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<a href="MRMFeatureFinderScoring_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>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <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>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Hannes Roest $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Hannes Roest $</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_OPENSWATH_MRMFEATUREFINDERSCORING_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_OPENSWATH_MRMFEATUREFINDERSCORING_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"><a class="line" href="MRMFeatureFinderScoring_8h.html#a1f18f099a1e85e5ad0256530ab97cd3a"> 38</a></span> <span class="preprocessor">#define run_identifier "unique_run_identifier"</span></div>
<div class="line"><a name="l00039"></a><span class="lineno"><a class="line" href="MRMFeatureFinderScoring_8h.html#a11009be58e0d38179204ebd339593f8b"> 39</a></span> <span class="preprocessor"></span><span class="preprocessor">#define USE_SP_INTERFACE</span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="comment">// move to TOPPTool</span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="MzMLFile_8h.html">OpenMS/FORMAT/MzMLFile.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="FeatureXMLFile_8h.html">OpenMS/FORMAT/FeatureXMLFile.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="TransformationXMLFile_8h.html">OpenMS/FORMAT/TransformationXMLFile.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="TraMLFile_8h.html">OpenMS/FORMAT/TraMLFile.h</a>></span></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="preprocessor">#include <<a class="code" href="MRMTransitionGroup_8h.html">OpenMS/KERNEL/MRMTransitionGroup.h</a>></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <<a class="code" href="MRMFeature_8h.html">OpenMS/KERNEL/MRMFeature.h</a>></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <<a class="code" href="MSSpectrum_8h.html">OpenMS/KERNEL/MSSpectrum.h</a>></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#include <<a class="code" href="MSChromatogram_8h.html">OpenMS/KERNEL/MSChromatogram.h</a>></span></div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="comment">// peak picking & noise estimation</span></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#include <<a class="code" href="SignalToNoiseEstimatorMedian_8h.html">OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.h</a>></span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="preprocessor">#include <<a class="code" href="MRMTransitionGroupPicker_8h.html">OpenMS/ANALYSIS/OPENSWATH/MRMTransitionGroupPicker.h</a>></span></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="comment">// data access</span></div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor">#include <<a class="code" href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2DataStructures_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h</a>></span></div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="preprocessor">#include <<a class="code" href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h</a>></span></div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> <span class="preprocessor">#include <<a class="code" href="TransitionExperiment_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h</a>></span></div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="preprocessor">#include <<a class="code" href="SimpleOpenMSSpectraAccessFactory_8h.html">OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SimpleOpenMSSpectraAccessFactory.h</a>></span></div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> <span class="preprocessor">#include <<a class="code" href="MRMFeatureAccessOpenMS_8h.html">OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/MRMFeatureAccessOpenMS.h</a>></span></div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="comment">// scoring</span></div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="preprocessor">#include <<a class="code" href="EmgScoring_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgScoring.h</a>></span></div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="preprocessor">#include <<a class="code" href="Scoring_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/ALGO/Scoring.h</a>></span></div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="preprocessor">#include <<a class="code" href="MRMScoring_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/ALGO/MRMScoring.h</a>></span></div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="preprocessor">#include <<a class="code" href="DIAScoring_8h.html">OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h</a>></span></div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="comment">// auxiliary</span></div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="preprocessor">#include <<a class="code" href="SpectrumAddition_8h.html">OpenMS/ANALYSIS/OPENSWATH/SpectrumAddition.h</a>></span></div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="preprocessor">#ifdef _OPENMP</span></div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="preprocessor"></span><span class="preprocessor">#include <omp.h></span></div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="keywordtype">bool</span> <a class="code" href="MRMFeatureFinderScoring_8h.html#ac179205eda67e461049ab7112f3de1e9">SortDoubleDoublePairFirst</a>(<span class="keyword">const</span> std::pair<double, double>& left, <span class="keyword">const</span> std::pair<double, double>& right);</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> {</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html"> 85</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1OpenSwath__Scores.html">OpenSwath_Scores</a></div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  {</div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#ac7a01742e0b867bc9ab9d91829d0d890"> 87</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ac7a01742e0b867bc9ab9d91829d0d890">elution_model_fit_score</a>;</div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#a4d7c492ccfc19c4162d9616011a060da"> 88</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a4d7c492ccfc19c4162d9616011a060da">library_corr</a>;</div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#aba3edbdb6d99fdd71b262d1e938b4e89"> 89</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aba3edbdb6d99fdd71b262d1e938b4e89">library_rmsd</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#a2d04130c2720f68f9dd1b541b0e5eaba"> 90</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a2d04130c2720f68f9dd1b541b0e5eaba">norm_rt_score</a>;</div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#a78dbcf0489fbf0d53d650d37c74ee164"> 91</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a78dbcf0489fbf0d53d650d37c74ee164">isotope_correlation</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#a3f0b0d733e7992afe009dd65591e0a2e"> 92</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a3f0b0d733e7992afe009dd65591e0a2e">isotope_overlap</a>;</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#ad86382490f14d6cc1b62611513b5e27f"> 93</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ad86382490f14d6cc1b62611513b5e27f">massdev_score</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#ab8dfbfc3eaa57313e0e5481894017995"> 94</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ab8dfbfc3eaa57313e0e5481894017995">xcorr_coelution_score</a>;</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#aa050ad09c86fd7f50842c59d49e6fea7"> 95</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aa050ad09c86fd7f50842c59d49e6fea7">xcorr_shape_score</a>;</div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#ad17f08a1a1d14810389bf7f585e95e8b"> 96</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ad17f08a1a1d14810389bf7f585e95e8b">yseries_score</a>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#a3626f9b563a3d7134f3849e62579c03b"> 97</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a3626f9b563a3d7134f3849e62579c03b">log_sn_score</a>;</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#aeb40871b8728dab160318bc38fc23e3a"> 99</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aeb40871b8728dab160318bc38fc23e3a">get_quick_lda_score</a>(<span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a4d7c492ccfc19c4162d9616011a060da">library_corr</a>, <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aba3edbdb6d99fdd71b262d1e938b4e89">library_rmsd</a>, <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a2d04130c2720f68f9dd1b541b0e5eaba">norm_rt_score</a>, <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ab8dfbfc3eaa57313e0e5481894017995">xcorr_coelution_score</a>,</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aa050ad09c86fd7f50842c59d49e6fea7">xcorr_shape_score</a>, <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a3626f9b563a3d7134f3849e62579c03b">log_sn_score</a>)</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>  <span class="comment">// some scores based on manual evaluation of 80 chromatograms</span></div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// quick LDA average model on 100 2xCrossvalidated runs (0.85 TPR/0.17 FDR)</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="comment">// true: mean 4.2 with sd 1.055</span></div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="comment">// false: mean -0.07506772 with sd 1.055</span></div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="comment">// below -0.5 removes around 30% of the peaks</span></div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="comment">// below 0 removes around 50% of the peaks</span></div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="comment">// below 0.5 removes around 70% of the peaks</span></div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="comment">// below 1.0 removes around 85% of the peaks</span></div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="comment">// below 1.5 removes around 93% of the peaks</span></div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="comment">// below 2.0 removes around 97% of the peaks</span></div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordtype">double</span> lda_quick_score =</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  library_corr * -0.5319046 +</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  library_rmsd * 2.1643962 +</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  norm_rt_score * 8.0353047 +</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  xcorr_coelution_score * 0.1458914 +</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  xcorr_shape_score * -1.6901925 +</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  log_sn_score * -0.8002824;</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keywordflow">return</span> lda_quick_score;</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  }</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#aca437d1a16d43a1e055a4fc295a2aa1e"> 122</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aca437d1a16d43a1e055a4fc295a2aa1e">calculate_lda_prescore</a>(<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html">OpenSwath_Scores</a> scores)</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  {</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="comment">// LDA average model on 100 2xCrossvalidated runs (0.91 TPR/0.20 FDR)</span></div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="comment">/*</span></div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> <span class="comment"> double xx_old_lda_prescore =</span></div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> <span class="comment"> intensity_score * -2.296679 +</span></div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="comment"> library_corr * -0.1223876 +</span></div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> <span class="comment"> library_rmsd * 2.013638 +</span></div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> <span class="comment"> nr_peaks_score * 0.01683357 +</span></div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="comment"> rt_score * 0.00143999 +</span></div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="comment"> sn_score * -0.1619762 +</span></div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> <span class="comment"> total_xic_score * 0.00000003697898 +</span></div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> <span class="comment"> xcorr_coelution_score * 0.05909583 +</span></div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> <span class="comment"> xcorr_shape_score * -0.4699841;</span></div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keywordflow">return</span> scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a4d7c492ccfc19c4162d9616011a060da">library_corr</a> * -0.34664267 +</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aba3edbdb6d99fdd71b262d1e938b4e89">library_rmsd</a> * 2.98700722 +</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a2d04130c2720f68f9dd1b541b0e5eaba">norm_rt_score</a> * 7.05496384 +</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ab8dfbfc3eaa57313e0e5481894017995">xcorr_coelution_score</a> * 0.09445371 +</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aa050ad09c86fd7f50842c59d49e6fea7">xcorr_shape_score</a> * -5.71823862 +</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a3626f9b563a3d7134f3849e62579c03b">log_sn_score</a> * -0.72989582 +</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ac7a01742e0b867bc9ab9d91829d0d890">elution_model_fit_score</a> * 1.88443209;</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  }</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> </div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OpenSwath__Scores.html#a6509c5d12cc9ba3417f9d46314345bc9"> 148</a></span>  <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a6509c5d12cc9ba3417f9d46314345bc9">calculate_swath_lda_prescore</a>(<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html">OpenSwath_Scores</a> scores)</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> </div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="comment">// Swath - LDA average model on 100 2xCrossvalidated runs (0.76 TPR/0.20 FDR) [without elution model]</span></div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="comment">/*</span></div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> <span class="comment"> double xx_old_swath_prescore =</span></div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> <span class="comment"> intensity_score * -3.148838e+00 +</span></div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span> <span class="comment"> library_corr * -7.562403e-02 +</span></div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> <span class="comment"> library_rmsd * 1.786286e+00 +</span></div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span> <span class="comment"> nr_peaks_score * -7.674263e-03 +</span></div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> <span class="comment"> rt_score * 1.748377e-03 +</span></div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> <span class="comment"> sn_score * -1.372636e-01 +</span></div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> <span class="comment"> total_xic_score * 7.278437e-08 +</span></div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <span class="comment"> xcorr_coelution_score * 1.181813e-01 +</span></div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> <span class="comment"> weighted_coelution_score * -7.661783e-02 +</span></div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> <span class="comment"> xcorr_shape_score * -6.903933e-02 +</span></div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="comment"> weighted_xcorr_shape * -4.234820e-01 +</span></div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> <span class="comment"> bseries_score * -2.022380e-02 +</span></div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> <span class="comment"> massdev_score * 2.844948e-02 +</span></div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span> <span class="comment"> massdev_score_weighted * 1.133209e-02 +</span></div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span> <span class="comment"> yseries_score * -9.510874e-02 +</span></div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="comment"> isotope_corr * -1.619902e+00 +</span></div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span> <span class="comment"> isotope_overlap * 2.890688e-01 ;</span></div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> </div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordflow">return</span> scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a4d7c492ccfc19c4162d9616011a060da">library_corr</a> * -0.19011762 +</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aba3edbdb6d99fdd71b262d1e938b4e89">library_rmsd</a> * 2.47298914 +</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a2d04130c2720f68f9dd1b541b0e5eaba">norm_rt_score</a> * 5.63906731 +</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a78dbcf0489fbf0d53d650d37c74ee164">isotope_correlation</a> * -0.62640133 +</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a3f0b0d733e7992afe009dd65591e0a2e">isotope_overlap</a> * 0.36006925 +</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ad86382490f14d6cc1b62611513b5e27f">massdev_score</a> * 0.08814003 +</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ab8dfbfc3eaa57313e0e5481894017995">xcorr_coelution_score</a> * 0.13978311 +</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aa050ad09c86fd7f50842c59d49e6fea7">xcorr_shape_score</a> * -1.16475032 +</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ad17f08a1a1d14810389bf7f585e95e8b">yseries_score</a> * -0.19267813 +</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a3626f9b563a3d7134f3849e62579c03b">log_sn_score</a> * -0.61712054;</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  }</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span> </div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  };</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> </div>
<div class="line"><a name="l00200"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html"> 200</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html">MRMFeatureFinderScoring</a> :</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>,</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></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> </div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> </div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span> </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="comment">// All the filters expect MSSpectrum<PeakT>, thus we give it an "MSSpectrum"</span></div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="comment">// but filled with Chromatogram Peaks.</span></div>
<div class="line"><a name="l00212"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a4910016b262f6723b82c4b1c4d6cdde7"> 212</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<ChromatogramPeak></a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a4910016b262f6723b82c4b1c4d6cdde7">RichPeakChromatogram</a>; <span class="comment">// this is the type in which we store the chromatograms for this analysis</span></div>
<div class="line"><a name="l00213"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a8497becf96cdfaf51ba301262d81f126"> 213</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenSwath_1_1LightTransition.html">OpenSwath::LightTransition</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a8497becf96cdfaf51ba301262d81f126">TransitionType</a>;</div>
<div class="line"><a name="l00214"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ab93154c1962d6ccb0a7d8f548ea0a9da"> 214</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ab93154c1962d6ccb0a7d8f548ea0a9da">TargetedExpType</a>;</div>
<div class="line"><a name="l00215"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#af71c1f3e928ced2c6264ed63155d8de0"> 215</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenSwath_1_1LightPeptide.html">OpenSwath::LightPeptide</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#af71c1f3e928ced2c6264ed63155d8de0">PeptideType</a>;</div>
<div class="line"><a name="l00216"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1e9fb94f05f21667db64366fe31b4357"> 216</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenSwath_1_1LightProtein.html">OpenSwath::LightProtein</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1e9fb94f05f21667db64366fe31b4357">ProteinType</a>;</div>
<div class="line"><a name="l00217"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae3c1ad9ec2bbfe5e9e7bac70731091fb"> 217</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenSwath_1_1LightModification.html">OpenSwath::LightModification</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae3c1ad9ec2bbfe5e9e7bac70731091fb">ModificationType</a>;</div>
<div class="line"><a name="l00218"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0f6b08b724983b516b2529790b798a9f"> 218</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup<MSSpectrum <ChromatogramPeak></a>, <a class="code" href="structOpenSwath_1_1LightTransition.html">TransitionType</a>> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0f6b08b724983b516b2529790b798a9f">MRMTransitionGroupType</a>; <span class="comment">// a transition group holds the MSSpectra with the Chromatogram peaks from above</span></div>
<div class="line"><a name="l00219"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7"> 219</a></span>  <span class="keyword">typedef</span> std::map<String, MRMTransitionGroupType> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7">TransitionGroupMapType</a>;</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html">MRMFeatureFinderScoring</a>();</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span> </div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  ~<a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html">MRMFeatureFinderScoring</a>();</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="comment">// pick features in one experiment containing chromatograms</span></div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <span class="comment">// (easy function for wrapping in Python, only uses OpenMS datastructures</span></div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <span class="comment">// and does not return the map)</span></div>
<div class="line"><a name="l00231"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#af879ba2bc9bcc83bed021af39c24e9d6"> 231</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#af879ba2bc9bcc83bed021af39c24e9d6">pickExperiment</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<Peak1D></a> & chromatograms, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<Feature></a>& output, <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a>& transition_exp_,</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> trafo, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<Peak1D></a>& swath_map)</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  {</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> transition_exp;</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <a class="code" href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a0476f3ea925f584d9064efee48c7db6a">OpenSwathDataAccessHelper::convertTargetedExp</a>(transition_exp_, transition_exp);</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7">TransitionGroupMapType</a> transition_group_map;</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span> </div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <a class="code" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> chromatogram_ptr = <a class="code" href="classOpenMS_1_1SimpleOpenMSSpectraFactory.html#a645eefe3725b60ffcf44f9ae01f0c19d">SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr</a>(chromatograms);</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <a class="code" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> empty_swath_ptr = <a class="code" href="classOpenMS_1_1SimpleOpenMSSpectraFactory.html#a645eefe3725b60ffcf44f9ae01f0c19d">SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr</a>(swath_map);</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span> </div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  pickExperiment(chromatogram_ptr, output, transition_exp, trafo, empty_swath_ptr, transition_group_map);</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  }</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>  <span class="comment">// pick features in one experiment containing chromatograms</span></div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a21e38df433d05118f343c33af60816e9"> 245</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a21e38df433d05118f343c33af60816e9">pickExperiment</a>(<a class="code" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> input, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<Feature></a>& output, <a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a>& transition_exp,</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> trafo, <a class="code" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> swath_map, <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7">TransitionGroupMapType</a>& transition_group_map)</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>  updateMembers_();</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="comment">//</span></div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <span class="comment">// Step 1</span></div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="comment">// Store the peptide retention times in an intermediate map</span></div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  PeptideRTMap_.clear();</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < transition_exp.<a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html#a75e5e77ae24708d28d8f3df92fcb84de">getPeptides</a>().size(); i++)</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  {</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <a class="code" href="structOpenSwath_1_1LightPeptide.html">PeptideType</a> pep = transition_exp.<a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html#a75e5e77ae24708d28d8f3df92fcb84de">getPeptides</a>()[i];</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  PeptideRTMap_[pep.<a class="code" href="structOpenSwath_1_1LightPeptide.html#afd0d68c6d31ff249f3ae8662162663c3">id</a>] = pep.<a class="code" href="structOpenSwath_1_1LightPeptide.html#ae5ee906bf451a6150d80754f4068dc58">rt</a>;</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  PeptideRefMap_[pep.<a class="code" href="structOpenSwath_1_1LightPeptide.html#afd0d68c6d31ff249f3ae8662162663c3">id</a>] = &transition_exp.<a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html#a75e5e77ae24708d28d8f3df92fcb84de">getPeptides</a>()[i];</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  }</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>  <span class="comment">// Store the proteins from the input in the output feature map</span></div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  std::vector<ProteinHit> protein_hits;</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < transition_exp.<a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html#a6d58ec7403247e88dbee94e859389c19">getProteins</a>().size(); i++)</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  {</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="keyword">const</span> <a class="code" href="structOpenSwath_1_1LightProtein.html">ProteinType</a>& prot = transition_exp.<a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html#a6d58ec7403247e88dbee94e859389c19">getProteins</a>()[i];</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  ProteinRefMap_[transition_exp.<a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html#a6d58ec7403247e88dbee94e859389c19">getProteins</a>()[i].id] = &transition_exp.<a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html#a6d58ec7403247e88dbee94e859389c19">getProteins</a>()[i];</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <a class="code" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> prot_hit = <a class="code" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a>();</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  prot_hit.<a class="code" href="classOpenMS_1_1ProteinHit.html#a2b8bf5f3febdb76461bdea9ff39d6b6d">setSequence</a>(prot.<a class="code" href="structOpenSwath_1_1LightProtein.html#a9a2b94a2b0e3195ef7ea3a13187c17b9">sequence</a>);</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  prot_hit.<a class="code" href="classOpenMS_1_1ProteinHit.html#aba1fff7a176ff80d53f932769e606980">setAccession</a>(prot.<a class="code" href="structOpenSwath_1_1LightProtein.html#afd0d68c6d31ff249f3ae8662162663c3">id</a>);</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  protein_hits.push_back(prot_hit);</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</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>  <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> prot_id = <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>();</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  prot_id.<a class="code" href="classOpenMS_1_1ProteinIdentification.html#a86f5c6d7c17c3aa94ec734e2a4fb50fa">setHits</a>(protein_hits);</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  prot_id.<a class="code" href="classOpenMS_1_1ProteinIdentification.html#a00f1456779f764c2738c35be2c04f6e8">setIdentifier</a>(<a class="code" href="MRMFeatureFinderScoring_8h.html#a1f18f099a1e85e5ad0256530ab97cd3a">run_identifier</a>);</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  output.<a class="code" href="classOpenMS_1_1FeatureMap.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>().push_back(prot_id);</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span> </div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <span class="comment">// Step 2</span></div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="comment">// Create all MRM transition groups from the individual transitions.</span></div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  mapExperimentToTransitionList(input, transition_exp, transition_group_map, trafo, rt_extraction_window_);</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="keywordtype">int</span> counter = 0;</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <span class="keywordflow">for</span> (TransitionGroupMapType::iterator trgroup_it = transition_group_map.begin(); trgroup_it != transition_group_map.end(); trgroup_it++)</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  {</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="keywordflow">if</span> (trgroup_it->second.getChromatograms().size() > 0) {counter++; }</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>  std::cout << <span class="stringliteral">"Will analyse "</span> << counter << <span class="stringliteral">" peptides with a total of "</span> << transition_exp.<a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html#a23a85c8da00a9f39f0c9ce6e15bc5a32">getTransitions</a>().size() << <span class="stringliteral">" transitions "</span> << std::endl;</div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span> </div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <span class="comment">// Step 3</span></div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="comment">// Go through all transition groups: first create consensus features, then score them</span></div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> progress = 0;</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  startProgress(0, transition_group_map.size(), <span class="stringliteral">"picking peaks"</span>);</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="keywordflow">for</span> (TransitionGroupMapType::iterator trgroup_it = transition_group_map.begin(); trgroup_it != transition_group_map.end(); trgroup_it++)</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> </div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  setProgress(++progress);</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroupType</a>& transition_group = trgroup_it->second;</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="keywordflow">if</span> (transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">getChromatograms</a>().size() == 0 || transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">getTransitions</a>().size() == 0)</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="keywordflow">continue</span>;</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  }</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span> </div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html">MRMTransitionGroupPicker</a> trgroup_picker;</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  trgroup_picker.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(param_.copy(<span class="stringliteral">"TransitionGroupPicker:"</span>, <span class="keyword">true</span>));</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  trgroup_picker.<a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#acce2a9f0fe8d27893f6a027a4598e8ba">pickTransitionGroup</a>(transition_group);</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  scorePeakgroups_(trgroup_it->second, trafo, swath_map, output);</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span> </div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  }</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  endProgress();</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span> </div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <span class="comment">//output.sortByPosition(); // if the exact same order is needed</span></div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  }</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="comment">// Map an input experiment (mzML) and transition list (TraML) onto each other</span></div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="comment">// when they share identifiers, e.g. if the transition id is the same as the</span></div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="comment">// chromatogram native id.</span></div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  <span class="keywordtype">void</span> mapExperimentToTransitionList(<a class="code" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> input, <a class="code" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a>& transition_exp,</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  TransitionGroupMapType& transition_group_map, <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> trafo, <span class="keywordtype">double</span> rt_extraction_window);</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span> </div>
<div class="line"><a name="l00325"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a9ac530b577855511cc32791aef8de7e4"> 325</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a9ac530b577855511cc32791aef8de7e4">setStrictFlag</a>(<span class="keywordtype">bool</span> f)</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  {</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  strict_ = f;</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  }</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="keyword">private</span>:</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span> </div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumT, <span class="keyword">typename</span> TransitionT></div>
<div class="line"><a name="l00334"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1d7f11c2be93f8140f508487ba0ae718"> 334</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1d7f11c2be93f8140f508487ba0ae718">scorePeakgroups_</a>(<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup<SpectrumT, TransitionT></a> & transition_group, <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> & trafo,</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <a class="code" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> swath_map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<Feature></a>& output)</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>  <span class="comment">//std::vector<SignalToNoiseEstimatorMedian<RichPeakChromatogram> > signal_noise_estimators;</span></div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup<SpectrumT, TransitionT>::PeakType</a> <a class="code" href="classPeakT.html">PeakT</a>;</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  std::vector<OpenSwath::ISignalToNoisePtr> signal_noise_estimators;</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  std::vector<MRMFeature> feature_list;</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span> </div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span> </div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <a class="code" href="classdouble.html">DoubleReal</a> sn_win_len_ = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)param_.getValue(<span class="stringliteral">"TransitionGroupPicker:sn_win_len"</span>);</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <a class="code" href="classdouble.html">DoubleReal</a> sn_bin_count_ = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)param_.getValue(<span class="stringliteral">"TransitionGroupPicker:sn_bin_count"</span>);</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> < transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">getChromatograms</a>().size(); <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>++)</div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  {</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <a class="code" href="namespaceOpenSwath.html#a657df1b62b2200d972968d1151992d7f">OpenSwath::ISignalToNoisePtr</a> snptr(<span class="keyword">new</span> <a class="code" href="classOpenMS_1_1SignalToNoiseOpenMS.html">OpenMS::SignalToNoiseOpenMS< PeakT ></a>(transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">getChromatograms</a>()[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>], sn_win_len_, sn_bin_count_));</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  signal_noise_estimators.push_back(snptr);</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  }</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span> </div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="comment">// get the expected rt value for this peptide</span></div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  <span class="keywordtype">double</span> expected_rt = PeptideRTMap_[transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#aedcd02941cf31e259bb9394850653bbc">getTransitionGroupID</a>()];</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> newtr = trafo;</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  newtr.<a class="code" href="classOpenMS_1_1TransformationDescription.html#a7fa1616cc61c19a5efcc863c950f7f30">invert</a>();</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  expected_rt = newtr.<a class="code" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">apply</a>(expected_rt);</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span> </div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <span class="comment">// Go through all peak groups (found MRM features) and score them</span></div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  <span class="keywordflow">for</span> (std::vector<MRMFeature>::iterator mrmfeature = transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a5c92d3ef5e22a80e2188a8fd81af3e5a">getFeaturesMuteable</a>().begin();</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  mrmfeature != transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a5c92d3ef5e22a80e2188a8fd81af3e5a">getFeaturesMuteable</a>().end(); mrmfeature++)</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> </div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  <a class="code" href="classOpenSwath_1_1IMRMFeature.html">OpenSwath::IMRMFeature</a>* imrmfeature;</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  imrmfeature = <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1MRMFeatureOpenMS.html">MRMFeatureOpenMS</a>(*mrmfeature);</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span> </div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  <a class="code" href="structOpenSwath_1_1ITransitionGroup.html">OpenSwath::ITransitionGroup</a>* itransition_group;</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  itransition_group = <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1TransitionGroupOpenMS.html">TransitionGroupOpenMS<SpectrumT, TransitionT></a>(transition_group);</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span> </div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span> <span class="preprocessor">#ifdef DEBUG_MRMPEAKPICKER</span></div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"000000000000000000000000000000000000000000000000000000000000000000000000000 "</span> << std::endl;</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  std::cout << <span class="stringliteral">"scoring feature "</span> << (*mrmfeature) << <span class="stringliteral">" == "</span> << mrmfeature->getMetaValue(<span class="stringliteral">"PeptideRef"</span>) <<</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <span class="stringliteral">"[ expected RT "</span> << PeptideRTMap_[mrmfeature->getMetaValue(<span class="stringliteral">"PeptideRef"</span>)] << <span class="stringliteral">" / "</span> << expected_rt << <span class="stringliteral">" ]"</span> <<</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  <span class="stringliteral">" with "</span> << transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() << <span class="stringliteral">" nr transitions and nr chromats "</span> << transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">getChromatograms</a>().size() << std::endl;</div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  <span class="keywordtype">int</span> group_size = boost::numeric_cast<<span class="keywordtype">int</span>>(transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="keywordflow">if</span> (group_size == 0)</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  {</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__,</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="stringliteral">"Error: Transition group "</span> + transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#aedcd02941cf31e259bb9394850653bbc">getTransitionGroupID</a>() + <span class="stringliteral">" has no chromatograms."</span>);</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  }</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  <span class="keywordflow">if</span> (group_size < 2)</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  {</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  std::cerr << <span class="stringliteral">"Error: transition group "</span> << transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#aedcd02941cf31e259bb9394850653bbc">getTransitionGroupID</a>() << <span class="stringliteral">" has less than 2 chromatograms. It has "</span> << group_size << std::endl;</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  <span class="comment">//throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Error: transition group " + transition_group.getTransitionGroupID() + " has less than 2 chromatograms.");</span></div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  }</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span> </div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  <span class="comment">// calculate the normalized library intensity (expected value of the intensities)</span></div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  std::vector<double> normalized_library_intensity;</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#aff73c863c0c2c6ff6173deac72567709">getLibraryIntensity</a>(normalized_library_intensity);</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  <a class="code" href="namespaceOpenSwath_1_1Scoring.html#afa39e794c622d1fdfc2d702517fffc80">OpenSwath::Scoring::normalize_sum</a>(&normalized_library_intensity[0], boost::numeric_cast<int>(normalized_library_intensity.size()));</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span> </div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  <span class="comment">// calcxcorr -> for each lag do the correlation, normally use lag 0</span></div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <span class="comment">// xcorr_matrix => correlate chromatogram i with chromatogram j</span></div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">normalize</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  mrmscore_.initializeXCorrMatrix(imrmfeature, itransition_group, normalize);</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span> </div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <span class="comment">// XCorr score (coelution)</span></div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  <span class="keywordtype">double</span> xcorr_coelution_score = 0;</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  <span class="keywordflow">if</span> (use_coelution_score_)</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>  xcorr_coelution_score = mrmscore_.calcXcorrCoelutionScore();</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  mrmfeature->addScore(<span class="stringliteral">"var_xcorr_coelution"</span>, xcorr_coelution_score);</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  }</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span> </div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  <span class="keywordtype">double</span> weighted_coelution_score = 0;</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  <span class="keywordflow">if</span> (use_coelution_score_)</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  {</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  weighted_coelution_score = mrmscore_.calcXcorrCoelutionScore_weighted(normalized_library_intensity);</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  mrmfeature->addScore(<span class="stringliteral">"var_xcorr_coelution_weighted "</span>, weighted_coelution_score);</div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  }</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span> </div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  <span class="comment">// XCorr score (shape)</span></div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  <span class="comment">// mean over the intensities at the max of the crosscorrelation</span></div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  <span class="comment">// FEATURE : weigh by the intensity as done by mQuest</span></div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <span class="comment">// FEATURE : normalize with the intensity at the peak group apex?</span></div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  <span class="keywordtype">double</span> xcorr_shape_score = 0;</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  <span class="keywordflow">if</span> (use_shape_score_)</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>  xcorr_shape_score = mrmscore_.calcXcorrShape_score();</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  mrmfeature->addScore(<span class="stringliteral">"var_xcorr_shape"</span>, xcorr_shape_score);</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  }</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span> </div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  <span class="keywordtype">double</span> weighted_xcorr_shape = 0;</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  <span class="keywordflow">if</span> (use_shape_score_)</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>  weighted_xcorr_shape = mrmscore_.calcXcorrShape_score_weighted(normalized_library_intensity);</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  mrmfeature->addScore(<span class="stringliteral">"var_xcorr_shape_weighted"</span>, weighted_xcorr_shape);</div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  }</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span> </div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="comment">// FEATURE : how should we best calculate correlation between library and experiment?</span></div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="comment">// FEATURE : spectral angle</span></div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <span class="keywordtype">double</span> library_corr = 0, library_rmsd = 0;</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  <span class="keywordtype">double</span> library_manhattan, library_dotprod;</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  <span class="keywordflow">if</span> (use_library_score_)</div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  {</div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  mrmscore_.calcLibraryScore(imrmfeature, transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">getTransitions</a>(), library_corr, library_rmsd, library_manhattan, library_dotprod);</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  mrmfeature->addScore(<span class="stringliteral">"var_library_corr"</span>, library_corr);</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  mrmfeature->addScore(<span class="stringliteral">"var_library_rmsd"</span>, library_rmsd);</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  mrmfeature->addScore(<span class="stringliteral">"var_library_manhattan"</span>, library_manhattan); <span class="comment">// new score</span></div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  mrmfeature->addScore(<span class="stringliteral">"var_library_dotprod"</span>, library_dotprod); <span class="comment">// new score</span></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> </div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <span class="comment">// Retention time score</span></div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="keywordtype">double</span> rt_score = 0, norm_rt_score = 0;</div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  <span class="keywordflow">if</span> (use_rt_score_)</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>  <span class="comment">// get the id, then get the expected and the experimental retention time</span></div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> native_id = transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">getChromatograms</a>()[0].getNativeID();</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  <a class="code" href="structOpenSwath_1_1LightTransition.html">TransitionType</a> tr = transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a72f3eb6e4f2beacf59fb94d10fffd9ba">getTransition</a>(native_id);</div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  <span class="keyword">const</span> <a class="code" href="structOpenSwath_1_1LightPeptide.html">PeptideType</a>* pep = PeptideRefMap_[tr.<a class="code" href="structOpenSwath_1_1LightTransition.html#a4c4914efae99b51076cec9814268707c">getPeptideRef</a>()];</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  <span class="keywordtype">double</span> experimental_rt = mrmfeature->getFeature(native_id).getRT();</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keywordtype">double</span> normalized_experimental_rt = trafo.<a class="code" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">apply</a>(experimental_rt);</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  <span class="comment">// rt score is delta iRT</span></div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  rt_score = mrmscore_.calcRTScore(*pep, normalized_experimental_rt);</div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  norm_rt_score = rt_score / rt_normalization_factor_;</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  mrmfeature->addScore(<span class="stringliteral">"delta_rt"</span>, mrmfeature->getRT() - expected_rt);</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  mrmfeature->addScore(<span class="stringliteral">"assay_rt"</span>, expected_rt);</div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  mrmfeature->addScore(<span class="stringliteral">"norm_RT"</span>, normalized_experimental_rt);</div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  mrmfeature->addScore(<span class="stringliteral">"rt_score"</span>, rt_score);</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  mrmfeature->addScore(<span class="stringliteral">"var_norm_rt_score"</span>, norm_rt_score);</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> </div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="comment">// Intensity score</span></div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  <span class="keywordtype">double</span> intensity_score = 0;</div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <span class="keywordflow">if</span> (use_intensity_score_)</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>  intensity_score = mrmfeature->getIntensity() / (<a class="code" href="classdouble.html">double</a>)mrmfeature->getMetaValue(<span class="stringliteral">"total_xic"</span>);</div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  mrmfeature->addScore(<span class="stringliteral">"var_intensity_score"</span>, intensity_score);</div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  }</div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span> </div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  <span class="keywordtype">double</span> total_xic_score = 0;</div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  <span class="keywordflow">if</span> (use_total_xic_score_)</div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  {</div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  total_xic_score = (<a class="code" href="classdouble.html">double</a>)mrmfeature->getMetaValue(<span class="stringliteral">"total_xic"</span>);</div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  mrmfeature->addScore(<span class="stringliteral">"total_xic"</span>, total_xic_score);</div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  }</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>  <span class="keywordtype">double</span> nr_peaks_score = 0;</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  <span class="keywordflow">if</span> (use_nr_peaks_score_)</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>  nr_peaks_score = group_size;</div>
<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  mrmfeature->addScore(<span class="stringliteral">"nr_peaks"</span>, nr_peaks_score);</div>
<div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  }</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="keywordtype">double</span> sn_score = 0, log_sn_score = 0;</div>
<div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  <span class="keywordflow">if</span> (use_sn_score_)</div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  {</div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  sn_score = mrmscore_.calcSNScore(imrmfeature, signal_noise_estimators);</div>
<div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  <span class="keywordflow">if</span> (sn_score < 1) <span class="comment">// fix to make sure, that log(sn_score = 0) = -inf does not occur</span></div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  {</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  log_sn_score = 0;</div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  }</div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  {</div>
<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  log_sn_score = std::log(sn_score);</div>
<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  }</div>
<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  mrmfeature->addScore(<span class="stringliteral">"sn_ratio"</span>, sn_score);</div>
<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  mrmfeature->addScore(<span class="stringliteral">"var_log_sn_score"</span>, log_sn_score);</div>
<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  }</div>
<div class="line"><a name="l00501"></a><span class="lineno"> 501</span> </div>
<div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html">OpenSwath_Scores</a> scores;</div>
<div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  <span class="keywordtype">double</span> quick_lda_dismiss = 0;</div>
<div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  <span class="keywordtype">double</span> lda_quick_score = -scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aeb40871b8728dab160318bc38fc23e3a">get_quick_lda_score</a>(library_corr, library_rmsd, norm_rt_score, xcorr_coelution_score, xcorr_shape_score, log_sn_score);</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>  <span class="keywordflow">if</span> (lda_quick_score < quick_lda_dismiss)</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">// continue;</span></div>
<div class="line"><a name="l00509"></a><span class="lineno"> 509</span>  }</div>
<div class="line"><a name="l00510"></a><span class="lineno"> 510</span> </div>
<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  <span class="keywordtype">double</span> elution_model_fit_score = 0;</div>
<div class="line"><a name="l00512"></a><span class="lineno"> 512</span>  <span class="keywordflow">if</span> (use_elution_model_score_)</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>  elution_model_fit_score = emgscoring_.calcElutionFitScore((*mrmfeature), transition_group);</div>
<div class="line"><a name="l00515"></a><span class="lineno"> 515</span>  mrmfeature->addScore(<span class="stringliteral">"var_elution_model_fit_score"</span>, elution_model_fit_score);</div>
<div class="line"><a name="l00516"></a><span class="lineno"> 516</span>  }</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>  <span class="keywordtype">double</span> xx_lda_prescore;</div>
<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a4d7c492ccfc19c4162d9616011a060da">library_corr</a> = library_corr;</div>
<div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aba3edbdb6d99fdd71b262d1e938b4e89">library_rmsd</a> = library_rmsd;</div>
<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a2d04130c2720f68f9dd1b541b0e5eaba">norm_rt_score</a> = norm_rt_score;</div>
<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ac7a01742e0b867bc9ab9d91829d0d890">elution_model_fit_score</a> = elution_model_fit_score;</div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a3626f9b563a3d7134f3849e62579c03b">log_sn_score</a> = log_sn_score;</div>
<div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ab8dfbfc3eaa57313e0e5481894017995">xcorr_coelution_score</a> = xcorr_coelution_score;</div>
<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aa050ad09c86fd7f50842c59d49e6fea7">xcorr_shape_score</a> = xcorr_shape_score;</div>
<div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  xx_lda_prescore = -scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#aca437d1a16d43a1e055a4fc295a2aa1e">calculate_lda_prescore</a>(scores);</div>
<div class="line"><a name="l00527"></a><span class="lineno"> 527</span> </div>
<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  <span class="keywordtype">bool</span> swath_present = (swath_map->getNrSpectra() > 0);</div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  <span class="keywordflow">if</span> (!swath_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>  mrmfeature->addScore(<span class="stringliteral">"main_var_xx_lda_prelim_score"</span>, xx_lda_prescore);</div>
<div class="line"><a name="l00532"></a><span class="lineno"> 532</span>  mrmfeature->setOverallQuality(xx_lda_prescore);</div>
<div class="line"><a name="l00533"></a><span class="lineno"> 533</span>  }</div>
<div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  {</div>
<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  mrmfeature->addScore(<span class="stringliteral">"xx_lda_prelim_score"</span>, xx_lda_prescore);</div>
<div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  }</div>
<div class="line"><a name="l00538"></a><span class="lineno"> 538</span> </div>
<div class="line"><a name="l00539"></a><span class="lineno"> 539</span>  <span class="keywordflow">if</span> (swath_present)</div>
<div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  {</div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  calculateSwathScores_(transition_group, *mrmfeature, swath_map, normalized_library_intensity, scores);</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> </div>
<div class="line"><a name="l00544"></a><span class="lineno"> 544</span> <span class="preprocessor">#if 0</span></div>
<div class="line"><a name="l00545"></a><span class="lineno"> 545</span> <span class="preprocessor"></span> <span class="keywordflow">if</span> (do_local_fdr_)</div>
<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  {</div>
<div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  calculate_local_fdr_scores(transition_group, *mrmfeature, trafo);</div>
<div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  }</div>
<div class="line"><a name="l00549"></a><span class="lineno"> 549</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00550"></a><span class="lineno"> 550</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  <span class="comment">// add the peptide hit information to the feature</span></div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span> <span class="comment"></span></div>
<div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  <span class="keyword">const</span> <a class="code" href="structOpenSwath_1_1LightPeptide.html">PeptideType</a>* pep = PeptideRefMap_[transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">getTransitions</a>()[0].getPeptideRef()];</div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  <span class="keyword">const</span> <a class="code" href="structOpenSwath_1_1LightProtein.html">ProteinType</a>* prot = ProteinRefMap_[pep-><a class="code" href="structOpenSwath_1_1LightPeptide.html#a85ef381b973761bfb8afbe31ba8c010f">protein_ref</a>];</div>
<div class="line"><a name="l00557"></a><span class="lineno"> 557</span> </div>
<div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> pep_id_ = <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>();</div>
<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> pep_hit_ = <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a>();</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>  <span class="keywordflow">if</span> (pep-><a class="code" href="structOpenSwath_1_1LightPeptide.html#a49ce0caa2ae22c1439eaf0fd861bf37f">getChargeState</a>() != -1)</div>
<div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  {</div>
<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  pep_hit_.<a class="code" href="classOpenMS_1_1PeptideHit.html#aca40a4630f5f8a0568899b74a62dcd4b">setCharge</a>(pep-><a class="code" href="structOpenSwath_1_1LightPeptide.html#a49ce0caa2ae22c1439eaf0fd861bf37f">getChargeState</a>());</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>  pep_hit_.<a class="code" href="classOpenMS_1_1PeptideHit.html#a2e9b7c12f6d8fa7415aa0aca69208f42">setScore</a>(xx_lda_prescore);</div>
<div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  <span class="keywordflow">if</span> (swath_present)</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>  pep_hit_.<a class="code" href="classOpenMS_1_1PeptideHit.html#a2e9b7c12f6d8fa7415aa0aca69208f42">setScore</a>(mrmfeature->getScore(<span class="stringliteral">"xx_swath_prelim_score"</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>  pep_hit_.<a class="code" href="classOpenMS_1_1PeptideHit.html#a209d1e10f38a766c3f73c9666e89e14d">setSequence</a>((<a class="code" href="classOpenMS_1_1String.html">String</a>)pep-><a class="code" href="structOpenSwath_1_1LightPeptide.html#a9a2b94a2b0e3195ef7ea3a13187c17b9">sequence</a>);</div>
<div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  pep_hit_.<a class="code" href="classOpenMS_1_1PeptideHit.html#a49d90d2fa65c45386e5725386d7741fe">addProteinAccession</a>(prot-><a class="code" href="structOpenSwath_1_1LightProtein.html#afd0d68c6d31ff249f3ae8662162663c3">id</a>);</div>
<div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  pep_id_.<a class="code" href="classOpenMS_1_1PeptideIdentification.html#ae558057222f754e972e0257de2fe3c2d">insertHit</a>(pep_hit_);</div>
<div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  pep_id_.<a class="code" href="classOpenMS_1_1PeptideIdentification.html#a00f1456779f764c2738c35be2c04f6e8">setIdentifier</a>(<a class="code" href="MRMFeatureFinderScoring_8h.html#a1f18f099a1e85e5ad0256530ab97cd3a">run_identifier</a>);</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>  mrmfeature->getPeptideIdentifications().push_back(pep_id_);</div>
<div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  mrmfeature->ensureUniqueId();</div>
<div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  mrmfeature->setMetaValue(<span class="stringliteral">"PrecursorMZ"</span>, transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">getTransitions</a>()[0].getPrecursorMZ());</div>
<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  mrmfeature->setSubordinates(mrmfeature->getFeatures()); <span class="comment">// add all the subfeatures as subordinates</span></div>
<div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  <span class="keywordtype">double</span> total_intensity = 0, total_peak_apices = 0;</div>
<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="keywordflow">for</span> (std::vector<Feature>::iterator sub_it = mrmfeature->getSubordinates().begin(); sub_it != mrmfeature->getSubordinates().end(); sub_it++)</div>
<div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  {</div>
<div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  <span class="keywordflow">if</span> (!write_convex_hull_) {sub_it->getConvexHulls().clear(); }</div>
<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  sub_it->ensureUniqueId();</div>
<div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  <span class="keywordflow">if</span> (sub_it->getMZ() > quantification_cutoff_)</div>
<div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  {</div>
<div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  total_intensity += sub_it->getIntensity();</div>
<div class="line"><a name="l00587"></a><span class="lineno"> 587</span>  total_peak_apices += (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)sub_it->getMetaValue(<span class="stringliteral">"peak_apex_int"</span>);</div>
<div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  }</div>
<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  }</div>
<div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  <span class="comment">// overwrite the reported intensities with those above the m/z cutoff</span></div>
<div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  mrmfeature->setIntensity(total_intensity);</div>
<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  mrmfeature->setMetaValue(<span class="stringliteral">"peak_apices_sum"</span>, total_peak_apices);</div>
<div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  feature_list.push_back((*mrmfeature));</div>
<div class="line"><a name="l00594"></a><span class="lineno"> 594</span> </div>
<div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  <span class="keyword">delete</span> imrmfeature;</div>
<div class="line"><a name="l00596"></a><span class="lineno"> 596</span>  <span class="keyword">delete</span> itransition_group;</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> </div>
<div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  <span class="comment">// Order by quality</span></div>
<div class="line"><a name="l00600"></a><span class="lineno"> 600</span>  std::sort(feature_list.begin(), feature_list.end(), <a class="code" href="classOpenMS_1_1Feature.html#a076172c5ec2a42850e27a7de01b2b910">OpenMS::Feature::OverallQualityLess</a>());</div>
<div class="line"><a name="l00601"></a><span class="lineno"> 601</span>  std::reverse(feature_list.begin(), feature_list.end());</div>
<div class="line"><a name="l00602"></a><span class="lineno"> 602</span> </div>
<div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < feature_list.size(); i++)</div>
<div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  {</div>
<div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  <span class="keywordflow">if</span> (stop_report_after_feature_ >= 0 && i >= (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>)stop_report_after_feature_) {<span class="keywordflow">break</span>; }</div>
<div class="line"><a name="l00606"></a><span class="lineno"> 606</span>  output.push_back(feature_list[i]);</div>
<div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  }</div>
<div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  }</div>
<div class="line"><a name="l00609"></a><span class="lineno"> 609</span> </div>
<div class="line"><a name="l00611"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a392c2beaccf8b9d8e6f5d3e766f1bc72"> 611</a></span>  <a class="code" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a392c2beaccf8b9d8e6f5d3e766f1bc72">getAddedSpectra_</a>(<a class="code" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> swath_map, <span class="keywordtype">double</span> RT, <span class="keywordtype">int</span> nr_spectra_to_add)</div>
<div class="line"><a name="l00612"></a><span class="lineno"> 612</span>  {</div>
<div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  std::vector<std::size_t> indices = swath_map->getSpectraByRT(RT, 0.0);</div>
<div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  <span class="keywordtype">int</span> closest_idx = boost::numeric_cast<<span class="keywordtype">int</span>>(indices[0]);</div>
<div class="line"><a name="l00615"></a><span class="lineno"> 615</span>  <span class="keywordflow">if</span> (indices[0] != 0 &&</div>
<div class="line"><a name="l00616"></a><span class="lineno"> 616</span>  std::fabs(swath_map->getSpectrumMetaById(boost::numeric_cast<int>(indices[0]) - 1).RT - RT) <</div>
<div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  std::fabs(swath_map->getSpectrumMetaById(boost::numeric_cast<int>(indices[0])).RT - RT))</div>
<div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  {</div>
<div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  closest_idx--;</div>
<div class="line"><a name="l00620"></a><span class="lineno"> 620</span>  }</div>
<div class="line"><a name="l00621"></a><span class="lineno"> 621</span> </div>
<div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  <span class="keywordflow">if</span> (nr_spectra_to_add == 1)</div>
<div class="line"><a name="l00623"></a><span class="lineno"> 623</span>  {</div>
<div class="line"><a name="l00624"></a><span class="lineno"> 624</span>  <a class="code" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> spectrum_ = swath_map->getSpectrumById(closest_idx);</div>
<div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  <span class="keywordflow">return</span> spectrum_;</div>
<div class="line"><a name="l00626"></a><span class="lineno"> 626</span>  }</div>
<div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  <span class="keywordflow">else</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>  std::vector<OpenSwath::SpectrumPtr> all_spectra;</div>
<div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  <span class="comment">// always add the spectrum 0, then add those right and left</span></div>
<div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  all_spectra.push_back(swath_map->getSpectrumById(closest_idx));</div>
<div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 1; i <= nr_spectra_to_add / 2; i++) <span class="comment">// cast to int is intended!</span></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>  all_spectra.push_back(swath_map->getSpectrumById(closest_idx - i));</div>
<div class="line"><a name="l00635"></a><span class="lineno"> 635</span>  all_spectra.push_back(swath_map->getSpectrumById(closest_idx + i));</div>
<div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  }</div>
<div class="line"><a name="l00637"></a><span class="lineno"> 637</span>  <a class="code" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> spectrum_ = <a class="code" href="classOpenMS_1_1SpectrumAddition.html#a66af26742cdb048bacaed720d147f7fb">SpectrumAddition::addUpSpectra</a>(all_spectra, spacing_for_spectra_resampling_, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  <span class="keywordflow">return</span> spectrum_;</div>
<div class="line"><a name="l00639"></a><span class="lineno"> 639</span>  }</div>
<div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  }</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>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumT, <span class="keyword">typename</span> TransitionT></div>
<div class="line"><a name="l00643"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a7aa7123edb723725ec69f259c69d46d0"> 643</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a7aa7123edb723725ec69f259c69d46d0">calculateSwathScores_</a>(<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup<SpectrumT, TransitionT></a> & transition_group, <a class="code" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a> & mrmfeature_,</div>
<div class="line"><a name="l00644"></a><span class="lineno"> 644</span>  <a class="code" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> swath_map, std::vector<double>& normalized_library_intensity, <a class="code" href="structOpenMS_1_1OpenSwath__Scores.html">OpenSwath_Scores</a> scores)</div>
<div class="line"><a name="l00645"></a><span class="lineno"> 645</span>  {</div>
<div class="line"><a name="l00646"></a><span class="lineno"> 646</span>  <a class="code" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a>* mrmfeature = &mrmfeature_;</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="comment">// parameters</span></div>
<div class="line"><a name="l00649"></a><span class="lineno"> 649</span>  <span class="keywordtype">int</span> by_charge_state = 1; <span class="comment">// for which charge states should we check b/y series</span></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="comment">// find spectrum that is closest to the apex of the peak using binary search</span></div>
<div class="line"><a name="l00652"></a><span class="lineno"> 652</span>  <a class="code" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> spectrum_ = getAddedSpectra_(swath_map, mrmfeature-><a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>(), add_up_spectra_);</div>
<div class="line"><a name="l00653"></a><span class="lineno"> 653</span>  <a class="code" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a>* spectrum = &spectrum_;</div>
<div class="line"><a name="l00654"></a><span class="lineno"> 654</span> </div>
<div class="line"><a name="l00655"></a><span class="lineno"> 655</span>  <span class="comment">// Isotope correlation / overlap score: Is this peak part of an</span></div>
<div class="line"><a name="l00656"></a><span class="lineno"> 656</span>  <span class="comment">// isotopic pattern or is it the monoisotopic peak in an isotopic</span></div>
<div class="line"><a name="l00657"></a><span class="lineno"> 657</span>  <span class="comment">// pattern?</span></div>
<div class="line"><a name="l00658"></a><span class="lineno"> 658</span>  <a class="code" href="classOpenSwath_1_1IMRMFeature.html">OpenSwath::IMRMFeature</a>* imrmfeature = <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1MRMFeatureOpenMS.html">MRMFeatureOpenMS</a>(*mrmfeature);</div>
<div class="line"><a name="l00659"></a><span class="lineno"> 659</span>  <span class="keywordtype">double</span> isotope_corr = 0, isotope_overlap = 0;</div>
<div class="line"><a name="l00660"></a><span class="lineno"> 660</span>  diascoring_.dia_isotope_scores(transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">getTransitions</a>(),</div>
<div class="line"><a name="l00661"></a><span class="lineno"> 661</span>  (*spectrum), imrmfeature, isotope_corr, isotope_overlap);</div>
<div class="line"><a name="l00662"></a><span class="lineno"> 662</span>  <span class="comment">// Mass deviation score</span></div>
<div class="line"><a name="l00663"></a><span class="lineno"> 663</span>  <span class="keywordtype">double</span> ppm_score = 0, ppm_score_weighted = 0;</div>
<div class="line"><a name="l00664"></a><span class="lineno"> 664</span>  diascoring_.dia_massdiff_score(transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">getTransitions</a>(),</div>
<div class="line"><a name="l00665"></a><span class="lineno"> 665</span>  (*spectrum), normalized_library_intensity, ppm_score, ppm_score_weighted);</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>  <span class="comment">// Presence of b/y series score</span></div>
<div class="line"><a name="l00668"></a><span class="lineno"> 668</span>  <span class="keywordtype">double</span> bseries_score = 0, yseries_score = 0;</div>
<div class="line"><a name="l00669"></a><span class="lineno"> 669</span>  <a class="code" href="classOpenMS_1_1AASequence.html">OpenMS::AASequence</a> aas;</div>
<div class="line"><a name="l00670"></a><span class="lineno"> 670</span>  <a class="code" href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a8ae154a5964d69f913d864b169b7310e">OpenSwathDataAccessHelper::convertPeptideToAASequence</a>(*PeptideRefMap_[transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">getTransitions</a>()[0].getPeptideRef()], aas);</div>
<div class="line"><a name="l00671"></a><span class="lineno"> 671</span>  diascoring_.dia_by_ion_score((*spectrum), aas, by_charge_state, bseries_score, yseries_score);</div>
<div class="line"><a name="l00672"></a><span class="lineno"> 672</span>  mrmfeature-><a class="code" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">addScore</a>(<span class="stringliteral">"var_isotope_correlation_score"</span>, isotope_corr);</div>
<div class="line"><a name="l00673"></a><span class="lineno"> 673</span>  mrmfeature-><a class="code" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">addScore</a>(<span class="stringliteral">"var_isotope_overlap_score"</span>, isotope_overlap);</div>
<div class="line"><a name="l00674"></a><span class="lineno"> 674</span> <span class="preprocessor">#ifdef DEBUG_MRMPEAKPICKER</span></div>
<div class="line"><a name="l00675"></a><span class="lineno"> 675</span> <span class="preprocessor"></span> cout << <span class="stringliteral">"added corr isotope_score "</span> << isotope_corr << endl;</div>
<div class="line"><a name="l00676"></a><span class="lineno"> 676</span>  cout << <span class="stringliteral">"added overlap isotope_score "</span> << isotope_overlap << endl;</div>
<div class="line"><a name="l00677"></a><span class="lineno"> 677</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00678"></a><span class="lineno"> 678</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00679"></a><span class="lineno"> 679</span>  <span class="comment">// FEATURE we should not punish so much when one transition is missing!</span></div>
<div class="line"><a name="l00680"></a><span class="lineno"> 680</span>  <span class="keywordtype">double</span> massdev_score = ppm_score / transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>();</div>
<div class="line"><a name="l00681"></a><span class="lineno"> 681</span>  <span class="keywordtype">double</span> massdev_score_weighted = ppm_score_weighted;</div>
<div class="line"><a name="l00682"></a><span class="lineno"> 682</span>  mrmfeature-><a class="code" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">addScore</a>(<span class="stringliteral">"var_massdev_score"</span>, massdev_score);</div>
<div class="line"><a name="l00683"></a><span class="lineno"> 683</span>  mrmfeature-><a class="code" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">addScore</a>(<span class="stringliteral">"var_massdev_score_weighted"</span>, massdev_score_weighted);</div>
<div class="line"><a name="l00684"></a><span class="lineno"> 684</span> <span class="preprocessor">#ifdef DEBUG_MRMPEAKPICKER</span></div>
<div class="line"><a name="l00685"></a><span class="lineno"> 685</span> <span class="preprocessor"></span> cout << <span class="stringliteral">"added score massdev_score "</span> << massdev_score << endl;</div>
<div class="line"><a name="l00686"></a><span class="lineno"> 686</span>  cout << <span class="stringliteral">"added score weighted massdev_score "</span> << massdev_score_weighted << endl;</div>
<div class="line"><a name="l00687"></a><span class="lineno"> 687</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00688"></a><span class="lineno"> 688</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00689"></a><span class="lineno"> 689</span>  mrmfeature-><a class="code" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">addScore</a>(<span class="stringliteral">"var_bseries_score"</span>, bseries_score);</div>
<div class="line"><a name="l00690"></a><span class="lineno"> 690</span>  mrmfeature-><a class="code" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">addScore</a>(<span class="stringliteral">"var_yseries_score"</span>, yseries_score);</div>
<div class="line"><a name="l00691"></a><span class="lineno"> 691</span> <span class="preprocessor">#ifdef DEBUG_MRMPEAKPICKER</span></div>
<div class="line"><a name="l00692"></a><span class="lineno"> 692</span> <span class="preprocessor"></span> cout << <span class="stringliteral">"added score bseries_score "</span> << bseries_score << endl;</div>
<div class="line"><a name="l00693"></a><span class="lineno"> 693</span>  cout << <span class="stringliteral">"added score yseries_score "</span> << yseries_score << endl;</div>
<div class="line"><a name="l00694"></a><span class="lineno"> 694</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00695"></a><span class="lineno"> 695</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00696"></a><span class="lineno"> 696</span>  <span class="keywordtype">double</span> dotprod_score_dia;</div>
<div class="line"><a name="l00697"></a><span class="lineno"> 697</span>  <span class="keywordtype">double</span> manhatt_score_dia;</div>
<div class="line"><a name="l00698"></a><span class="lineno"> 698</span> </div>
<div class="line"><a name="l00699"></a><span class="lineno"> 699</span>  diascoring_.score_with_isotopes((*spectrum), transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">getTransitions</a>(), dotprod_score_dia, manhatt_score_dia);</div>
<div class="line"><a name="l00700"></a><span class="lineno"> 700</span> </div>
<div class="line"><a name="l00701"></a><span class="lineno"> 701</span>  mrmfeature-><a class="code" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">addScore</a>(<span class="stringliteral">"var_dotprod_score"</span>, dotprod_score_dia);</div>
<div class="line"><a name="l00702"></a><span class="lineno"> 702</span>  mrmfeature-><a class="code" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">addScore</a>(<span class="stringliteral">"var_manhatt_score"</span>, manhatt_score_dia);</div>
<div class="line"><a name="l00703"></a><span class="lineno"> 703</span> </div>
<div class="line"><a name="l00704"></a><span class="lineno"> 704</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ad17f08a1a1d14810389bf7f585e95e8b">yseries_score</a> = yseries_score;</div>
<div class="line"><a name="l00705"></a><span class="lineno"> 705</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a78dbcf0489fbf0d53d650d37c74ee164">isotope_correlation</a> = isotope_corr;</div>
<div class="line"><a name="l00706"></a><span class="lineno"> 706</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a3f0b0d733e7992afe009dd65591e0a2e">isotope_overlap</a> = isotope_overlap;</div>
<div class="line"><a name="l00707"></a><span class="lineno"> 707</span>  scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#ad86382490f14d6cc1b62611513b5e27f">massdev_score</a> = massdev_score;</div>
<div class="line"><a name="l00708"></a><span class="lineno"> 708</span>  <span class="keywordtype">double</span> xx_swath_prescore = -scores.<a class="code" href="structOpenMS_1_1OpenSwath__Scores.html#a6509c5d12cc9ba3417f9d46314345bc9">calculate_swath_lda_prescore</a>(scores);</div>
<div class="line"><a name="l00709"></a><span class="lineno"> 709</span>  mrmfeature-><a class="code" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">addScore</a>(<span class="stringliteral">"main_var_xx_swath_prelim_score"</span>, xx_swath_prescore);</div>
<div class="line"><a name="l00710"></a><span class="lineno"> 710</span>  mrmfeature-><a class="code" href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">setOverallQuality</a>(xx_swath_prescore);</div>
<div class="line"><a name="l00711"></a><span class="lineno"> 711</span> <span class="preprocessor">#ifdef DEBUG_MRMPEAKPICKER</span></div>
<div class="line"><a name="l00712"></a><span class="lineno"> 712</span> <span class="preprocessor"></span> cout << <span class="stringliteral">"added xx_swath_prescore (everything above 2 is good) "</span> << xx_swath_prescore << endl;</div>
<div class="line"><a name="l00713"></a><span class="lineno"> 713</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00714"></a><span class="lineno"> 714</span> <span class="preprocessor"></span> <span class="keyword">delete</span> imrmfeature;</div>
<div class="line"><a name="l00715"></a><span class="lineno"> 715</span>  }</div>
<div class="line"><a name="l00716"></a><span class="lineno"> 716</span> </div>
<div class="line"><a name="l00717"></a><span class="lineno"> 717</span>  <span class="comment">// void handle_params();</span></div>
<div class="line"><a name="l00718"></a><span class="lineno"> 718</span> </div>
<div class="line"><a name="l00720"></a><span class="lineno"> 720</span>  <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00721"></a><span class="lineno"> 721</span> </div>
<div class="line"><a name="l00722"></a><span class="lineno"> 722</span>  <span class="comment">// Variables</span></div>
<div class="line"><a name="l00723"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a22f959483c21d84714446ca1dda67305"> 723</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a22f959483c21d84714446ca1dda67305">rt_extraction_window_</a>;</div>
<div class="line"><a name="l00724"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ab5e0c18f8afa7476f40274195da56a95"> 724</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ab5e0c18f8afa7476f40274195da56a95">quantification_cutoff_</a>;</div>
<div class="line"><a name="l00725"></a><span class="lineno"> 725</span> </div>
<div class="line"><a name="l00726"></a><span class="lineno"> 726</span>  <span class="comment">// Which scores to use</span></div>
<div class="line"><a name="l00727"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a4a1ef597bca1204743aea62db7e5854c"> 727</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a4a1ef597bca1204743aea62db7e5854c">use_coelution_score_</a>;</div>
<div class="line"><a name="l00728"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae129fad3b127a2c3b2e326957d8790f6"> 728</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae129fad3b127a2c3b2e326957d8790f6">use_shape_score_</a>;</div>
<div class="line"><a name="l00729"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a02cbed9db0f88714f00b408ce1b2cd89"> 729</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a02cbed9db0f88714f00b408ce1b2cd89">use_rt_score_</a>;</div>
<div class="line"><a name="l00730"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a9f60459941531734092771fbffbbff74"> 730</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a9f60459941531734092771fbffbbff74">use_library_score_</a>;</div>
<div class="line"><a name="l00731"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac8d7f0bcfd4cb2e7d52cab65e7df6158"> 731</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac8d7f0bcfd4cb2e7d52cab65e7df6158">use_elution_model_score_</a>;</div>
<div class="line"><a name="l00732"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a576420b6d768fd10d4346e472d5fd2aa"> 732</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a576420b6d768fd10d4346e472d5fd2aa">use_intensity_score_</a>;</div>
<div class="line"><a name="l00733"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a75a21d4281da11d37c8da3535d1d84b6"> 733</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a75a21d4281da11d37c8da3535d1d84b6">use_total_xic_score_</a>;</div>
<div class="line"><a name="l00734"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac64852f39c2bec2f316e47ae6dec9252"> 734</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac64852f39c2bec2f316e47ae6dec9252">use_nr_peaks_score_</a>;</div>
<div class="line"><a name="l00735"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#aea920562de500ac98b46bbb0e89ccdfc"> 735</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#aea920562de500ac98b46bbb0e89ccdfc">use_sn_score_</a>;</div>
<div class="line"><a name="l00736"></a><span class="lineno"> 736</span> </div>
<div class="line"><a name="l00737"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a5014ed66263ea3caf2b85109c996ebb4"> 737</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a5014ed66263ea3caf2b85109c996ebb4">stop_report_after_feature_</a>;</div>
<div class="line"><a name="l00738"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a2b03153c17ac2f3ace8b5d471a98dd53"> 738</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a2b03153c17ac2f3ace8b5d471a98dd53">add_up_spectra_</a>;</div>
<div class="line"><a name="l00739"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a22727bee734eaaa5b46b0c81d64de04f"> 739</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a22727bee734eaaa5b46b0c81d64de04f">spacing_for_spectra_resampling_</a>;</div>
<div class="line"><a name="l00740"></a><span class="lineno"> 740</span> </div>
<div class="line"><a name="l00741"></a><span class="lineno"> 741</span>  <span class="comment">// bool do_local_fdr_;</span></div>
<div class="line"><a name="l00742"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a67ca9455fcfa3f2bf40502a88ea0b776"> 742</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a67ca9455fcfa3f2bf40502a88ea0b776">write_convex_hull_</a>;</div>
<div class="line"><a name="l00743"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0ae9ca9c54d967fe064dd3b5939dabd2"> 743</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0ae9ca9c54d967fe064dd3b5939dabd2">strict_</a>;</div>
<div class="line"><a name="l00744"></a><span class="lineno"> 744</span> </div>
<div class="line"><a name="l00745"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a18149f9f24aaea0ec584e290620fbd20"> 745</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a18149f9f24aaea0ec584e290620fbd20">rt_normalization_factor_</a>;</div>
<div class="line"><a name="l00746"></a><span class="lineno"> 746</span> </div>
<div class="line"><a name="l00747"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae505eef01d0c7c8b342bac83fcd81f23"> 747</a></span>  std::map<OpenMS::String, double> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae505eef01d0c7c8b342bac83fcd81f23">PeptideRTMap_</a>;</div>
<div class="line"><a name="l00748"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a7f80a0cb2acd6063fc093e3d79aa04b0"> 748</a></span>  std::map<OpenMS::String, const PeptideType*> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a7f80a0cb2acd6063fc093e3d79aa04b0">PeptideRefMap_</a>;</div>
<div class="line"><a name="l00749"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#abfbb890cd21227a2434d240018c1e7a8"> 749</a></span>  std::map<OpenMS::String, const ProteinType*> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#abfbb890cd21227a2434d240018c1e7a8">ProteinRefMap_</a>;</div>
<div class="line"><a name="l00750"></a><span class="lineno"> 750</span> </div>
<div class="line"><a name="l00751"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac63df47f07bf98212d84b4edb37d1a86"> 751</a></span>  <a class="code" href="classOpenSwath_1_1MRMScoring.html">OpenSwath::MRMScoring</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac63df47f07bf98212d84b4edb37d1a86">mrmscore_</a>;</div>
<div class="line"><a name="l00752"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a608c6b3c9c5f225e40f35260f1f6cc9e"> 752</a></span>  <a class="code" href="classOpenMS_1_1DIAScoring.html">OpenMS::DIAScoring</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a608c6b3c9c5f225e40f35260f1f6cc9e">diascoring_</a>;</div>
<div class="line"><a name="l00753"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a40b8bcf6f0f15147e7e6e88a46e1e35f"> 753</a></span>  <a class="code" href="classOpenMS_1_1EmgScoring.html">OpenMS::EmgScoring</a> <a class="code" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a40b8bcf6f0f15147e7e6e88a46e1e35f">emgscoring_</a>;</div>
<div class="line"><a name="l00754"></a><span class="lineno"> 754</span>  };</div>
<div class="line"><a name="l00755"></a><span class="lineno"> 755</span> }</div>
<div class="line"><a name="l00756"></a><span class="lineno"> 756</span> </div>
<div class="line"><a name="l00757"></a><span class="lineno"> 757</span> <span class="preprocessor">#undef run_identifier</span></div>
<div class="line"><a name="l00758"></a><span class="lineno"> 758</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_a3f0b0d733e7992afe009dd65591e0a2e"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#a3f0b0d733e7992afe009dd65591e0a2e">OpenMS::OpenSwath_Scores::isotope_overlap</a></div><div class="ttdeci">double isotope_overlap</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_aea920562de500ac98b46bbb0e89ccdfc"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#aea920562de500ac98b46bbb0e89ccdfc">OpenMS::MRMFeatureFinderScoring::use_sn_score_</a></div><div class="ttdeci">bool use_sn_score_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:735</div></div>
<div class="ttc" id="structOpenSwath_1_1LightTransition_html_a4c4914efae99b51076cec9814268707c"><div class="ttname"><a href="structOpenSwath_1_1LightTransition.html#a4c4914efae99b51076cec9814268707c">OpenSwath::LightTransition::getPeptideRef</a></div><div class="ttdeci">std::string getPeptideRef() const </div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:66</div></div>
<div class="ttc" id="structOpenSwath_1_1LightTargetedExperiment_html_a6d58ec7403247e88dbee94e859389c19"><div class="ttname"><a href="structOpenSwath_1_1LightTargetedExperiment.html#a6d58ec7403247e88dbee94e859389c19">OpenSwath::LightTargetedExperiment::getProteins</a></div><div class="ttdeci">std::vector< LightProtein > & getProteins()</div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:135</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a93a8dc068053ec44ee7e45864ef969f7"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a></div><div class="ttdeci">const double k</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html">OpenMS::ProteinIdentification</a></div><div class="ttdoc">Representation of a protein identification run. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:61</div></div>
<div class="ttc" id="structOpenSwath_1_1LightProtein_html_afd0d68c6d31ff249f3ae8662162663c3"><div class="ttname"><a href="structOpenSwath_1_1LightProtein.html#afd0d68c6d31ff249f3ae8662162663c3">OpenSwath::LightProtein::id</a></div><div class="ttdeci">std::string id</div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:116</div></div>
<div class="ttc" id="MRMScoring_8h_html"><div class="ttname"><a href="MRMScoring_8h.html">MRMScoring.h</a></div></div>
<div class="ttc" id="EmgScoring_8h_html"><div class="ttname"><a href="EmgScoring_8h.html">EmgScoring.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_a78dbcf0489fbf0d53d650d37c74ee164"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#a78dbcf0489fbf0d53d650d37c74ee164">OpenMS::OpenSwath_Scores::isotope_correlation</a></div><div class="ttdeci">double isotope_correlation</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:91</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="structOpenSwath_1_1LightPeptide_html_a49ce0caa2ae22c1439eaf0fd861bf37f"><div class="ttname"><a href="structOpenSwath_1_1LightPeptide.html#a49ce0caa2ae22c1439eaf0fd861bf37f">OpenSwath::LightPeptide::getChargeState</a></div><div class="ttdeci">int getChargeState() const </div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:106</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html_a3599bdfacba1b03fa680b7e183dc80ce"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">OpenMS::MRMTransitionGroup::getTransitions</a></div><div class="ttdeci">const std::vector< TransitionType > & getTransitions() const </div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:122</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_1PeptideIdentification_html_a00f1456779f764c2738c35be2c04f6e8"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html#a00f1456779f764c2738c35be2c04f6e8">OpenMS::PeptideIdentification::setIdentifier</a></div><div class="ttdeci">void setIdentifier(const String &id)</div><div class="ttdoc">sets the indentifier </div></div>
<div class="ttc" id="classOpenMS_1_1PeptideHit_html_a2e9b7c12f6d8fa7415aa0aca69208f42"><div class="ttname"><a href="classOpenMS_1_1PeptideHit.html#a2e9b7c12f6d8fa7415aa0aca69208f42">OpenMS::PeptideHit::setScore</a></div><div class="ttdeci">void setScore(DoubleReal score)</div><div class="ttdoc">sets the score of the peptide hit </div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a86f5c6d7c17c3aa94ec734e2a4fb50fa"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a86f5c6d7c17c3aa94ec734e2a4fb50fa">OpenMS::ProteinIdentification::setHits</a></div><div class="ttdeci">void setHits(const std::vector< ProteinHit > &hits)</div><div class="ttdoc">Sets the protein hits. </div></div>
<div class="ttc" id="MRMFeature_8h_html"><div class="ttname"><a href="MRMFeature_8h.html">MRMFeature.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MRMTransitionGroup::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_af71c1f3e928ced2c6264ed63155d8de0"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#af71c1f3e928ced2c6264ed63155d8de0">OpenMS::MRMFeatureFinderScoring::PeptideType</a></div><div class="ttdeci">OpenSwath::LightPeptide PeptideType</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:215</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_ae129fad3b127a2c3b2e326957d8790f6"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae129fad3b127a2c3b2e326957d8790f6">OpenMS::MRMFeatureFinderScoring::use_shape_score_</a></div><div class="ttdeci">bool use_shape_score_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:728</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_acef58bf2531b77d0191c4780739281c6"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#acef58bf2531b77d0191c4780739281c6">OpenMS::FeatureMap::getProteinIdentifications</a></div><div class="ttdeci">const std::vector< ProteinIdentification > & getProteinIdentifications() const </div><div class="ttdoc">non-mutable access to the protein identifications </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:410</div></div>
<div class="ttc" id="classOpenSwath_1_1MRMScoring_html"><div class="ttname"><a href="classOpenSwath_1_1MRMScoring.html">OpenSwath::MRMScoring</a></div><div class="ttdoc">This class implements different scores for peaks found in SRM/MRM. </div><div class="ttdef"><b>Definition:</b> MRMScoring.h:75</div></div>
<div class="ttc" id="classPeakT_html"><div class="ttname"><a href="classPeakT.html">PeakT</a></div></div>
<div class="ttc" id="SimpleOpenMSSpectraAccessFactory_8h_html"><div class="ttname"><a href="SimpleOpenMSSpectraAccessFactory_8h.html">SimpleOpenMSSpectraAccessFactory.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ProteinHit_html_a2b8bf5f3febdb76461bdea9ff39d6b6d"><div class="ttname"><a href="classOpenMS_1_1ProteinHit.html#a2b8bf5f3febdb76461bdea9ff39d6b6d">OpenMS::ProteinHit::setSequence</a></div><div class="ttdeci">void setSequence(const String &sequence)</div><div class="ttdoc">sets the protein sequence </div></div>
<div class="ttc" id="Scoring_8h_html"><div class="ttname"><a href="Scoring_8h.html">Scoring.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html">OpenMS::EmgScoring</a></div><div class="ttdoc">Scoring of an elution peak using an exponentially modified gaussian distribution model. </div><div class="ttdef"><b>Definition:</b> EmgScoring.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a0f6b08b724983b516b2529790b798a9f"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0f6b08b724983b516b2529790b798a9f">OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType</a></div><div class="ttdeci">MRMTransitionGroup< MSSpectrum< ChromatogramPeak >, TransitionType > MRMTransitionGroupType</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:218</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a608c6b3c9c5f225e40f35260f1f6cc9e"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a608c6b3c9c5f225e40f35260f1f6cc9e">OpenMS::MRMFeatureFinderScoring::diascoring_</a></div><div class="ttdeci">OpenMS::DIAScoring diascoring_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:752</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a392c2beaccf8b9d8e6f5d3e766f1bc72"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a392c2beaccf8b9d8e6f5d3e766f1bc72">OpenMS::MRMFeatureFinderScoring::getAddedSpectra_</a></div><div class="ttdeci">OpenSwath::SpectrumPtr getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add)</div><div class="ttdoc">Returns the addition of &quot;nr_spectra_to_add&quot; spectra around the given RT. </div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:611</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_ac63df47f07bf98212d84b4edb37d1a86"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac63df47f07bf98212d84b4edb37d1a86">OpenMS::MRMFeatureFinderScoring::mrmscore_</a></div><div class="ttdeci">OpenSwath::MRMScoring mrmscore_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:751</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html_a84fbe2b625d0885f5e93397ed2122202"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">OpenMS::MRMTransitionGroup::getChromatograms</a></div><div class="ttdeci">const std::vector< SpectrumType > & getChromatograms() const </div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap</a></div><div class="ttdoc">A container for features. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a8497becf96cdfaf51ba301262d81f126"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a8497becf96cdfaf51ba301262d81f126">OpenMS::MRMFeatureFinderScoring::TransitionType</a></div><div class="ttdeci">OpenSwath::LightTransition TransitionType</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:213</div></div>
<div class="ttc" id="classOpenMS_1_1OpenSwathDataAccessHelper_html_a8ae154a5964d69f913d864b169b7310e"><div class="ttname"><a href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a8ae154a5964d69f913d864b169b7310e">OpenMS::OpenSwathDataAccessHelper::convertPeptideToAASequence</a></div><div class="ttdeci">static void convertPeptideToAASequence(const OpenSwath::LightPeptide &peptide, AASequence &aa_sequence)</div><div class="ttdoc">convert from the LightPeptide to an OpenMS AASequence (with correct modifications) ...</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_ae505eef01d0c7c8b342bac83fcd81f23"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae505eef01d0c7c8b342bac83fcd81f23">OpenMS::MRMFeatureFinderScoring::PeptideRTMap_</a></div><div class="ttdeci">std::map< OpenMS::String, double > PeptideRTMap_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:747</div></div>
<div class="ttc" id="TransitionExperiment_8h_html"><div class="ttname"><a href="TransitionExperiment_8h.html">TransitionExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TransitionGroupOpenMS_html"><div class="ttname"><a href="classOpenMS_1_1TransitionGroupOpenMS.html">OpenMS::TransitionGroupOpenMS</a></div><div class="ttdoc">An implementation of the OpenSWATH Transition Group Access interface using OpenMS. </div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:109</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html">OpenMS::MRMFeatureFinderScoring</a></div><div class="ttdoc">The MRMFeatureFinder finds and scores peaks of transitions that coelute. </div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:200</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a67ca9455fcfa3f2bf40502a88ea0b776"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a67ca9455fcfa3f2bf40502a88ea0b776">OpenMS::MRMFeatureFinderScoring::write_convex_hull_</a></div><div class="ttdeci">bool write_convex_hull_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:742</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a2b03153c17ac2f3ace8b5d471a98dd53"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a2b03153c17ac2f3ace8b5d471a98dd53">OpenMS::MRMFeatureFinderScoring::add_up_spectra_</a></div><div class="ttdeci">int add_up_spectra_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:738</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_adc7399590e54bd7f438d16a0372803e7"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7">OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType</a></div><div class="ttdeci">std::map< String, MRMTransitionGroupType > TransitionGroupMapType</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:219</div></div>
<div class="ttc" id="MRMFeatureFinderScoring_8h_html_a1f18f099a1e85e5ad0256530ab97cd3a"><div class="ttname"><a href="MRMFeatureFinderScoring_8h.html#a1f18f099a1e85e5ad0256530ab97cd3a">run_identifier</a></div><div class="ttdeci">#define run_identifier</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:38</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_1MRMTransitionGroup_html_aff73c863c0c2c6ff6173deac72567709"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#aff73c863c0c2c6ff6173deac72567709">OpenMS::MRMTransitionGroup::getLibraryIntensity</a></div><div class="ttdeci">void getLibraryIntensity(std::vector< double > &result) const </div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:189</div></div>
<div class="ttc" id="classOpenMS_1_1AASequence_html"><div class="ttname"><a href="classOpenMS_1_1AASequence.html">OpenMS::AASequence</a></div><div class="ttdoc">Representation of a peptide/protein sequence. </div><div class="ttdef"><b>Definition:</b> AASequence.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a076172c5ec2a42850e27a7de01b2b910"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a076172c5ec2a42850e27a7de01b2b910">OpenMS::Feature::OverallQualityLess</a></div><div class="ttdeci">QualityLess OverallQualityLess</div><div class="ttdoc">Compare by quality. </div><div class="ttdef"><b>Definition:</b> Feature.h:97</div></div>
<div class="ttc" id="structOpenSwath_1_1LightPeptide_html_a85ef381b973761bfb8afbe31ba8c010f"><div class="ttname"><a href="structOpenSwath_1_1LightPeptide.html#a85ef381b973761bfb8afbe31ba8c010f">OpenSwath::LightPeptide::protein_ref</a></div><div class="ttdeci">std::string protein_ref</div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:104</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab4e0f356f837ce58e57695da114adce3"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">OpenMS::Peak2D::getRT</a></div><div class="ttdeci">CoordinateType getRT() const </div><div class="ttdoc">Returns the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:203</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_abc8067511cfc949ae942ea2b08588f81"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">OpenMS::DefaultParamHandler::setParameters</a></div><div class="ttdeci">void setParameters(const Param &param)</div><div class="ttdoc">Sets the parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a40b8bcf6f0f15147e7e6e88a46e1e35f"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a40b8bcf6f0f15147e7e6e88a46e1e35f">OpenMS::MRMFeatureFinderScoring::emgscoring_</a></div><div class="ttdeci">OpenMS::EmgScoring emgscoring_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:753</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a546b9a9117f4207e3cfc9ef2ea4aad3d"><div class="ttname"><a href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">OpenSwath::normalize</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)</div><div class="ttdoc">Normalize intensities in vector by normalization_factor. </div></div>
<div class="ttc" id="structOpenSwath_1_1ITransitionGroup_html"><div class="ttname"><a href="structOpenSwath_1_1ITransitionGroup.html">OpenSwath::ITransitionGroup</a></div><div class="ttdef"><b>Definition:</b> ITransition.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_ac64852f39c2bec2f316e47ae6dec9252"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac64852f39c2bec2f316e47ae6dec9252">OpenMS::MRMFeatureFinderScoring::use_nr_peaks_score_</a></div><div class="ttdeci">bool use_nr_peaks_score_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:734</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html">OpenMS::MRMTransitionGroup</a></div><div class="ttdoc">The representation of a transition group that has information about the individual chromatograms as w...</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a5014ed66263ea3caf2b85109c996ebb4"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a5014ed66263ea3caf2b85109c996ebb4">OpenMS::MRMFeatureFinderScoring::stop_report_after_feature_</a></div><div class="ttdeci">int stop_report_after_feature_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:737</div></div>
<div class="ttc" id="namespaceOpenSwath_1_1Scoring_html_afa39e794c622d1fdfc2d702517fffc80"><div class="ttname"><a href="namespaceOpenSwath_1_1Scoring.html#afa39e794c622d1fdfc2d702517fffc80">OpenSwath::Scoring::normalize_sum</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI void normalize_sum(double x[], unsigned int n)</div><div class="ttdoc">divide each element of x by the sum of the vector </div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a1e9fb94f05f21667db64366fe31b4357"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1e9fb94f05f21667db64366fe31b4357">OpenMS::MRMFeatureFinderScoring::ProteinType</a></div><div class="ttdeci">OpenSwath::LightProtein ProteinType</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:216</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_aba3edbdb6d99fdd71b262d1e938b4e89"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#aba3edbdb6d99fdd71b262d1e938b4e89">OpenMS::OpenSwath_Scores::library_rmsd</a></div><div class="ttdeci">double library_rmsd</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:89</div></div>
<div class="ttc" id="MSSpectrum_8h_html"><div class="ttname"><a href="MSSpectrum_8h.html">MSSpectrum.h</a></div></div>
<div class="ttc" id="structOpenSwath_1_1LightPeptide_html"><div class="ttname"><a href="structOpenSwath_1_1LightPeptide.html">OpenSwath::LightPeptide</a></div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:99</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a1d7f11c2be93f8140f508487ba0ae718"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1d7f11c2be93f8140f508487ba0ae718">OpenMS::MRMFeatureFinderScoring::scorePeakgroups_</a></div><div class="ttdeci">void scorePeakgroups_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, TransformationDescription &trafo, OpenSwath::SpectrumAccessPtr swath_map, FeatureMap< Feature > &output)</div><div class="ttdoc">Score all peak groups. </div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:334</div></div>
<div class="ttc" id="structOpenSwath_1_1LightProtein_html_a9a2b94a2b0e3195ef7ea3a13187c17b9"><div class="ttname"><a href="structOpenSwath_1_1LightProtein.html#a9a2b94a2b0e3195ef7ea3a13187c17b9">OpenSwath::LightProtein::sequence</a></div><div class="ttdeci">std::string sequence</div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum</a></div><div class="ttdoc">The representation of a 1D spectrum. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1IllegalArgument_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1IllegalArgument.html">OpenMS::Exception::IllegalArgument</a></div><div class="ttdoc">A method or algorithm argument contains illegal values. </div><div class="ttdef"><b>Definition:</b> Exception.h:634</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a63af68177a01f914ee1944977ba796ee"><div class="ttname"><a href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr</div><div class="ttdef"><b>Definition:</b> ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:73</div></div>
<div class="ttc" id="structOpenSwath_1_1LightTargetedExperiment_html_a23a85c8da00a9f39f0c9ce6e15bc5a32"><div class="ttname"><a href="structOpenSwath_1_1LightTargetedExperiment.html#a23a85c8da00a9f39f0c9ce6e15bc5a32">OpenSwath::LightTargetedExperiment::getTransitions</a></div><div class="ttdeci">std::vector< LightTransition > & getTransitions()</div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:125</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a22727bee734eaaa5b46b0c81d64de04f"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a22727bee734eaaa5b46b0c81d64de04f">OpenMS::MRMFeatureFinderScoring::spacing_for_spectra_resampling_</a></div><div class="ttdeci">DoubleReal spacing_for_spectra_resampling_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:739</div></div>
<div class="ttc" id="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2DataStructures_8h_html"><div class="ttname"><a href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2DataStructures_8h.html">DataStructures.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PeptideHit_html_aca40a4630f5f8a0568899b74a62dcd4b"><div class="ttname"><a href="classOpenMS_1_1PeptideHit.html#aca40a4630f5f8a0568899b74a62dcd4b">OpenMS::PeptideHit::setCharge</a></div><div class="ttdeci">void setCharge(Int charge)</div><div class="ttdoc">sets the charge of the peptide </div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html">OpenMS::MRMTransitionGroupPicker</a></div><div class="ttdoc">The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors...</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_ab5e0c18f8afa7476f40274195da56a95"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#ab5e0c18f8afa7476f40274195da56a95">OpenMS::MRMFeatureFinderScoring::quantification_cutoff_</a></div><div class="ttdeci">DoubleReal quantification_cutoff_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:724</div></div>
<div class="ttc" id="DIAScoring_8h_html"><div class="ttname"><a href="DIAScoring_8h.html">DIAScoring.h</a></div></div>
<div class="ttc" id="namespaceOpenSwath_html_a93e7d6a13eb66ccae0357dbae6f33523"><div class="ttname"><a href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< Spectrum > SpectrumPtr</div><div class="ttdef"><b>Definition:</b> ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:227</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideHit_html"><div class="ttname"><a href="classOpenMS_1_1PeptideHit.html">OpenMS::PeptideHit</a></div><div class="ttdoc">Representation of a peptide hit. </div><div class="ttdef"><b>Definition:</b> PeptideHit.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1SimpleOpenMSSpectraFactory_html_a645eefe3725b60ffcf44f9ae01f0c19d"><div class="ttname"><a href="classOpenMS_1_1SimpleOpenMSSpectraFactory.html#a645eefe3725b60ffcf44f9ae01f0c19d">OpenMS::SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr</a></div><div class="ttdeci">static OpenSwath::SpectrumAccessPtr getSpectrumAccessOpenMSPtr(OpenMS::MSExperiment< OpenMS::Peak1D > &exp)</div><div class="ttdoc">Simple Factory method to get a SpectrumAccess Ptr from an MSExperiment. </div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_a3626f9b563a3d7134f3849e62579c03b"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#a3626f9b563a3d7134f3849e62579c03b">OpenMS::OpenSwath_Scores::log_sn_score</a></div><div class="ttdeci">double log_sn_score</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:97</div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseOpenMS_html"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseOpenMS.html">OpenMS::SignalToNoiseOpenMS</a></div><div class="ttdoc">An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS. </div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:152</div></div>
<div class="ttc" id="classOpenMS_1_1DIAScoring_html"><div class="ttname"><a href="classOpenMS_1_1DIAScoring.html">OpenMS::DIAScoring</a></div><div class="ttdoc">Scoring of an spectrum at the peak apex of an chromatographic elution peak. </div><div class="ttdef"><b>Definition:</b> DIAScoring.h:76</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_ad86382490f14d6cc1b62611513b5e27f"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#ad86382490f14d6cc1b62611513b5e27f">OpenMS::OpenSwath_Scores::massdev_score</a></div><div class="ttdeci">double massdev_score</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a4a1ef597bca1204743aea62db7e5854c"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a4a1ef597bca1204743aea62db7e5854c">OpenMS::MRMFeatureFinderScoring::use_coelution_score_</a></div><div class="ttdeci">bool use_coelution_score_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:727</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a18149f9f24aaea0ec584e290620fbd20"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a18149f9f24aaea0ec584e290620fbd20">OpenMS::MRMFeatureFinderScoring::rt_normalization_factor_</a></div><div class="ttdeci">DoubleReal rt_normalization_factor_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:745</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_aeb40871b8728dab160318bc38fc23e3a"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#aeb40871b8728dab160318bc38fc23e3a">OpenMS::OpenSwath_Scores::get_quick_lda_score</a></div><div class="ttdeci">double get_quick_lda_score(double library_corr, double library_rmsd, double norm_rt_score, double xcorr_coelution_score, double xcorr_shape_score, double log_sn_score)</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:99</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_ad17f08a1a1d14810389bf7f585e95e8b"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#ad17f08a1a1d14810389bf7f585e95e8b">OpenMS::OpenSwath_Scores::yseries_score</a></div><div class="ttdeci">double yseries_score</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:96</div></div>
<div class="ttc" id="MRMTransitionGroup_8h_html"><div class="ttname"><a href="MRMTransitionGroup_8h.html">MRMTransitionGroup.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a7f80a0cb2acd6063fc093e3d79aa04b0"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a7f80a0cb2acd6063fc093e3d79aa04b0">OpenMS::MRMFeatureFinderScoring::PeptideRefMap_</a></div><div class="ttdeci">std::map< OpenMS::String, const PeptideType * > PeptideRefMap_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:748</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html_a5c92d3ef5e22a80e2188a8fd81af3e5a"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#a5c92d3ef5e22a80e2188a8fd81af3e5a">OpenMS::MRMTransitionGroup::getFeaturesMuteable</a></div><div class="ttdeci">std::vector< MRMFeature > & getFeaturesMuteable()</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:179</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a9ac530b577855511cc32791aef8de7e4"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a9ac530b577855511cc32791aef8de7e4">OpenMS::MRMFeatureFinderScoring::setStrictFlag</a></div><div class="ttdeci">void setStrictFlag(bool f)</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:325</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a02cbed9db0f88714f00b408ce1b2cd89"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a02cbed9db0f88714f00b408ce1b2cd89">OpenMS::MRMFeatureFinderScoring::use_rt_score_</a></div><div class="ttdeci">bool use_rt_score_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:729</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationDescription_html_aa280f8d4730c216c58a3edd091b99767"><div class="ttname"><a href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">OpenMS::TransformationDescription::apply</a></div><div class="ttdeci">DoubleReal apply(DoubleReal value) const </div><div class="ttdoc">Applies the transformation to value. </div></div>
<div class="ttc" id="MRMTransitionGroupPicker_8h_html"><div class="ttname"><a href="MRMTransitionGroupPicker_8h.html">MRMTransitionGroupPicker.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1OpenSwathDataAccessHelper_html_a0476f3ea925f584d9064efee48c7db6a"><div class="ttname"><a href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a0476f3ea925f584d9064efee48c7db6a">OpenMS::OpenSwathDataAccessHelper::convertTargetedExp</a></div><div class="ttdeci">static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)</div><div class="ttdoc">convert from the OpenMS Targeted experiment to the light Targeted Experiment </div></div>
<div class="ttc" id="structOpenSwath_1_1LightPeptide_html_afd0d68c6d31ff249f3ae8662162663c3"><div class="ttname"><a href="structOpenSwath_1_1LightPeptide.html#afd0d68c6d31ff249f3ae8662162663c3">OpenSwath::LightPeptide::id</a></div><div class="ttdeci">std::string id</div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:105</div></div>
<div class="ttc" id="SignalToNoiseEstimatorMedian_8h_html"><div class="ttname"><a href="SignalToNoiseEstimatorMedian_8h.html">SignalToNoiseEstimatorMedian.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a7aa7123edb723725ec69f259c69d46d0"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a7aa7123edb723725ec69f259c69d46d0">OpenMS::MRMFeatureFinderScoring::calculateSwathScores_</a></div><div class="ttdeci">void calculateSwathScores_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, MRMFeature &mrmfeature_, OpenSwath::SpectrumAccessPtr swath_map, std::vector< double > &normalized_library_intensity, OpenSwath_Scores scores)</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:643</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_ab8dfbfc3eaa57313e0e5481894017995"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#ab8dfbfc3eaa57313e0e5481894017995">OpenMS::OpenSwath_Scores::xcorr_coelution_score</a></div><div class="ttdeci">double xcorr_coelution_score</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideHit_html_a209d1e10f38a766c3f73c9666e89e14d"><div class="ttname"><a href="classOpenMS_1_1PeptideHit.html#a209d1e10f38a766c3f73c9666e89e14d">OpenMS::PeptideHit::setSequence</a></div><div class="ttdeci">void setSequence(const AASequence &sequence)</div><div class="ttdoc">sets the peptide sequence </div></div>
<div class="ttc" id="classOpenMS_1_1ProteinHit_html_aba1fff7a176ff80d53f932769e606980"><div class="ttname"><a href="classOpenMS_1_1ProteinHit.html#aba1fff7a176ff80d53f932769e606980">OpenMS::ProteinHit::setAccession</a></div><div class="ttdeci">void setAccession(const String &accession)</div><div class="ttdoc">sets the accession of the protein </div></div>
<div class="ttc" id="classOpenMS_1_1ProteinHit_html"><div class="ttname"><a href="classOpenMS_1_1ProteinHit.html">OpenMS::ProteinHit</a></div><div class="ttdoc">Representation of a protein hit. </div><div class="ttdef"><b>Definition:</b> ProteinHit.h:54</div></div>
<div class="ttc" id="structOpenSwath_1_1LightTransition_html"><div class="ttname"><a href="structOpenSwath_1_1LightTransition.html">OpenSwath::LightTransition</a></div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:46</div></div>
<div class="ttc" id="structOpenSwath_1_1LightTargetedExperiment_html_a75e5e77ae24708d28d8f3df92fcb84de"><div class="ttname"><a href="structOpenSwath_1_1LightTargetedExperiment.html#a75e5e77ae24708d28d8f3df92fcb84de">OpenSwath::LightTargetedExperiment::getPeptides</a></div><div class="ttdeci">std::vector< LightPeptide > & getPeptides()</div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:130</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment< Peak1D ></a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a22f959483c21d84714446ca1dda67305"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a22f959483c21d84714446ca1dda67305">OpenMS::MRMFeatureFinderScoring::rt_extraction_window_</a></div><div class="ttdeci">DoubleReal rt_extraction_window_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:723</div></div>
<div class="ttc" id="classOpenSwath_1_1IMRMFeature_html"><div class="ttname"><a href="classOpenSwath_1_1IMRMFeature.html">OpenSwath::IMRMFeature</a></div><div class="ttdef"><b>Definition:</b> ITransition.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_abfbb890cd21227a2434d240018c1e7a8"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#abfbb890cd21227a2434d240018c1e7a8">OpenMS::MRMFeatureFinderScoring::ProteinRefMap_</a></div><div class="ttdeci">std::map< OpenMS::String, const ProteinType * > ProteinRefMap_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:749</div></div>
<div class="ttc" id="MRMFeatureAccessOpenMS_8h_html"><div class="ttname"><a href="MRMFeatureAccessOpenMS_8h.html">MRMFeatureAccessOpenMS.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_af879ba2bc9bcc83bed021af39c24e9d6"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#af879ba2bc9bcc83bed021af39c24e9d6">OpenMS::MRMFeatureFinderScoring::pickExperiment</a></div><div class="ttdeci">void pickExperiment(MSExperiment< Peak1D > &chromatograms, FeatureMap< Feature > &output, TargetedExperiment &transition_exp_, TransformationDescription trafo, MSExperiment< Peak1D > &swath_map)</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:231</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_aeba0cded976431f70fbea5499218ce18"><div class="ttname"><a href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">OpenMS::Feature::setOverallQuality</a></div><div class="ttdeci">void setOverallQuality(QualityType q)</div><div class="ttdoc">Set the overall quality. </div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html">OpenMS::OpenSwath_Scores</a></div><div class="ttdoc">A structure to hold the different scores computed by the FeatureFinder. </div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:85</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_ab93154c1962d6ccb0a7d8f548ea0a9da"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#ab93154c1962d6ccb0a7d8f548ea0a9da">OpenMS::MRMFeatureFinderScoring::TargetedExpType</a></div><div class="ttdeci">OpenSwath::LightTargetedExperiment TargetedExpType</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:214</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a576420b6d768fd10d4346e472d5fd2aa"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a576420b6d768fd10d4346e472d5fd2aa">OpenMS::MRMFeatureFinderScoring::use_intensity_score_</a></div><div class="ttdeci">bool use_intensity_score_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:732</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeature_html_a8d4bb3e3b2f22cdaa1855d09f5d98a41"><div class="ttname"><a href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">OpenMS::MRMFeature::addScore</a></div><div class="ttdeci">void addScore(const String &score_name, double score)</div><div class="ttdoc">set a single peakgroup score </div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_aa050ad09c86fd7f50842c59d49e6fea7"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#aa050ad09c86fd7f50842c59d49e6fea7">OpenMS::OpenSwath_Scores::xcorr_shape_score</a></div><div class="ttdeci">double xcorr_shape_score</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_acce2a9f0fe8d27893f6a027a4598e8ba"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#acce2a9f0fe8d27893f6a027a4598e8ba">OpenMS::MRMTransitionGroupPicker::pickTransitionGroup</a></div><div class="ttdeci">void pickTransitionGroup(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group)</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:202</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_a6509c5d12cc9ba3417f9d46314345bc9"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#a6509c5d12cc9ba3417f9d46314345bc9">OpenMS::OpenSwath_Scores::calculate_swath_lda_prescore</a></div><div class="ttdeci">double calculate_swath_lda_prescore(OpenSwath_Scores scores)</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a></div><div class="ttdoc">This class stores an prediction of an SRM/MRM transition. </div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:53</div></div>
<div class="ttc" id="MRMFeatureFinderScoring_8h_html_ac179205eda67e461049ab7112f3de1e9"><div class="ttname"><a href="MRMFeatureFinderScoring_8h.html#ac179205eda67e461049ab7112f3de1e9">SortDoubleDoublePairFirst</a></div><div class="ttdeci">bool SortDoubleDoublePairFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_a2d04130c2720f68f9dd1b541b0e5eaba"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#a2d04130c2720f68f9dd1b541b0e5eaba">OpenMS::OpenSwath_Scores::norm_rt_score</a></div><div class="ttdeci">double norm_rt_score</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:90</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a657df1b62b2200d972968d1151992d7f"><div class="ttname"><a href="namespaceOpenSwath.html#a657df1b62b2200d972968d1151992d7f">OpenSwath::ISignalToNoisePtr</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< ISignalToNoise > ISignalToNoisePtr</div><div class="ttdef"><b>Definition:</b> ITransition.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_ae3c1ad9ec2bbfe5e9e7bac70731091fb"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae3c1ad9ec2bbfe5e9e7bac70731091fb">OpenMS::MRMFeatureFinderScoring::ModificationType</a></div><div class="ttdeci">OpenSwath::LightModification ModificationType</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:217</div></div>
<div class="ttc" id="MSChromatogram_8h_html"><div class="ttname"><a href="MSChromatogram_8h.html">MSChromatogram.h</a></div></div>
<div class="ttc" id="SpectrumAddition_8h_html"><div class="ttname"><a href="SpectrumAddition_8h.html">SpectrumAddition.h</a></div></div>
<div class="ttc" id="TraMLFile_8h_html"><div class="ttname"><a href="TraMLFile_8h.html">TraMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TransformationDescription_html"><div class="ttname"><a href="classOpenMS_1_1TransformationDescription.html">OpenMS::TransformationDescription</a></div><div class="ttdoc">Generic description of a coordinate transformation. </div><div class="ttdef"><b>Definition:</b> TransformationDescription.h:59</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="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h_html"><div class="ttname"><a href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h.html">ISpectrumAccess.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html_ae558057222f754e972e0257de2fe3c2d"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html#ae558057222f754e972e0257de2fe3c2d">OpenMS::PeptideIdentification::insertHit</a></div><div class="ttdeci">void insertHit(const PeptideHit &hit)</div><div class="ttdoc">Appends a peptide hit. </div></div>
<div class="ttc" id="structOpenSwath_1_1LightPeptide_html_ae5ee906bf451a6150d80754f4068dc58"><div class="ttname"><a href="structOpenSwath_1_1LightPeptide.html#ae5ee906bf451a6150d80754f4068dc58">OpenSwath::LightPeptide::rt</a></div><div class="ttdeci">double rt</div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:101</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_ac7a01742e0b867bc9ab9d91829d0d890"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#ac7a01742e0b867bc9ab9d91829d0d890">OpenMS::OpenSwath_Scores::elution_model_fit_score</a></div><div class="ttdeci">double elution_model_fit_score</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:87</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a75a21d4281da11d37c8da3535d1d84b6"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a75a21d4281da11d37c8da3535d1d84b6">OpenMS::MRMFeatureFinderScoring::use_total_xic_score_</a></div><div class="ttdeci">bool use_total_xic_score_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:733</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideHit_html_a49d90d2fa65c45386e5725386d7741fe"><div class="ttname"><a href="classOpenMS_1_1PeptideHit.html#a49d90d2fa65c45386e5725386d7741fe">OpenMS::PeptideHit::addProteinAccession</a></div><div class="ttdeci">void addProteinAccession(const String &accession)</div><div class="ttdoc">adds an accession of a protein which contains this peptide hit </div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeature_html"><div class="ttname"><a href="classOpenMS_1_1MRMFeature.html">OpenMS::MRMFeature</a></div><div class="ttdoc">A multi-chromatogram MRM feature. </div><div class="ttdef"><b>Definition:</b> MRMFeature.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_ac8d7f0bcfd4cb2e7d52cab65e7df6158"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac8d7f0bcfd4cb2e7d52cab65e7df6158">OpenMS::MRMFeatureFinderScoring::use_elution_model_score_</a></div><div class="ttdeci">bool use_elution_model_score_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:731</div></div>
<div class="ttc" id="TransformationXMLFile_8h_html"><div class="ttname"><a href="TransformationXMLFile_8h.html">TransformationXMLFile.h</a></div></div>
<div class="ttc" id="structOpenSwath_1_1LightProtein_html"><div class="ttname"><a href="structOpenSwath_1_1LightProtein.html">OpenSwath::LightProtein</a></div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:114</div></div>
<div class="ttc" id="structOpenSwath_1_1LightTargetedExperiment_html"><div class="ttname"><a href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a></div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html_aedcd02941cf31e259bb9394850653bbc"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#aedcd02941cf31e259bb9394850653bbc">OpenMS::MRMTransitionGroup::getTransitionGroupID</a></div><div class="ttdeci">const String & getTransitionGroupID() const </div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:112</div></div>
<div class="ttc" id="MzMLFile_8h_html"><div class="ttname"><a href="MzMLFile_8h.html">MzMLFile.h</a></div></div>
<div class="ttc" id="structOpenSwath_1_1LightPeptide_html_a9a2b94a2b0e3195ef7ea3a13187c17b9"><div class="ttname"><a href="structOpenSwath_1_1LightPeptide.html#a9a2b94a2b0e3195ef7ea3a13187c17b9">OpenSwath::LightPeptide::sequence</a></div><div class="ttdeci">std::string sequence</div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:103</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_a4d7c492ccfc19c4162d9616011a060da"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#a4d7c492ccfc19c4162d9616011a060da">OpenMS::OpenSwath_Scores::library_corr</a></div><div class="ttdeci">double library_corr</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a4910016b262f6723b82c4b1c4d6cdde7"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a4910016b262f6723b82c4b1c4d6cdde7">OpenMS::MRMFeatureFinderScoring::RichPeakChromatogram</a></div><div class="ttdeci">MSSpectrum< ChromatogramPeak > RichPeakChromatogram</div><div class="ttdoc">Type definitions. </div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:212</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html_a72f3eb6e4f2beacf59fb94d10fffd9ba"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#a72f3eb6e4f2beacf59fb94d10fffd9ba">OpenMS::MRMTransitionGroup::getTransition</a></div><div class="ttdeci">const TransitionType & getTransition(String key)</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:138</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationDescription_html_a7fa1616cc61c19a5efcc863c950f7f30"><div class="ttname"><a href="classOpenMS_1_1TransformationDescription.html#a7fa1616cc61c19a5efcc863c950f7f30">OpenMS::TransformationDescription::invert</a></div><div class="ttdeci">void invert()</div><div class="ttdoc">Computes an (approximate) inverse of the transformation. </div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a21e38df433d05118f343c33af60816e9"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a21e38df433d05118f343c33af60816e9">OpenMS::MRMFeatureFinderScoring::pickExperiment</a></div><div class="ttdeci">void pickExperiment(OpenSwath::SpectrumAccessPtr input, FeatureMap< Feature > &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType &transition_group_map)</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:245</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumAddition_html_a66af26742cdb048bacaed720d147f7fb"><div class="ttname"><a href="classOpenMS_1_1SpectrumAddition.html#a66af26742cdb048bacaed720d147f7fb">OpenMS::SpectrumAddition::addUpSpectra</a></div><div class="ttdeci">static OpenSwath::SpectrumPtr addUpSpectra(std::vector< OpenSwath::SpectrumPtr > all_spectra, double sampling_rate, double filter_zeros)</div><div class="ttdoc">adds up a list of Spectra by resampling them and then addition of intensities </div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a00f1456779f764c2738c35be2c04f6e8"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a00f1456779f764c2738c35be2c04f6e8">OpenMS::ProteinIdentification::setIdentifier</a></div><div class="ttdeci">void setIdentifier(const String &id)</div><div class="ttdoc">Sets the identifier. </div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html">OpenMS::PeptideIdentification</a></div><div class="ttdoc">Represents the peptide hits for a spectrum. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:63</div></div>
<div class="ttc" id="structOpenMS_1_1OpenSwath__Scores_html_aca437d1a16d43a1e055a4fc295a2aa1e"><div class="ttname"><a href="structOpenMS_1_1OpenSwath__Scores.html#aca437d1a16d43a1e055a4fc295a2aa1e">OpenMS::OpenSwath_Scores::calculate_lda_prescore</a></div><div class="ttdeci">double calculate_lda_prescore(OpenSwath_Scores scores)</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:122</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureFinderScoring_html_a9f60459941531734092771fbffbbff74"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a9f60459941531734092771fbffbbff74">OpenMS::MRMFeatureFinderScoring::use_library_score_</a></div><div class="ttdeci">bool use_library_score_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:730</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_1MRMFeatureFinderScoring_html_a0ae9ca9c54d967fe064dd3b5939dabd2"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0ae9ca9c54d967fe064dd3b5939dabd2">OpenMS::MRMFeatureFinderScoring::strict_</a></div><div class="ttdeci">bool strict_</div><div class="ttdef"><b>Definition:</b> MRMFeatureFinderScoring.h:743</div></div>
<div class="ttc" id="structOpenSwath_1_1LightModification_html"><div class="ttname"><a href="structOpenSwath_1_1LightModification.html">OpenSwath::LightModification</a></div><div class="ttdef"><b>Definition:</b> TransitionExperiment.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureOpenMS_html"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureOpenMS.html">OpenMS::MRMFeatureOpenMS</a></div><div class="ttdoc">An implementation of the OpenSWATH MRM Feature Access interface using OpenMS. </div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:84</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:17 using doxygen 1.8.5</font></TD>
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