840cc4b903f2958efca7aa1a"> 572</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#acca2e18b840cc4b903f2958efca7aa1a">OfflinePrecursorIonSelection::checkMassRanges_</a>(std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,</div>
<div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a>& experiment)</div>
<div class="line"><a name="l00574"></a><span class="lineno"> 574</span>  {</div>
<div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  std::vector<std::vector<std::pair<Size, Size> > > checked_mass_ranges;</div>
<div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  <a class="code" href="classdouble.html">DoubleReal</a> min_peak_distance = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"min_peak_distance"</span>);</div>
<div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  checked_mass_ranges.reserve(mass_ranges.size());</div>
<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> f = 0; f < mass_ranges.size(); ++f)</div>
<div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  {</div>
<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  std::vector<std::pair<Size, Size> > checked_mass_ranges_f;</div>
<div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s_idx = 0; s_idx < mass_ranges[f].size(); s_idx += 2)</div>
<div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  {</div>
<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = mass_ranges[f][s_idx].first;</div>
<div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  <span class="keywordtype">bool</span> overlapping_features = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  <span class="comment">// check if other features overlap with this feature in the current scan</span></div>
<div class="line"><a name="l00588"></a><span class="lineno"> 588</span> <span class="comment"></span> <span class="keyword">const</span> InputPeakType& peak_left_border = experiment[s][mass_ranges[f][s_idx].second];</div>
<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  <span class="keyword">const</span> InputPeakType& peak_right_border = experiment[s][mass_ranges[f][s_idx + 1].second];</div>
<div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> fmr = 0; fmr < mass_ranges.size(); ++fmr)</div>
<div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  {</div>
<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  <span class="keywordflow">if</span> (fmr == f)</div>
<div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00594"></a><span class="lineno"> 594</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> mr = 0; mr < mass_ranges[fmr].size(); mr += 2)</div>
<div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  {</div>
<div class="line"><a name="l00596"></a><span class="lineno"> 596</span>  <span class="keywordflow">if</span> (mass_ranges[fmr][mr].first == s) <span class="comment">// same spectrum</span></div>
<div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  {</div>
<div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  <span class="keyword">const</span> InputPeakType& tmp_peak_left = experiment[s][mass_ranges[fmr][mr].second];</div>
<div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  <span class="keyword">const</span> InputPeakType& tmp_peak_right = experiment[s][mass_ranges[fmr][mr + 1].second];</div>
<div class="line"><a name="l00600"></a><span class="lineno"> 600</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00601"></a><span class="lineno"> 601</span> <span class="preprocessor"></span> std::cout << tmp_peak_left.getMZ() << <span class="stringliteral">" < "</span></div>
<div class="line"><a name="l00602"></a><span class="lineno"> 602</span>  << peak_left_border.getMZ() - min_peak_distance << <span class="stringliteral">" && "</span></div>
<div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  << tmp_peak_right.getMZ() << <span class="stringliteral">" < "</span></div>
<div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  << peak_left_border.getMZ() - min_peak_distance << <span class="stringliteral">" ? "</span></div>
<div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  << (tmp_peak_left.getMZ() < peak_left_border.getMZ() - min_peak_distance &&</div>
<div class="line"><a name="l00606"></a><span class="lineno"> 606</span>  tmp_peak_right.getMZ() < peak_left_border.getMZ() - min_peak_distance)</div>
<div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  << <span class="stringliteral">" || "</span></div>
<div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  << tmp_peak_left.getMZ() << <span class="stringliteral">" > "</span></div>
<div class="line"><a name="l00609"></a><span class="lineno"> 609</span>  << peak_right_border.getMZ() + min_peak_distance << <span class="stringliteral">" && "</span></div>
<div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  << tmp_peak_right.getMZ() << <span class="stringliteral">" > "</span></div>
<div class="line"><a name="l00611"></a><span class="lineno"> 611</span>  << peak_right_border.getMZ() + min_peak_distance << <span class="stringliteral">" ? "</span></div>
<div class="line"><a name="l00612"></a><span class="lineno"> 612</span>  << (tmp_peak_left.getMZ() > peak_right_border.getMZ() + min_peak_distance &&</div>
<div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  tmp_peak_right.getMZ() > peak_right_border.getMZ() + min_peak_distance)</div>
<div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  << std::endl;</div>
<div class="line"><a name="l00615"></a><span class="lineno"> 615</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00616"></a><span class="lineno"> 616</span> <span class="preprocessor"></span> <span class="comment">// all other features have to be either completely left or</span></div>
<div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  <span class="comment">// right of the current feature</span></div>
<div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  <span class="keywordflow">if</span> (!((tmp_peak_left.getMZ() < peak_left_border.getMZ() - min_peak_distance &&</div>
<div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  tmp_peak_right.getMZ() < peak_left_border.getMZ() - min_peak_distance) ||</div>
<div class="line"><a name="l00620"></a><span class="lineno"> 620</span>  (tmp_peak_left.getMZ() > peak_right_border.getMZ() + min_peak_distance &&</div>
<div class="line"><a name="l00621"></a><span class="lineno"> 621</span>  tmp_peak_right.getMZ() > peak_right_border.getMZ() + min_peak_distance)))</div>
<div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  {</div>
<div class="line"><a name="l00623"></a><span class="lineno"> 623</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00624"></a><span class="lineno"> 624</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"found overlapping peak"</span> << std::endl;</div>
<div class="line"><a name="l00625"></a><span class="lineno"> 625</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00626"></a><span class="lineno"> 626</span> <span class="preprocessor"></span> overlapping_features = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00628"></a><span class="lineno"> 628</span>  }</div>
<div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  }</div>
<div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  }</div>
<div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  }</div>
<div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  <span class="keywordflow">if</span> (!overlapping_features)</div>
<div class="line"><a name="l00633"></a><span class="lineno"> 633</span>  {</div>
<div class="line"><a name="l00634"></a><span class="lineno"> 634</span> <span class="preprocessor">#ifdef DEBUG_OPS</span></div>
<div class="line"><a name="l00635"></a><span class="lineno"> 635</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"feature in spec ok"</span> << mass_ranges[f][s_idx].second << <span class="stringliteral">" in spec "</span></div>
<div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  << mass_ranges[f][s_idx].first << std::endl;</div>
<div class="line"><a name="l00637"></a><span class="lineno"> 637</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00638"></a><span class="lineno"> 638</span> <span class="preprocessor"></span> checked_mass_ranges_f.insert(checked_mass_ranges_f.end(),</div>
<div class="line"><a name="l00639"></a><span class="lineno"> 639</span>  mass_ranges[f].begin() + s_idx,</div>
<div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  mass_ranges[f].begin() + s_idx + 2);</div>
<div class="line"><a name="l00641"></a><span class="lineno"> 641</span>  }</div>
<div class="line"><a name="l00642"></a><span class="lineno"> 642</span>  }</div>
<div class="line"><a name="l00643"></a><span class="lineno"> 643</span>  checked_mass_ranges.push_back(checked_mass_ranges_f);</div>
<div class="line"><a name="l00644"></a><span class="lineno"> 644</span>  }</div>
<div class="line"><a name="l00645"></a><span class="lineno"> 645</span>  mass_ranges.swap(checked_mass_ranges);</div>
<div class="line"><a name="l00646"></a><span class="lineno"> 646</span>  }</div>
<div class="line"><a name="l00647"></a><span class="lineno"> 647</span> </div>
<div class="line"><a name="l00648"></a><span class="lineno"> 648</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> T></div>
<div class="line"><a name="l00649"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ac76fec6f118131b8d46e5e2885ad7d50"> 649</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ac76fec6f118131b8d46e5e2885ad7d50">OfflinePrecursorIonSelection::updateExclusionList_</a>(std::vector<std::pair<T, Size> >& exclusion_list)</div>
<div class="line"><a name="l00650"></a><span class="lineno"> 650</span>  {</div>
<div class="line"><a name="l00651"></a><span class="lineno"> 651</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < exclusion_list.size(); ++i)</div>
<div class="line"><a name="l00652"></a><span class="lineno"> 652</span>  {</div>
<div class="line"><a name="l00653"></a><span class="lineno"> 653</span>  <span class="keywordflow">if</span> (exclusion_list[i].second > 0)</div>
<div class="line"><a name="l00654"></a><span class="lineno"> 654</span>  --exclusion_list[i].second;</div>
<div class="line"><a name="l00655"></a><span class="lineno"> 655</span>  }</div>
<div class="line"><a name="l00656"></a><span class="lineno"> 656</span>  sort(exclusion_list.begin(), exclusion_list.end(), <a class="code" href="structOpenMS_1_1PairComparatorSecondElementMore.html">PairComparatorSecondElementMore<std::pair<T, Size></a> >());</div>
<div class="line"><a name="l00657"></a><span class="lineno"> 657</span>  <span class="keyword">typename</span> std::vector<std::pair<T, Size> >::iterator iter = exclusion_list.begin();</div>
<div class="line"><a name="l00658"></a><span class="lineno"> 658</span>  <span class="keywordflow">while</span> (iter != exclusion_list.end() && iter->second != 0)</div>
<div class="line"><a name="l00659"></a><span class="lineno"> 659</span>  ++iter;</div>
<div class="line"><a name="l00660"></a><span class="lineno"> 660</span>  exclusion_list.erase(iter, exclusion_list.end());</div>
<div class="line"><a name="l00661"></a><span class="lineno"> 661</span>  }</div>
<div class="line"><a name="l00662"></a><span class="lineno"> 662</span> </div>
<div class="line"><a name="l00663"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#a0a78199f092a6aa84227a6decad602ca"> 663</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ac76fec6f118131b8d46e5e2885ad7d50">OfflinePrecursorIonSelection::updateExclusionList_</a>(std::map<std::pair<DoubleReal, DoubleReal>, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="code" href="structOpenMS_1_1PairComparatorSecondElement.html">PairComparatorSecondElement</a><std::pair<DoubleReal, DoubleReal> > >& exclusion_list)</div>
<div class="line"><a name="l00664"></a><span class="lineno"> 664</span>  {</div>
<div class="line"><a name="l00665"></a><span class="lineno"> 665</span>  std::map<std::pair<DoubleReal, DoubleReal>, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="code" href="structOpenMS_1_1PairComparatorSecondElement.html">PairComparatorSecondElement<std::pair<DoubleReal, DoubleReal></a> > >::iterator it;</div>
<div class="line"><a name="l00666"></a><span class="lineno"> 666</span> </div>
<div class="line"><a name="l00667"></a><span class="lineno"> 667</span>  it = exclusion_list.begin();</div>
<div class="line"><a name="l00668"></a><span class="lineno"> 668</span> </div>
<div class="line"><a name="l00669"></a><span class="lineno"> 669</span>  <span class="keywordflow">while</span> (it != exclusion_list.end())</div>
<div class="line"><a name="l00670"></a><span class="lineno"> 670</span>  {</div>
<div class="line"><a name="l00671"></a><span class="lineno"> 671</span>  <span class="keywordflow">if</span> ((it->second--) == 1)</div>
<div class="line"><a name="l00672"></a><span class="lineno"> 672</span>  {</div>
<div class="line"><a name="l00673"></a><span class="lineno"> 673</span>  exclusion_list.erase(it++);</div>
<div class="line"><a name="l00674"></a><span class="lineno"> 674</span>  }</div>
<div class="line"><a name="l00675"></a><span class="lineno"> 675</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00676"></a><span class="lineno"> 676</span>  {</div>
<div class="line"><a name="l00677"></a><span class="lineno"> 677</span>  ++it;</div>
<div class="line"><a name="l00678"></a><span class="lineno"> 678</span>  }</div>
<div class="line"><a name="l00679"></a><span class="lineno"> 679</span>  }</div>
<div class="line"><a name="l00680"></a><span class="lineno"> 680</span>  }</div>
<div class="line"><a name="l00681"></a><span class="lineno"> 681</span> </div>
<div class="line"><a name="l00682"></a><span class="lineno"> 682</span> }</div>
<div class="line"><a name="l00683"></a><span class="lineno"> 683</span> </div>
<div class="line"><a name="l00684"></a><span class="lineno"> 684</span> <span class="preprocessor">#endif // OPENMS_ANALYSIS_ID_OFFLINEPRECURSORIONSELECTION_H</span></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_a1e8f4d69eddc6bd53fb8b1101e24f765"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a1e8f4d69eddc6bd53fb8b1101e24f765">OpenMS::Internal::DIntervalBase::maxY</a></div><div class="ttdeci">CoordinateType maxY() const </div><div class="ttdoc">Accessor for max_ coordinate maximum. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:258</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_a135a7e818125b31198a8a65d9ac7a3d1"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">OpenMS::MetaInfoInterface::setMetaValue</a></div><div class="ttdeci">void setMetaValue(const String &name, const DataValue &value)</div><div class="ttdoc">sets the DataValue corresponding to a name </div></div>
<div class="ttc" id="FeatureXMLFile_8h_html"><div class="ttname"><a href="FeatureXMLFile_8h.html">FeatureXMLFile.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_1Precursor_html"><div class="ttname"><a href="classOpenMS_1_1Precursor.html">OpenMS::Precursor</a></div><div class="ttdoc">Precursor meta information. </div><div class="ttdef"><b>Definition:</b> Precursor.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_a3faa28974e310e9743446f1c184496a6"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a3faa28974e310e9743446f1c184496a6">OpenMS::Internal::DIntervalBase::setMinY</a></div><div class="ttdeci">void setMinY(CoordinateType const c)</div><div class="ttdoc">Mutator for max_ coordinate of the smaller point. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:271</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_1DefaultParamHandler_html_a28c73e623c63a4fe3bfceb1ae8274f39"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">OpenMS::DefaultParamHandler::param_</a></div><div class="ttdeci">Param param_</div><div class="ttdoc">Container for current parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:148</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"><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<></a></div></div>
<div class="ttc" id="group__Conditions_html_ga45a74ea28109e7e1ed992fbd2ee97778"><div class="ttname"><a href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a></div><div class="ttdeci">#define OPENMS_PRECONDITION(condition, message)</div><div class="ttdoc">Precondition macro. </div><div class="ttdef"><b>Definition:</b> Macros.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_a71b4e57973d9ad60975b774f4eeaef06"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a71b4e57973d9ad60975b774f4eeaef06">OpenMS::Internal::DIntervalBase::setMaxY</a></div><div class="ttdeci">void setMaxY(CoordinateType const c)</div><div class="ttdoc">Mutator for max_ coordinate of the larger point. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:285</div></div>
<div class="ttc" id="classOpenMS_1_1OfflinePrecursorIonSelection_html_ac945a0966726a3a644d194b81c28d960"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ac945a0966726a3a644d194b81c28d960">OpenMS::OfflinePrecursorIonSelection::getLPSolver</a></div><div class="ttdeci">LPWrapper::SOLVER getLPSolver()</div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:106</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_a6fefef82aae7a3208e71648e763d5ea4"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">OpenMS::Peak1D::getMZ</a></div><div class="ttdeci">CoordinateType getMZ() const </div><div class="ttdoc">Non-mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a4895afe86c2aa0747ae0411c58c82114"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">OpenMS::MSSpectrum::ConstIterator</a></div><div class="ttdeci">ContainerType::const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:125</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a2387033802383edbdc95f9bbb12a707e"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">OpenMS::MSExperiment::begin</a></div><div class="ttdeci">Iterator begin()</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:147</div></div>
<div class="ttc" id="namespaceOpenMS_html_aa36b2ed6c06f4252dec15cd4f6d72635"><div class="ttname"><a href="namespaceOpenMS.html#aa36b2ed6c06f4252dec15cd4f6d72635">OpenMS::enclosesBoundingBox</a></div><div class="ttdeci">bool enclosesBoundingBox(const Feature &f, typename MSExperiment< InputPeakType >::CoordinateType rt, typename MSExperiment< InputPeakType >::CoordinateType mz)</div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:138</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_1Peak1D_html_ab9c4ce5d172a75d6de2c6f5f1847c9ab"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">OpenMS::Peak1D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType mz)</div><div class="ttdoc">Mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::Peak1D::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> Peak1D.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_aecc2b466c4b527df363f5b1287a5e646"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#aecc2b466c4b527df363f5b1287a5e646">OpenMS::MSExperiment::RTEnd</a></div><div class="ttdeci">ConstIterator RTEnd(CoordinateType rt) const </div><div class="ttdoc">Fast search for spectrum range end (returns the past-the-end iterator) </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:363</div></div>
<div class="ttc" id="structOpenMS_1_1PairComparatorSecondElementMore_html"><div class="ttname"><a href="structOpenMS_1_1PairComparatorSecondElementMore.html">OpenMS::PairComparatorSecondElementMore</a></div><div class="ttdoc">Class for comparison of std::pair using second ONLY e.g. for use with std::sort. </div><div class="ttdef"><b>Definition:</b> ComparatorUtils.h:368</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ab45dae688fc5d8983727abffa4389003"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">OpenMS::MSExperiment::end</a></div><div class="ttdeci">Iterator end()</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:157</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_adb2f0f3e10754ca4dc7be677f15689a3"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">OpenMS::MSExperiment::RTBegin</a></div><div class="ttdeci">ConstIterator RTBegin(CoordinateType rt) const </div><div class="ttdoc">Fast search for spectrum range begin. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:349</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="classOpenMS_1_1Internal_1_1DIntervalBase_html_ad7c0ea2d4aceb7723ebcf33ae386634f"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ad7c0ea2d4aceb7723ebcf33ae386634f">OpenMS::Internal::DIntervalBase::minY</a></div><div class="ttdeci">CoordinateType minY() const </div><div class="ttdoc">Accessor for max_ coordinate minimum. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:246</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< PeakType ></a></div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_abd0f5571675ec99e1aa647b39e2a8711"><div class="ttname"><a href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">OpenMS::Param::getValue</a></div><div class="ttdeci">const DataValue & getValue(const String &key) const </div><div class="ttdoc">Returns a value of a parameter. </div></div>
<div class="ttc" id="classOpenMS_1_1OfflinePrecursorIonSelection_html_ac76fec6f118131b8d46e5e2885ad7d50"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ac76fec6f118131b8d46e5e2885ad7d50">OpenMS::OfflinePrecursorIonSelection::updateExclusionList_</a></div><div class="ttdeci">void updateExclusionList_(std::vector< std::pair< T, Size > > &exclusion_list)</div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:649</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition< 2 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_ad99bb8ba2103d6c52ee10ae6369b46e7"><div class="ttname"><a href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">OpenMS::Feature::getConvexHulls</a></div><div class="ttdeci">const std::vector< ConvexHull2D > & getConvexHulls() const </div><div class="ttdoc">Non-mutable access to the convex hulls. </div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a93f1c9f620403aec160d98e83e125502"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a93f1c9f620403aec160d98e83e125502">OpenMS::MSSpectrum::sortByIntensity</a></div><div class="ttdeci">void sortByIntensity(bool reverse=false)</div><div class="ttdoc">Lexicographically sorts the peaks by their intensity. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:314</div></div>
<div class="ttc" id="classOpenMS_1_1OfflinePrecursorIonSelection_html_afc3ec85793adf0cdaacc5803e59f6c17"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html#afc3ec85793adf0cdaacc5803e59f6c17">OpenMS::OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap</a></div><div class="ttdeci">void makePrecursorSelectionForKnownLCMSMap(const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, MSExperiment< InputPeakType > &ms2, std::set< Int > &charges_set, bool feature_based)</div><div class="ttdoc">Makes the precursor selection for a given feature map, either feature or scan based. </div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:342</div></div>
<div class="ttc" id="classOpenMS_1_1OfflinePrecursorIonSelection_html_afb8f1202d548f01394d85fbeb51f9adf"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html#afb8f1202d548f01394d85fbeb51f9adf">OpenMS::OfflinePrecursorIonSelection::solver_</a></div><div class="ttdeci">LPWrapper::SOLVER solver_</div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:134</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a24f081fe74bbbf773533ad19e96d8358"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a24f081fe74bbbf773533ad19e96d8358">OpenMS::MSSpectrum::setMSLevel</a></div><div class="ttdeci">void setMSLevel(UInt ms_level)</div><div class="ttdoc">Sets the MS level. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:237</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_1OfflinePrecursorIonSelection_html_a2b206fdbe8649b90b854129f37fc594a"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html#a2b206fdbe8649b90b854129f37fc594a">OpenMS::OfflinePrecursorIonSelection::setLPSolver</a></div><div class="ttdeci">void setLPSolver(LPWrapper::SOLVER solver)</div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:100</div></div>
<div class="ttc" id="IDMapper_8h_html"><div class="ttname"><a href="IDMapper_8h.html">IDMapper.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ae9dafbb74a1a4c430ceef03e25ab8e10"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ae9dafbb74a1a4c430ceef03e25ab8e10">OpenMS::MSExperiment::addSpectrum</a></div><div class="ttdeci">void addSpectrum(const MSSpectrum< PeakT > &spectrum)</div><div class="ttdoc">adds a spectra to the list </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:738</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1InvalidSize_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1InvalidSize.html">OpenMS::Exception::InvalidSize</a></div><div class="ttdoc">Invalid UInt exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:304</div></div>
<div class="ttc" id="classOpenMS_1_1OfflinePrecursorIonSelection_html_acca2e18b840cc4b903f2958efca7aa1a"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html#acca2e18b840cc4b903f2958efca7aa1a">OpenMS::OfflinePrecursorIonSelection::checkMassRanges_</a></div><div class="ttdeci">void checkMassRanges_(std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const MSExperiment< InputPeakType > &experiment)</div><div class="ttdoc">Eliminates overlapping peaks. </div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:572</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_1MSExperiment_html_aee0a1a68d0fab63eefa6e14010b4a7f0"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">OpenMS::MSExperiment::ConstIterator</a></div><div class="ttdeci">std::vector< SpectrumType >::const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1OfflinePrecursorIonSelection_html"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html">OpenMS::OfflinePrecursorIonSelection</a></div><div class="ttdoc">Implements different algorithms for precursor ion selection. </div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ad85e4e6fe1ec77097d9108f38a8e57ae"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ad85e4e6fe1ec77097d9108f38a8e57ae">OpenMS::SpectrumSettings::setPrecursors</a></div><div class="ttdeci">void setPrecursors(const std::vector< Precursor > &precursors)</div><div class="ttdoc">sets the precursors </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<> &features, const MSExperiment< InputPeakType > &experiment, std::vector< IndexTriple > &variable_indices, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::set< Int > &charges_set, UInt ms2_spectra_per_rt_bin, std::vector< int > &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="classOpenMS_1_1OfflinePrecursorIonSelection_html_ae895e8f290c7f5869249e59a7b53c417"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html#ae895e8f290c7f5869249e59a7b53c417">OpenMS::OfflinePrecursorIonSelection::getMassRanges</a></div><div class="ttdeci">void getMassRanges(const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, std::vector< std::vector< std::pair< Size, Size > > > &indices)</div><div class="ttdoc">Calculates the mass ranges for each feature and stores them as indices of the raw data...</div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:154</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_aac8c50f318154e9e5b7b01aee806e17f"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">OpenMS::MSSpectrum::setRT</a></div><div class="ttdeci">void setRT(DoubleReal rt)</div><div class="ttdoc">Sets the absolute retention time (is seconds) </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:221</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="structOpenMS_1_1PairComparatorSecondElement_html"><div class="ttname"><a href="structOpenMS_1_1PairComparatorSecondElement.html">OpenMS::PairComparatorSecondElement</a></div><div class="ttdoc">Class for comparison of std::pair using second ONLY e.g. for use with std::sort. </div><div class="ttdef"><b>Definition:</b> ComparatorUtils.h:340</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ac6e61de369e994009e36f344f99c15ad"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">OpenMS::MSExperiment::empty</a></div><div class="ttdeci">bool empty() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1IntList_html_ac244d9a257aab1a24c1a622ccacab745"><div class="ttname"><a href="classOpenMS_1_1IntList.html#ac244d9a257aab1a24c1a622ccacab745">OpenMS::IntList::create</a></div><div class="ttdeci">static IntList create(const String &list)</div><div class="ttdoc">Returns a list that is created by splitting the given comma-separated string (String are not trimmed!...</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_aca40a4630f5f8a0568899b74a62dcd4b"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#aca40a4630f5f8a0568899b74a62dcd4b">OpenMS::Precursor::setCharge</a></div><div class="ttdeci">void setCharge(Int charge)</div><div class="ttdoc">Mutable access to the charge. </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_1DBoundingBox_html"><div class="ttname"><a href="classOpenMS_1_1DBoundingBox.html">OpenMS::DBoundingBox</a></div><div class="ttdoc">A D-dimensional bounding box. </div><div class="ttdef"><b>Definition:</b> DBoundingBox.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1OfflinePrecursorIonSelection_html_aff2cbb90bd3ebac2208d25616c0ecf7f"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html#aff2cbb90bd3ebac2208d25616c0ecf7f">OpenMS::OfflinePrecursorIonSelection::IndexTriple</a></div><div class="ttdeci">PSLPFormulation::IndexTriple IndexTriple</div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a3da529bd3240fa0d7148484bbef0b9d7"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">OpenMS::MSSpectrum::getRT</a></div><div class="ttdeci">DoubleReal getRT() const </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:215</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="PSLPFormulation_8h_html"><div class="ttname"><a href="PSLPFormulation_8h.html">PSLPFormulation.h</a></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_1DoubleList_html"><div class="ttname"><a href="classOpenMS_1_1DoubleList.html">OpenMS::DoubleList</a></div><div class="ttdoc">DoubleReal list. </div><div class="ttdef"><b>Definition:</b> DoubleList.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1OfflinePrecursorIonSelection_html_a09cf655b910fa7166cd8b27d17e02453"><div class="ttname"><a href="classOpenMS_1_1OfflinePrecursorIonSelection.html#a09cf655b910fa7166cd8b27d17e02453">OpenMS::OfflinePrecursorIonSelection::calculateXICs_</a></div><div class="ttdeci">void calculateXICs_(const FeatureMap<> &features, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const MSExperiment< InputPeakType > &experiment, const std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, DoubleReal > > > &xics)</div><div class="ttdoc">Calculate the sum of intensities of relevant features for each scan separately. </div><div class="ttdef"><b>Definition:</b> OfflinePrecursorIonSelection.h:305</div></div>
<div class="ttc" id="group__Concept_html_gace75bfb1aba684e874dffee13738bd15"><div class="ttname"><a href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">OpenMS::DoubleReal</a></div><div class="ttdeci">double DoubleReal</div><div class="ttdoc">Double-precision real type. </div><div class="ttdef"><b>Definition:</b> Types.h:118</div></div>
<div class="ttc" id="classOpenMS_1_1IntList_html"><div class="ttname"><a href="classOpenMS_1_1IntList.html">OpenMS::IntList</a></div><div class="ttdoc">Int list. </div><div class="ttdef"><b>Definition:</b> IntList.h:56</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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