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<a href="MRMTransitionGroupPicker_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_MRMTRANSITIONGROUPPICKER_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_MRMTRANSITIONGROUPPICKER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="MRMTransitionGroup_8h.html">OpenMS/KERNEL/MRMTransitionGroup.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="MRMFeature_8h.html">OpenMS/KERNEL/MRMFeature.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="MSSpectrum_8h.html">OpenMS/KERNEL/MSSpectrum.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="MSChromatogram_8h.html">OpenMS/KERNEL/MSChromatogram.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="ChromatogramPeak_8h.html">OpenMS/KERNEL/ChromatogramPeak.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</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="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="SavitzkyGolayFilter_8h.html">OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h</a>></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <<a class="code" href="GaussFilter_8h.html">OpenMS/FILTERING/SMOOTHING/GaussFilter.h</a>></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <<a class="code" href="LinearResampler_8h.html">OpenMS/FILTERING/TRANSFORMERS/LinearResampler.h</a>></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <<a class="code" href="LinearResamplerAlign_8h.html">OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h</a>></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#include <<a class="code" href="PeakPickerHiRes_8h.html">OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h</a>></span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="comment">//#define DEBUG_TRANSITIONGROUPPICKER</span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> {</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html"> 76</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html">MRMTransitionGroupPicker</a> :</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  {</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> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="comment">// this is the type in which we store the chromatograms for this analysis</span></div>
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a4910016b262f6723b82c4b1c4d6cdde7"> 83</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<ChromatogramPeak></a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a4910016b262f6723b82c4b1c4d6cdde7">RichPeakChromatogram</a>; </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a415ee0df10ca0e1baf2ca18897c56463"> 86</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a415ee0df10ca0e1baf2ca18897c56463">sgolay_frame_length_</a>;</div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#acd8ce7700143488fdc293038f4636501"> 87</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#acd8ce7700143488fdc293038f4636501">sgolay_polynomial_order_</a>;</div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a6f89e0fa6d66ca2eef569f155a6eab15"> 88</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a6f89e0fa6d66ca2eef569f155a6eab15">gauss_width_</a>;</div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a6114587cf1dac7812059d2ae1b380808"> 89</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a6114587cf1dac7812059d2ae1b380808">use_gauss_</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> </div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a417a0fdec8dd7dfd838f0505a6aeec0b"> 91</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a417a0fdec8dd7dfd838f0505a6aeec0b">background_subtraction_</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a5e938e031680cf43ee3b1547ab6d1b1b"> 93</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a5e938e031680cf43ee3b1547ab6d1b1b">peak_width_</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#af9f4408f7c0f04e170ae1b4ba0571652"> 94</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#af9f4408f7c0f04e170ae1b4ba0571652">signal_to_noise_</a>;</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#aefa4cb42918dba37edfb78209ce2b512"> 96</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#aefa4cb42918dba37edfb78209ce2b512">sn_win_len_</a>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#ad0001b2cab5c5b4749188a5a1cffb2c0"> 97</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#ad0001b2cab5c5b4749188a5a1cffb2c0">sn_bin_count_</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="classOpenMS_1_1MRMTransitionGroupPicker.html#a813dbc0d8c14384b69c3bd1a658cac07"> 99</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a813dbc0d8c14384b69c3bd1a658cac07">stop_after_feature_</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a12f045950aed547386f4755a60004bea"> 100</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a12f045950aed547386f4755a60004bea">stop_after_intensity_ratio_</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"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#addd481a2f79201012bea9bc69a64fcce"> 102</a></span>  std::vector<RichPeakChromatogram> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#addd481a2f79201012bea9bc69a64fcce">picked_chroms_</a>;</div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a4fb9add89f346a8d64fe774536b5ad76"> 103</a></span>  std::vector<RichPeakChromatogram> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a4fb9add89f346a8d64fe774536b5ad76">smoothed_chroms_</a>;</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumT, <span class="keyword">typename</span> TransitionT></div>
<div class="line"><a name="l00109"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#abcb96765de1c995e5d9ef3d517682cad"> 109</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#abcb96765de1c995e5d9ef3d517682cad">prepareMasterContainer_</a>(<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup<SpectrumT, TransitionT></a> & transition_group,</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  SpectrumT & master_peak_container, <span class="keywordtype">int</span> chr_idx, <span class="keywordtype">double</span> best_left, <span class="keywordtype">double</span> best_right)</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  {</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keyword">const</span> SpectrumT & ref_chromatogram = transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">getChromatograms</a>()[chr_idx];</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="comment">// search for begin / end of the reference chromatogram (and add one more point)</span></div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keyword">typename</span> SpectrumT::const_iterator begin = ref_chromatogram.begin();</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keywordflow">while</span> (begin != ref_chromatogram.end() && begin->getMZ() < best_left) {begin++; }</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keywordflow">if</span> (begin != ref_chromatogram.begin()) {begin--; }</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keyword">typename</span> SpectrumT::const_iterator end = begin;</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordflow">while</span> (end != ref_chromatogram.end() && end->getMZ() < best_right) {end++; }</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordflow">if</span> (end != ref_chromatogram.end()) {end++; }</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span> </div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="comment">// resize the master container and set the m/z values to the ones of the master container</span></div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  master_peak_container.resize(distance(begin, end));</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keyword">typename</span> SpectrumT::iterator it = master_peak_container.begin();</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordflow">for</span> (<span class="keyword">typename</span> SpectrumT::const_iterator chrom_it = begin; chrom_it != end; chrom_it++, it++)</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  {</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  it->setMZ(chrom_it->getMZ());</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  }</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  }</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumT></div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#ac8e7c04f7fed4ad2ba53408e9b5cca76"> 134</a></span>  SpectrumT <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#ac8e7c04f7fed4ad2ba53408e9b5cca76">resampleChromatogram_</a>(<span class="keyword">const</span> SpectrumT & chromatogram,</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  SpectrumT & master_peak_container, <span class="keywordtype">double</span> best_left, <span class="keywordtype">double</span> best_right)</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  {</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="comment">// get the start / end point of this chromatogram => go one past</span></div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="comment">// best_left / best_right to make the resampling accurate also at the</span></div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">// edge.</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keyword">typename</span> SpectrumT::const_iterator begin = chromatogram.begin();</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keywordflow">while</span> (begin != chromatogram.end() && begin->getMZ() < best_left) {begin++; }</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordflow">if</span> (begin != chromatogram.begin()) {begin--; }</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span> </div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keyword">typename</span> SpectrumT::const_iterator end = begin;</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordflow">while</span> (end != chromatogram.end() && end->getMZ() < best_right) {end++; }</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordflow">if</span> (end != chromatogram.end()) {end++; }</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> </div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  SpectrumT resampled_peak_container = master_peak_container; <span class="comment">// copy the master container, which contains the RT values</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <a class="code" href="classOpenMS_1_1LinearResamplerAlign.html">LinearResamplerAlign</a> lresampler;</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  lresampler.<a class="code" href="classOpenMS_1_1LinearResamplerAlign.html#ac0856b2b1e7528e72df9b2b64c367b72">raster</a>(begin, end, resampled_peak_container.begin(), resampled_peak_container.end());</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> <span class="preprocessor">#if DEBUG_TRANSITIONGROUPPICKER</span></div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> <span class="preprocessor"></span> {</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  std::cout << <span class="stringliteral">"=========================================================================== "</span> << std::endl;</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">double</span> tot;</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  tot = 0;</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="keywordflow">for</span> (<span class="keyword">typename</span> SpectrumT::const_iterator it = begin; it != end; it++)</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  {</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  std::cout << <span class="stringliteral">" before resampl "</span> << *it << std::endl;</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  tot += it->getIntensity();</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  }</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  std::cout << <span class="stringliteral">" total "</span> << tot << std::endl;</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  tot = 0;</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">for</span> (<span class="keyword">typename</span> SpectrumT::iterator it = resampled_peak_container.begin(); it != resampled_peak_container.end(); it++)</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  {</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  std::cout << <span class="stringliteral">" resampl "</span> << *it << std::endl;</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  tot += it->getIntensity();</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  }</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  std::cout << <span class="stringliteral">" total "</span> << tot << std::endl;</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  std::cout << <span class="stringliteral">" resampled size "</span> << resampled_peak_container.size() << std::endl;</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="preprocessor">#endif</span></div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> <span class="preprocessor"></span> <span class="keywordflow">return</span> resampled_peak_container;</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  }</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> </div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span> </div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="keywordtype">double</span> calculateBgEstimation_(<span class="keyword">const</span> RichPeakChromatogram& smoothed_chromat, <span class="keywordtype">double</span> best_left, <span class="keywordtype">double</span> best_right);</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span> </div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html">MRMTransitionGroupPicker</a>& operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html">MRMTransitionGroupPicker</a>& rhs);</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span> </div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html">MRMTransitionGroupPicker</a>();</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span> </div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  ~<a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html">MRMTransitionGroupPicker</a>();</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> </div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumT, <span class="keyword">typename</span> TransitionT></div>
<div class="line"><a name="l00202"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#acce2a9f0fe8d27893f6a027a4598e8ba"> 202</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#acce2a9f0fe8d27893f6a027a4598e8ba">pickTransitionGroup</a>(<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup<SpectrumT, TransitionT></a> & transition_group)</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  {</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="comment">// Pick chromatograms</span></div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  picked_chroms_.clear();</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</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="l00207"></a><span class="lineno"> 207</span>  {</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakChromatogram</a>& chromatogram = transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">getChromatograms</a>()[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>];</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <span class="keywordflow">if</span> (!chromatogram.<a class="code" href="classOpenMS_1_1MSSpectrum.html#ada8ccbfae8ad9120b791b43000fc6dda">isSorted</a>()) { chromatogram.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a86f7b200260209865e730a2e4fcaa628">sortByPosition</a>(); }</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span> </div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="comment">// pickChromatogram will return the picked and the smoothed chromatogram</span></div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakChromatogram</a> picked_chrom, smoothed_chrom;</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  pickChromatogram(chromatogram, smoothed_chrom, picked_chrom);</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  picked_chrom.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a93f1c9f620403aec160d98e83e125502">sortByIntensity</a>(); <span class="comment">// we could do without that</span></div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  picked_chroms_.push_back(picked_chrom);</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  smoothed_chroms_.push_back(smoothed_chrom);</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  }</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="comment">// Find features (peak groups) in this group of transitions.</span></div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="comment">// While there are still peaks left, one will be picked and used to create</span></div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <span class="comment">// a feature. Whenever we run out of peaks, we will get -1 back as index</span></div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="comment">// and terminate.</span></div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <span class="keywordtype">int</span> chr_idx, peak_idx, cnt = 0;</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="keywordflow">while</span> (<span class="keyword">true</span>)</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  {</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  chr_idx = -1; peak_idx = -1;</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  findLargestPeak(picked_chroms_, chr_idx, peak_idx);</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="keywordflow">if</span> (chr_idx == -1 && peak_idx == -1) <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> </div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <span class="comment">/*</span></div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span> <span class="comment"> // FEATURE (hroest) check that this left/right do not collide with any already present features -- if so, re-set the left/right</span></div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span> <span class="comment"> double best_left = picked_chroms[chr_idx].getFloatDataArrays()[1][peak_idx];</span></div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span> <span class="comment"> double best_right = picked_chroms[chr_idx].getFloatDataArrays()[2][peak_idx];</span></div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span> </div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="comment">// get feature, prevent non-extended zero features to be added</span></div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <a class="code" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a> mrm_feature = createMRMFeature(transition_group, picked_chroms_, chr_idx, peak_idx);</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keywordflow">if</span> (mrm_feature.<a class="code" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>() > 0)</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  {</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#ad54c2606255628d4fe2af3793b1b3da4">addFeature</a>(mrm_feature);</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  }</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span> </div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  cnt++;</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="keywordflow">if</span> ((stop_after_feature_ > 0 && cnt > stop_after_feature_) && mrm_feature.<a class="code" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>() / (<a class="code" href="classdouble.html">double</a>)mrm_feature.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"total_xic"</span>) < stop_after_intensity_ratio_)</div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  {</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keywordflow">break</span>;</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>  }</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> </div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="comment">// This function will return a smoothed chromatogram and a picked chromatogram</span></div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordtype">void</span> pickChromatogram(<span class="keyword">const</span> RichPeakChromatogram& chromatogram, RichPeakChromatogram& smoothed_chrom, RichPeakChromatogram& picked_chrom);</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span> </div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumT, <span class="keyword">typename</span> TransitionT></div>
<div class="line"><a name="l00257"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#aea36708606fb59bad2006482d927b061"> 257</a></span>  <a class="code" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#aea36708606fb59bad2006482d927b061">createMRMFeature</a>(<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup<SpectrumT, TransitionT></a> & transition_group,</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  std::vector<SpectrumT> & picked_chroms, <span class="keywordtype">int</span> & chr_idx, <span class="keywordtype">int</span> & peak_idx)</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  {</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <a class="code" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a> mrmFeature;</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <span class="keyword">const</span> <span class="keywordtype">double</span> best_left = picked_chroms[chr_idx].getFloatDataArrays()[1][peak_idx];</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  <span class="keyword">const</span> <span class="keywordtype">double</span> best_right = picked_chroms[chr_idx].getFloatDataArrays()[2][peak_idx];</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="keyword">const</span> <span class="keywordtype">double</span> peak_apex = picked_chroms[chr_idx][peak_idx].getRT();</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span> </div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="comment">// Remove other, overlapping, picked peaks (in this and other</span></div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="comment">// chromatograms) and then ensure that at least one peak is set to zero</span></div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="comment">// (the currently best peak).</span></div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  remove_overlapping_features(picked_chroms, best_left, best_right);</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  picked_chroms[chr_idx][peak_idx].setIntensity(0.0);</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span> </div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="comment">// Prepare linear resampling of all the chromatograms, here creating the</span></div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="comment">// empty master_peak_container with the same RT (m/z) values as the reference</span></div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="comment">// chromatogram.</span></div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  SpectrumT master_peak_container;</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  prepareMasterContainer_(transition_group, master_peak_container, chr_idx, best_left, best_right);</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span> </div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keywordtype">double</span> total_intensity = 0; <span class="keywordtype">double</span> total_peak_apices = 0; <span class="keywordtype">double</span> total_xic = 0;</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</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="l00279"></a><span class="lineno"> 279</span>  {</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <span class="keyword">const</span> SpectrumT& chromatogram = transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">getChromatograms</a>()[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>];</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="keywordflow">for</span> (<span class="keyword">typename</span> SpectrumT::const_iterator it = chromatogram.begin(); it != chromatogram.end(); it++)</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  {</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  total_xic += it->getIntensity();</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  }</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span> </div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="comment">// resample the current chromatogram</span></div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="keyword">const</span> SpectrumT used_chromatogram = resampleChromatogram_(chromatogram, master_peak_container, best_left, best_right);</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="comment">// const SpectrumT& used_chromatogram = chromatogram; // instead of resampling</span></div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span> </div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> f;</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <span class="keywordtype">double</span> quality = 0;</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#a93cd3fc199fc903768e3b8d7fafaeb95">setQuality</a>(0, quality);</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">setOverallQuality</a>(quality);</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span> </div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <a class="code" href="classOpenMS_1_1ConvexHull2D.html#abdcce0f11b8d73a2b4da5b1a00457d7b">ConvexHull2D::PointArrayType</a> hull_points;</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  <a class="code" href="classdouble.html">DoubleReal</a> intensity_sum(0.0), rt_sum(0.0);</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="keywordtype">double</span> peak_apex_int = -1;</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  <span class="keywordtype">double</span> peak_apex_dist = std::fabs(used_chromatogram.begin()->getMZ() - peak_apex);</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <span class="comment">// FEATURE : use RTBegin / MZBegin -> for this we need to know whether the template param is a real chromatogram or a spectrum!</span></div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="keywordflow">for</span> (<span class="keyword">typename</span> SpectrumT::const_iterator it = used_chromatogram.begin(); it != used_chromatogram.end(); it++)</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  {</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="keywordflow">if</span> (it->getMZ() > best_left && it->getMZ() < best_right)</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>  <a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a> p;</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  p[0] = it->getMZ();</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  p[1] = it->getIntensity();</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  hull_points.push_back(p);</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keywordflow">if</span> (std::fabs(it->getMZ() - peak_apex) <= peak_apex_dist)</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  {</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  peak_apex_int = p[1];</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  peak_apex_dist = std::fabs(it->getMZ() - peak_apex);</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>  rt_sum += it->getMZ();</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  intensity_sum += it->getIntensity();</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  }</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  }</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>  <span class="keywordflow">if</span> (background_subtraction_ != <span class="stringliteral">"none"</span>)</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  {</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="keywordtype">double</span> background = 0;</div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="comment">// we use the smoothed chromatogram here to have a more accurate estimatation of the noise at the flanks of the peak</span></div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  <span class="keywordflow">if</span> (background_subtraction_ == <span class="stringliteral">"smoothed"</span>)</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  {</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keywordflow">if</span> (smoothed_chroms_.size() <= <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  {</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  std::cerr << <span class="stringliteral">"Tried to calculate background estimation without any smoothed chromatograms"</span> << std::endl;</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  background = 0;</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>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  {</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  background = calculateBgEstimation_(smoothed_chroms_[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>], best_left, best_right);</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  }</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  }</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (background_subtraction_ == <span class="stringliteral">"original"</span>)</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  {</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  background = calculateBgEstimation_(used_chromatogram, best_left, best_right);</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  }</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  intensity_sum -= background;</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  <span class="keywordflow">if</span> (intensity_sum < 0)</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  {</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  std::cerr << <span class="stringliteral">"Warning: Intensity was below 0 after background subtraction: "</span> << intensity_sum << <span class="stringliteral">". Setting it to 0."</span> << std::endl;</div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  intensity_sum = 0;</div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  }</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  }</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span> </div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  f.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>(picked_chroms[chr_idx][peak_idx].getMZ());</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  f.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(chromatogram.getMetaValue(<span class="stringliteral">"product_mz"</span>));</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(intensity_sum);</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <a class="code" href="classOpenMS_1_1ConvexHull2D.html">ConvexHull2D</a> hull;</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  hull.<a class="code" href="classOpenMS_1_1ConvexHull2D.html#a66469f20cdf9bda98df8e7dd611925a2">setHullPoints</a>(hull_points);</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>().push_back(hull);</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"MZ"</span>, chromatogram.getMetaValue(<span class="stringliteral">"product_mz"</span>));</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"native_id"</span>, chromatogram.getNativeID());</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"peak_apex_int"</span>, peak_apex_int);</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  <span class="comment">//f.setMetaValue("leftWidth", best_left);</span></div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  <span class="comment">//f.setMetaValue("rightWidth", best_right);</span></div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span> </div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  total_intensity += intensity_sum;</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  total_peak_apices += peak_apex_int;</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  mrmFeature.<a class="code" href="classOpenMS_1_1MRMFeature.html#afb0c149f5f33fa1a4284169a6164efa9">addFeature</a>(f, chromatogram.getNativeID()); <span class="comment">//map index and feature</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>  mrmFeature.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>(picked_chroms[chr_idx][peak_idx].getMZ());</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  mrmFeature.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(total_intensity);</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  mrmFeature.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"PeptideRef"</span>, transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#aedcd02941cf31e259bb9394850653bbc">getTransitionGroupID</a>());</div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  mrmFeature.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"leftWidth"</span>, best_left);</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  mrmFeature.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"rightWidth"</span>, best_right);</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  mrmFeature.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"total_xic"</span>, total_xic);</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  mrmFeature.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"peak_apices_sum"</span>, total_peak_apices);</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span> </div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keywordflow">return</span> mrmFeature;</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  }</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span> </div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  <span class="comment">// maybe private, but we have tests</span></div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span> </div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumT></div>
<div class="line"><a name="l00377"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a5ce5987c655ea5a3bba8d24d7833d323"> 377</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MRMTransitionGroupPicker.html#a5ce5987c655ea5a3bba8d24d7833d323">remove_overlapping_features</a>(std::vector<SpectrumT> & picked_chroms, <span class="keywordtype">double</span> best_left, <span class="keywordtype">double</span> best_right)</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  {</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="comment">// delete all seeds that lie within the current seed</span></div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> < picked_chroms.size(); <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>++)</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  {</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < picked_chroms[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].size(); i++)</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  {</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  <span class="keywordflow">if</span> (picked_chroms[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>][i].getMZ() >= best_left && picked_chroms[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>][i].getMZ() <= best_right)</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  {</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  picked_chroms[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>][i].setIntensity(0.0);</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>  }</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  }</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span> </div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  <span class="comment">// delete all seeds that overlap within the current seed</span></div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</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> < picked_chroms.size(); <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>++)</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  {</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < picked_chroms[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].size(); i++)</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  {</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  <span class="keywordtype">double</span> left = picked_chroms[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getFloatDataArrays()[1][i];</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  <span class="keywordtype">double</span> right = picked_chroms[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getFloatDataArrays()[2][i];</div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <span class="keywordflow">if</span> ((left >= best_left && left <= best_right)</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  || (right >= best_left && right <= best_right))</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  {</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  picked_chroms[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>][i].setIntensity(0.0);</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  }</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  }</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> </div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  <span class="keywordtype">void</span> findLargestPeak(std::vector<RichPeakChromatogram>& picked_chroms, <span class="keywordtype">int</span>& chr_idx, <span class="keywordtype">int</span>& peak_idx);</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  };</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span> }</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> <span class="preprocessor">#endif</span></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_1MetaInfoInterface_html_aae35ae2dfad88d673b03c787aafca83d"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">OpenMS::MetaInfoInterface::getMetaValue</a></div><div class="ttdeci">const DataValue & getMetaValue(const String &name) const </div><div class="ttdoc">returns the value corresponding to a string </div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1LinearResamplerAlign_html_ac0856b2b1e7528e72df9b2b64c367b72"><div class="ttname"><a href="classOpenMS_1_1LinearResamplerAlign.html#ac0856b2b1e7528e72df9b2b64c367b72">OpenMS::LinearResamplerAlign::raster</a></div><div class="ttdeci">void raster(SpecT< PeakType > &spectrum)</div><div class="ttdoc">Applies the resampling algorithm to an MSSpectrum. </div><div class="ttdef"><b>Definition:</b> LinearResamplerAlign.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_a135a7e818125b31198a8a65d9ac7a3d1"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">OpenMS::MetaInfoInterface::setMetaValue</a></div><div class="ttdeci">void setMetaValue(const String &name, const DataValue &value)</div><div class="ttdoc">sets the DataValue corresponding to a name </div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_a4fb9add89f346a8d64fe774536b5ad76"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a4fb9add89f346a8d64fe774536b5ad76">OpenMS::MRMTransitionGroupPicker::smoothed_chroms_</a></div><div class="ttdeci">std::vector< RichPeakChromatogram > smoothed_chroms_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_a417a0fdec8dd7dfd838f0505a6aeec0b"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a417a0fdec8dd7dfd838f0505a6aeec0b">OpenMS::MRMTransitionGroupPicker::background_subtraction_</a></div><div class="ttdeci">String background_subtraction_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:91</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="MRMFeature_8h_html"><div class="ttname"><a href="MRMFeature_8h.html">MRMFeature.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a2694f0775c46d9076355cb85d9815425"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">OpenMS::Peak2D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the m/z coordinate (index 1) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:197</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a86f7b200260209865e730a2e4fcaa628"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a86f7b200260209865e730a2e4fcaa628">OpenMS::MSSpectrum::sortByPosition</a></div><div class="ttdeci">void sortByPosition()</div><div class="ttdoc">Lexicographically sorts the peaks by their position. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:391</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a09903c7965f8ece31f2c1e07b41ae6dd"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">OpenMS::Peak2D::getIntensity</a></div><div class="ttdeci">IntensityType getIntensity() const </div><div class="ttdef"><b>Definition:</b> Peak2D.h:161</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_1ConvexHull2D_html_abdcce0f11b8d73a2b4da5b1a00457d7b"><div class="ttname"><a href="classOpenMS_1_1ConvexHull2D.html#abdcce0f11b8d73a2b4da5b1a00457d7b">OpenMS::ConvexHull2D::PointArrayType</a></div><div class="ttdeci">std::vector< PointType > PointArrayType</div><div class="ttdef"><b>Definition:</b> ConvexHull2D.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_ada8ccbfae8ad9120b791b43000fc6dda"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#ada8ccbfae8ad9120b791b43000fc6dda">OpenMS::MSSpectrum::isSorted</a></div><div class="ttdeci">bool isSorted() const </div><div class="ttdoc">Checks if all peaks are sorted with respect to ascending m/z. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:453</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_addd481a2f79201012bea9bc69a64fcce"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#addd481a2f79201012bea9bc69a64fcce">OpenMS::MRMTransitionGroupPicker::picked_chroms_</a></div><div class="ttdeci">std::vector< RichPeakChromatogram > picked_chroms_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:102</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="GaussFilter_8h_html"><div class="ttname"><a href="GaussFilter_8h.html">GaussFilter.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_a813dbc0d8c14384b69c3bd1a658cac07"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a813dbc0d8c14384b69c3bd1a658cac07">OpenMS::MRMTransitionGroupPicker::stop_after_feature_</a></div><div class="ttdeci">int stop_after_feature_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:99</div></div>
<div class="ttc" id="classOpenMS_1_1ConvexHull2D_html"><div class="ttname"><a href="classOpenMS_1_1ConvexHull2D.html">OpenMS::ConvexHull2D</a></div><div class="ttdoc">A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling...</div><div class="ttdef"><b>Definition:</b> ConvexHull2D.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_a6f89e0fa6d66ca2eef569f155a6eab15"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a6f89e0fa6d66ca2eef569f155a6eab15">OpenMS::MRMTransitionGroupPicker::gauss_width_</a></div><div class="ttdeci">DoubleReal gauss_width_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::Peak2D::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Non-mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:167</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_acd8ce7700143488fdc293038f4636501"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#acd8ce7700143488fdc293038f4636501">OpenMS::MRMTransitionGroupPicker::sgolay_polynomial_order_</a></div><div class="ttdeci">UInt sgolay_polynomial_order_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:87</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html">OpenMS::MRMTransitionGroup< SpectrumT, TransitionT ></a></div></div>
<div class="ttc" id="PeakPickerHiRes_8h_html"><div class="ttname"><a href="PeakPickerHiRes_8h.html">PeakPickerHiRes.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeature_html_afb0c149f5f33fa1a4284169a6164efa9"><div class="ttname"><a href="classOpenMS_1_1MRMFeature.html#afb0c149f5f33fa1a4284169a6164efa9">OpenMS::MRMFeature::addFeature</a></div><div class="ttdeci">void addFeature(Feature &feature, const String &key)</div><div class="ttdoc">Adds an feature from a single chromatogram into the feature. </div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_a6114587cf1dac7812059d2ae1b380808"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a6114587cf1dac7812059d2ae1b380808">OpenMS::MRMTransitionGroupPicker::use_gauss_</a></div><div class="ttdeci">bool use_gauss_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.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="classOpenMS_1_1MRMTransitionGroupPicker_html_aefa4cb42918dba37edfb78209ce2b512"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#aefa4cb42918dba37edfb78209ce2b512">OpenMS::MRMTransitionGroupPicker::sn_win_len_</a></div><div class="ttdeci">DoubleReal sn_win_len_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:96</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_1Peak2D_html_a396c5ebcac2e70f9b9a478bb2456985b"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">OpenMS::Peak2D::setRT</a></div><div class="ttdeci">void setRT(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:209</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_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition< 2 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_ad99bb8ba2103d6c52ee10ae6369b46e7"><div class="ttname"><a href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">OpenMS::Feature::getConvexHulls</a></div><div class="ttdeci">const std::vector< ConvexHull2D > & getConvexHulls() const </div><div class="ttdoc">Non-mutable access to the convex hulls. </div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a93f1c9f620403aec160d98e83e125502"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a93f1c9f620403aec160d98e83e125502">OpenMS::MSSpectrum::sortByIntensity</a></div><div class="ttdeci">void sortByIntensity(bool reverse=false)</div><div class="ttdoc">Lexicographically sorts the peaks by their intensity. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:314</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a93cd3fc199fc903768e3b8d7fafaeb95"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a93cd3fc199fc903768e3b8d7fafaeb95">OpenMS::Feature::setQuality</a></div><div class="ttdeci">void setQuality(Size index, QualityType q)</div><div class="ttdoc">Set the quality in dimension c. </div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_a415ee0df10ca0e1baf2ca18897c56463"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a415ee0df10ca0e1baf2ca18897c56463">OpenMS::MRMTransitionGroupPicker::sgolay_frame_length_</a></div><div class="ttdeci">UInt sgolay_frame_length_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:86</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_1LinearResamplerAlign_html"><div class="ttname"><a href="classOpenMS_1_1LinearResamplerAlign.html">OpenMS::LinearResamplerAlign</a></div><div class="ttdoc">Linear Resampling of raw data with alignment. </div><div class="ttdef"><b>Definition:</b> LinearResamplerAlign.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1ConvexHull2D_html_a66469f20cdf9bda98df8e7dd611925a2"><div class="ttname"><a href="classOpenMS_1_1ConvexHull2D.html#a66469f20cdf9bda98df8e7dd611925a2">OpenMS::ConvexHull2D::setHullPoints</a></div><div class="ttdeci">void setHullPoints(const PointArrayType &points)</div><div class="ttdoc">accessor for the outer(!) points (no checking is performed if this is actually a convex hull) ...</div></div>
<div class="ttc" id="LinearResamplerAlign_8h_html"><div class="ttname"><a href="LinearResamplerAlign_8h.html">LinearResamplerAlign.h</a></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_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</div></div>
<div class="ttc" id="ChromatogramPeak_8h_html"><div class="ttname"><a href="ChromatogramPeak_8h.html">ChromatogramPeak.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html_ad54c2606255628d4fe2af3793b1b3da4"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#ad54c2606255628d4fe2af3793b1b3da4">OpenMS::MRMTransitionGroup::addFeature</a></div><div class="ttdeci">void addFeature(MRMFeature &feature)</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:184</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_abcb96765de1c995e5d9ef3d517682cad"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#abcb96765de1c995e5d9ef3d517682cad">OpenMS::MRMTransitionGroupPicker::prepareMasterContainer_</a></div><div class="ttdeci">void prepareMasterContainer_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, SpectrumT &master_peak_container, int chr_idx, double best_left, double best_right)</div><div class="ttdoc">create an empty master peak container that has the correct mz / RT values set </div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:109</div></div>
<div class="ttc" id="SavitzkyGolayFilter_8h_html"><div class="ttname"><a href="SavitzkyGolayFilter_8h.html">SavitzkyGolayFilter.h</a></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="classOpenMS_1_1MRMTransitionGroupPicker_html_ac8e7c04f7fed4ad2ba53408e9b5cca76"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#ac8e7c04f7fed4ad2ba53408e9b5cca76">OpenMS::MRMTransitionGroupPicker::resampleChromatogram_</a></div><div class="ttdeci">SpectrumT resampleChromatogram_(const SpectrumT &chromatogram, SpectrumT &master_peak_container, double best_left, double best_right)</div><div class="ttdoc">use the master container from above to resample a chromatogram at those points stored in the master c...</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:134</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_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_1MRMTransitionGroupPicker_html_ad0001b2cab5c5b4749188a5a1cffb2c0"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#ad0001b2cab5c5b4749188a5a1cffb2c0">OpenMS::MRMTransitionGroupPicker::sn_bin_count_</a></div><div class="ttdeci">UInt sn_bin_count_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:97</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="classOpenMS_1_1MRMTransitionGroupPicker_html_a12f045950aed547386f4755a60004bea"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a12f045950aed547386f4755a60004bea">OpenMS::MRMTransitionGroupPicker::stop_after_intensity_ratio_</a></div><div class="ttdeci">DoubleReal stop_after_intensity_ratio_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_aea36708606fb59bad2006482d927b061"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#aea36708606fb59bad2006482d927b061">OpenMS::MRMTransitionGroupPicker::createMRMFeature</a></div><div class="ttdeci">MRMFeature createMRMFeature(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, std::vector< SpectrumT > &picked_chroms, int &chr_idx, int &peak_idx)</div><div class="ttdoc">Create feature from a vector of chromatograms and a specified peak. </div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:257</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_a5ce5987c655ea5a3bba8d24d7833d323"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a5ce5987c655ea5a3bba8d24d7833d323">OpenMS::MRMTransitionGroupPicker::remove_overlapping_features</a></div><div class="ttdeci">void remove_overlapping_features(std::vector< SpectrumT > &picked_chroms, double best_left, double best_right)</div><div class="ttdoc">Remove overlaping features that are within the current seed feature or overlap with it...</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:377</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_1MRMTransitionGroupPicker_html_a4910016b262f6723b82c4b1c4d6cdde7"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a4910016b262f6723b82c4b1c4d6cdde7">OpenMS::MRMTransitionGroupPicker::RichPeakChromatogram</a></div><div class="ttdeci">MSSpectrum< ChromatogramPeak > RichPeakChromatogram</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:83</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="LinearResampler_8h_html"><div class="ttname"><a href="LinearResampler_8h.html">LinearResampler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_a5e938e031680cf43ee3b1547ab6d1b1b"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#a5e938e031680cf43ee3b1547ab6d1b1b">OpenMS::MRMTransitionGroupPicker::peak_width_</a></div><div class="ttdeci">DoubleReal peak_width_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroupPicker_html_af9f4408f7c0f04e170ae1b4ba0571652"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroupPicker.html#af9f4408f7c0f04e170ae1b4ba0571652">OpenMS::MRMTransitionGroupPicker::signal_to_noise_</a></div><div class="ttdeci">DoubleReal signal_to_noise_</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroupPicker.h:94</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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