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<a href="ChromatogramExtractor_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_CHROMATOGRAMEXTRACTOR_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_CHROMATOGRAMEXTRACTOR_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="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="TargetedExperiment_8h.html">OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</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="TransformationXMLFile_8h.html">OpenMS/FORMAT/TransformationXMLFile.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="MzMLFile_8h.html">OpenMS/FORMAT/MzMLFile.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#ifdef _OPENMP</span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor"></span><span class="preprocessor">#include <omp.h></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> {</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html"> 61</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html">ChromatogramExtractor</a> :</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  {</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html#aebc0d6b93b7fbc4d7a7b1230d55489a0"> 68</a></span>  <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html#aebc0d6b93b7fbc4d7a7b1230d55489a0">ChromatogramExtractor</a>()</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  {</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  }</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html#a1409f6f0d2531350d7b9e7b0dd4601fc"> 73</a></span>  <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html#a1409f6f0d2531350d7b9e7b0dd4601fc">~ChromatogramExtractor</a>()</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  {</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  }</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> ExperimentT></div>
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html#ab8e5068d0d5799146b80ea6282ff0a6c"> 79</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html#ab8e5068d0d5799146b80ea6282ff0a6c">extractChromatograms</a>(<span class="keyword">const</span> ExperimentT& input, ExperimentT& output, <a class="code" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a>& transition_exp, <span class="keywordtype">double</span> extract_window, <span class="keywordtype">bool</span> ppm,</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> trafo, <span class="keywordtype">double</span> rt_extraction_window, <a class="code" href="classOpenMS_1_1String.html">String</a> filter)</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> </div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="comment">// invert the trafo because we want to transform nRT values to "real" RT values</span></div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  trafo.<a class="code" href="classOpenMS_1_1TransformationDescription.html#a7fa1616cc61c19a5efcc863c950f7f30">invert</a>();</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> input_size = input.size();</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordflow">if</span> (input_size < 1)</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  {</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  }</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <a class="code" href="classOpenMS_1_1SpectrumSettings.html">SpectrumSettings</a> settings = input[0];</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">int</span> used_filter = -1;</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordflow">if</span> (filter == <span class="stringliteral">"tophat"</span>)</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  {</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  used_filter = 1;</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  }</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (filter == <span class="stringliteral">"bartlett"</span>)</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  {</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  used_filter = 2;</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  }</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  {</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</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="l00104"></a><span class="lineno"> 104</span>  <span class="stringliteral">"Filter either needs to be tophat or bartlett"</span>);</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  }</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="comment">// Store the peptide retention times in an intermediate map</span></div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  PeptideRTMap_.clear();</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</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="classOpenMS_1_1TargetedExperiment.html#a81362aa067155119d3122af3555227f9">getPeptides</a>().size(); i++)</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  {</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">TargetedExperiment::Peptide</a>& pep = transition_exp.<a class="code" href="classOpenMS_1_1TargetedExperiment.html#a81362aa067155119d3122af3555227f9">getPeptides</a>()[i];</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordflow">if</span> (pep.<a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a04646756cfb9003cfa0fdbe7bafef165">rts</a>.empty() || pep.<a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a04646756cfb9003cfa0fdbe7bafef165">rts</a>[0].getCVTerms()[<span class="stringliteral">"MS:1000896"</span>].empty())</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">// we dont have retention times -> this is only a problem if we actually</span></div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="comment">// wanted to use the RT limit feature.</span></div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keywordflow">if</span> (rt_extraction_window >= 0)</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  {</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</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="l00119"></a><span class="lineno"> 119</span>  <span class="stringliteral">"Error: Peptide "</span> + pep.<a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a76010eef1edc0406cc2375c25d2a433d">id</a> + <span class="stringliteral">" does not have normalized retention times (term 1000896) which are necessary to perform an RT-limited extraction"</span>);</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>  <span class="keywordflow">continue</span>;</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>  PeptideRTMap_[pep.<a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a76010eef1edc0406cc2375c25d2a433d">id</a>] = pep.<a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a04646756cfb9003cfa0fdbe7bafef165">rts</a>[0].getCVTerms()[<span class="stringliteral">"MS:1000896"</span>][0].getValue().toString().toDouble();</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> </div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="comment">// sort the transition experiment by product mass</span></div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="comment">// this is essential because the algorithm assumes sorted transitions!</span></div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  transition_exp.<a class="code" href="classOpenMS_1_1TargetedExperiment.html#abc7d814820a48da344e780a775dfc5ac">sortTransitionsByProductMZ</a>();</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>  <span class="comment">// prepare all the spectra (but leave them empty)</span></div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  std::vector<typename ExperimentT::ChromatogramType> chromatograms;</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  prepareSpectra_(settings, chromatograms, transition_exp);</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="comment">//go through all spectra</span></div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  startProgress(0, input_size, <span class="stringliteral">"Extracting chromatograms"</span>);</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> scan_idx = 0; scan_idx < input_size; ++scan_idx)</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  {</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  setProgress(scan_idx);</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordflow">if</span> (input[scan_idx].size() == 0)</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span> </div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak_idx = 0;</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordtype">double</span> mz;</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordtype">double</span> integrated_intensity = 0;</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>  <span class="comment">// go through all transitions / chromatograms which are sorted by</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="comment">// ProductMZ. We can use this to step through the spectrum and at the</span></div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="comment">// same time step through the transitions. We increase the peak counter</span></div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="comment">// until we hit the next transition and then extract the signal.</span></div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</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> < chromatograms.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  {</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">double</span> current_rt = input[scan_idx].getRT();</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keywordflow">if</span> (outsideExtractionWindow_(transition_exp.<a class="code" href="classOpenMS_1_1TargetedExperiment.html#af3100e829c8edc47e845f2c73c0de0c2">getTransitions</a>()[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>], current_rt, trafo, rt_extraction_window))</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  {</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  }</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="keyword">typename</span> <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">ExperimentT::ChromatogramType::PeakType</a> p;</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  mz = transition_exp.<a class="code" href="classOpenMS_1_1TargetedExperiment.html#af3100e829c8edc47e845f2c73c0de0c2">getTransitions</a>()[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getProductMZ();</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="keywordflow">if</span> (used_filter == 1)</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  {</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  extract_value_tophat(input[scan_idx], mz, peak_idx, integrated_intensity, extract_window, ppm);</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  }</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (used_filter == 2)</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>  extract_value_bartlett(input[scan_idx], mz, peak_idx, integrated_intensity, extract_window, ppm);</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</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>  p.setRT(current_rt);</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  p.setIntensity(integrated_intensity);</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  chromatograms[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].push_back(p);</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  }</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  }</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  endProgress();</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span> </div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="comment">// add all the chromatograms to the output</span></div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  output.setChromatograms(chromatograms);</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  }</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> <span class="keyword">public</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>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumT></div>
<div class="line"><a name="l00187"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html#a476e590e0e0491b81412da274dd84eb8"> 187</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html#a476e590e0e0491b81412da274dd84eb8">extract_value_tophat</a>(<span class="keyword">const</span> SpectrumT& input, <span class="keyword">const</span> <span class="keywordtype">double</span>& mz, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>& peak_idx, <span class="keywordtype">double</span>& integrated_intensity, <span class="keyword">const</span> <span class="keywordtype">double</span>& extract_window, <span class="keyword">const</span> <span class="keywordtype">bool</span> ppm)</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  {</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  integrated_intensity = 0;</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <span class="keywordflow">if</span> (input.size() == 0)</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  {</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  }</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span> </div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="comment">// calculate extraction window</span></div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keywordtype">double</span> left, right;</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="keywordflow">if</span> (ppm)</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  {</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  left = mz - mz * extract_window / 2.0 * 1.0e-6;</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  right = mz + mz * extract_window / 2.0 * 1.0e-6;</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  }</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keywordflow">else</span></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>  left = mz - extract_window / 2.0;</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  right = mz + extract_window / 2.0;</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  }</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span> </div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> walker;</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">// advance the peak_idx until we hit the m/z value of the next transition</span></div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordflow">while</span> (peak_idx < input.size() && input[peak_idx].getMZ() < mz)</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  {</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  peak_idx++;</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  }</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  integrated_intensity = 0;</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>  <span class="comment">// walk right and left and add to our intensity</span></div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  walker = peak_idx;</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="comment">// if we moved past the end of the spectrum, we need to try the last peak of the spectrum (it could still be within the window)</span></div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <span class="keywordflow">if</span> (peak_idx >= input.size())</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  {</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  walker = input.size() - 1;</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</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>  <span class="comment">// add the current peak if it is between right and left</span></div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="keywordflow">if</span> (input[walker].getMZ() > left && input[walker].getMZ() < right)</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  {</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  integrated_intensity += input[walker].getIntensity();</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  }</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span> </div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="comment">// walk to the right until we go outside the window, then walk to the left until we are outside the window</span></div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  walker = peak_idx;</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keywordflow">if</span> (walker > 0)</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>  walker--;</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>  <span class="keywordflow">while</span> (walker > 0 && input[walker].getMZ() > left && input[walker].getMZ() < right)</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>  integrated_intensity += input[walker].getIntensity(); walker--;</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>  walker = peak_idx;</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="keywordflow">if</span> (walker < input.size() )</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  {</div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  walker++;</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  }</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <span class="keywordflow">while</span> (walker<input.size() && input[walker].getMZ()> left && input[walker].getMZ() < right)</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>  integrated_intensity += input[walker].getIntensity(); walker++;</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  }</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  }</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span> </div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumT></div>
<div class="line"><a name="l00254"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html#a8ae1f016ab62bf4c23427e15495e0784"> 254</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html#a8ae1f016ab62bf4c23427e15495e0784">extract_value_bartlett</a>(<span class="keyword">const</span> SpectrumT& input, <span class="keyword">const</span> <span class="keywordtype">double</span>& mz, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>& peak_idx, <span class="keywordtype">double</span>& integrated_intensity, <span class="keyword">const</span> <span class="keywordtype">double</span>& extract_window, <span class="keyword">const</span> <span class="keywordtype">bool</span> ppm)</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  {</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  integrated_intensity = 0;</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="keywordflow">if</span> (input.size() == 0)</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  {</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordflow">return</span>;</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">// calculate extraction window</span></div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="keywordtype">double</span> left, right, half_window_size, weight;</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="keywordflow">if</span> (ppm)</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>  half_window_size = mz * extract_window / 2.0 * 1.0e-6;</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  left = mz - mz * extract_window / 2.0 * 1.0e-6;</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  right = mz + mz * extract_window / 2.0 * 1.0e-6;</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  }</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  {</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  half_window_size = extract_window / 2.0;</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  left = mz - extract_window / 2.0;</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  right = mz + extract_window / 2.0;</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  }</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>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> walker;</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">// advance the peak_idx until we hit the m/z value of the next transition</span></div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <span class="keywordflow">while</span> (peak_idx < input.size() && input[peak_idx].getMZ() < mz)</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  {</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  peak_idx++;</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  }</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </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">// walk right and left and add to our intensity</span></div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  walker = peak_idx;</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="comment">// if we moved past the end of the spectrum, we need to try the last peak of the spectrum (it could still be within the window)</span></div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  <span class="keywordflow">if</span> (peak_idx >= input.size())</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>  walker = input.size() - 1;</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  }</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span> </div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="comment">// add the current peak if it is between right and left</span></div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <span class="keywordflow">if</span> (input[walker].getMZ() > left && input[walker].getMZ() < right)</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  {</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  weight = 1 - fabs(input[walker].getMZ() - mz) / half_window_size;</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  integrated_intensity += input[walker].getIntensity() * weight;</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> </div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="comment">// walk to the right until we go outside the window, then walk to the left until we are outside the window</span></div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  walker = peak_idx;</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <span class="keywordflow">if</span> (walker > 0 )</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  {</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  walker--;</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>  <span class="keywordflow">while</span> (walker > 0 && input[walker].getMZ() > left && input[walker].getMZ() < right)</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  {</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  weight = 1 - fabs(input[walker].getMZ() - mz) / half_window_size;</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  integrated_intensity += input[walker].getIntensity() * weight; walker--;</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>  walker = peak_idx;</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <span class="keywordflow">if</span> (walker < input.size() )</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>  walker++;</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>  <span class="keywordflow">while</span> (walker<input.size() && input[walker].getMZ()> left && input[walker].getMZ() < right)</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>  weight = 1 - fabs(input[walker].getMZ() - mz) / half_window_size;</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  integrated_intensity += input[walker].getIntensity() * weight; walker++;</div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  }</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</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"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html#a6935de84f69c85bfdf90e5119f705c07"> 324</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html#a6935de84f69c85bfdf90e5119f705c07">extract_value_tophat</a>(<span class="keyword">const</span> std::vector<double>::const_iterator& mz_start, std::vector<double>::const_iterator& mz_it,</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <span class="keyword">const</span> std::vector<double>::const_iterator& mz_end, std::vector<double>::const_iterator& int_it,</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>& mz, <span class="keywordtype">double</span>& integrated_intensity, <span class="keywordtype">double</span>& extract_window, <span class="keywordtype">bool</span> ppm)</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  {</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  integrated_intensity = 0;</div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="keywordflow">if</span> (mz_start == mz_end)</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>  <span class="keywordflow">return</span>;</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="comment">// calculate extraction window</span></div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="keywordtype">double</span> left, right;</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <span class="keywordflow">if</span> (ppm)</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>  left = mz - mz * extract_window / 2.0 * 1.0e-6;</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  right = mz + mz * extract_window / 2.0 * 1.0e-6;</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  }</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="keywordflow">else</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>  left = mz - extract_window / 2.0;</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  right = mz + extract_window / 2.0;</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> </div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  std::vector<double>::const_iterator mz_walker;</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  std::vector<double>::const_iterator int_walker;</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>  <span class="comment">// advance the mz / int iterator until we hit the m/z value of the next transition</span></div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="keywordflow">while</span> (mz_it != mz_end && (*mz_it) < mz)</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  {</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  mz_it++; int_it++;</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  }</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span> </div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  <span class="comment">// walk right and left and add to our intensity</span></div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  mz_walker = mz_it;</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  int_walker = int_it;</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> </div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  <span class="comment">// if we moved past the end of the spectrum, we need to try the last peak of the spectrum (it could still be within the window)</span></div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  <span class="keywordflow">if</span> (mz_it == mz_end)</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  {</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  mz_walker--; int_walker--;</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> </div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  <span class="comment">// add the current peak if it is between right and left</span></div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="keywordflow">if</span> ((*mz_walker) > left && (*mz_walker) < right)</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  {</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  integrated_intensity += (*int_walker);</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  }</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>  <span class="comment">// walk to the right until we go outside the window, then walk to the left until we are outside the window</span></div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  mz_walker = mz_it;</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  int_walker = int_it;</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  <span class="keywordflow">if</span> (mz_it != mz_start)</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  {</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  mz_walker--;</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  int_walker--;</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  }</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="keywordflow">while</span> (mz_walker != mz_start && (*mz_walker) > left && (*mz_walker) < right)</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>  integrated_intensity += (*int_walker); mz_walker--; int_walker--;</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>  mz_walker = mz_it;</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  int_walker = int_it;</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <span class="keywordflow">if</span> (mz_it != mz_end)</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>  mz_walker++;</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  int_walker++;</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="keywordflow">while</span> (mz_walker != mz_end && (*mz_walker) > left && (*mz_walker) < right)</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>  integrated_intensity += (*int_walker); mz_walker++; int_walker++;</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  }</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> </div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span> </div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  <span class="keyword">template</span> <<span class="keyword">class</span> SpectrumSettingsT, <span class="keyword">class</span> ChromatogramT></div>
<div class="line"><a name="l00401"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html#acc6dd6bb5820778b452b8adf9334421e"> 401</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html#acc6dd6bb5820778b452b8adf9334421e">prepareSpectra_</a>(SpectrumSettingsT& settings, std::vector<ChromatogramT>& chromatograms, <a class="code" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a>& transition_exp)</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>  <span class="comment">// first prepare all the spectra (but leave them empty)</span></div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</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="classOpenMS_1_1TargetedExperiment.html#af3100e829c8edc47e845f2c73c0de0c2">getTransitions</a>().size(); i++)</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  {</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ReactionMonitoringTransition.html">ReactionMonitoringTransition</a>* transition = &transition_exp.<a class="code" href="classOpenMS_1_1TargetedExperiment.html#af3100e829c8edc47e845f2c73c0de0c2">getTransitions</a>()[i];</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>  ChromatogramT chrom;</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="comment">// Create precursor and set</span></div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  <span class="comment">// 1) the target m/z</span></div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  <span class="comment">// 2) the isolation window (upper/lower)</span></div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  <span class="comment">// 3) the peptide sequence</span></div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a> prec;</div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  prec.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(transition-><a class="code" href="classOpenMS_1_1ReactionMonitoringTransition.html#aeaba1d2d17aad5f9a659c1b66ac77989">getPrecursorMZ</a>());</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <span class="keywordflow">if</span> (settings.getPrecursors().size() > 0)</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  {</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  prec.<a class="code" href="classOpenMS_1_1Precursor.html#a046066b9d4e7b06a0ce6b883346689f6">setIsolationWindowLowerOffset</a>(settings.getPrecursors()[0].getIsolationWindowLowerOffset());</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  prec.<a class="code" href="classOpenMS_1_1Precursor.html#a3c61b885b58c7b8ed6c09913229342d3">setIsolationWindowUpperOffset</a>(settings.getPrecursors()[0].getIsolationWindowUpperOffset());</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  }</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span> </div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="comment">//set precursor sequence</span></div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> pepref = transition-><a class="code" href="classOpenMS_1_1ReactionMonitoringTransition.html#a8d50acc4d8e15a1bb76c3d321679f300">getPeptideRef</a>();</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> pep_idx = 0; pep_idx < transition_exp.<a class="code" href="classOpenMS_1_1TargetedExperiment.html#a81362aa067155119d3122af3555227f9">getPeptides</a>().size(); pep_idx++)</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  {</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">OpenMS::TargetedExperiment::Peptide</a>* pep = &transition_exp.<a class="code" href="classOpenMS_1_1TargetedExperiment.html#a81362aa067155119d3122af3555227f9">getPeptides</a>()[pep_idx];</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="keywordflow">if</span> (pep-><a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a76010eef1edc0406cc2375c25d2a433d">id</a> == pepref)</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  {</div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  prec.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"peptide_sequence"</span>, pep-><a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a3d81a52752fe56b49914dbe273521b5d">sequence</a>);</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  }</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  }</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <span class="comment">// add precursor to spectrum</span></div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  chrom.setPrecursor(prec);</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span> </div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  <span class="comment">// Create product and set its m/z</span></div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  <a class="code" href="classOpenMS_1_1Product.html">Product</a> prod;</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  prod.<a class="code" href="classOpenMS_1_1Product.html#a94893c6a36a1281bfd8ff45c0199bd35">setMZ</a>(transition-><a class="code" href="classOpenMS_1_1ReactionMonitoringTransition.html#ac6730e2e483fad81620fb1adfde156e8">getProductMZ</a>());</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  chrom.setProduct(prod);</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span> </div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <span class="comment">// Set the rest of the meta-data</span></div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  chrom.setInstrumentSettings(settings.getInstrumentSettings());</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  chrom.setAcquisitionInfo(settings.getAcquisitionInfo());</div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  chrom.setSourceFile(settings.getSourceFile());</div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span> </div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < settings.getDataProcessing().size(); ++i)</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>  <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> dp = settings.getDataProcessing()[i];</div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  dp.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"performed_on_spectra"</span>, <span class="stringliteral">"true"</span>);</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  chrom.getDataProcessing().push_back(dp);</div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  }</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span> </div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="comment">// Set the id of the chromatogram, using the id of the transition (this gives directly the mapping of the two)</span></div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  chrom.setNativeID(transition-><a class="code" href="classOpenMS_1_1ReactionMonitoringTransition.html#ad368341c22d3447e324134c47adff081">getNativeID</a>());</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  chrom.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  chromatograms.push_back(chrom);</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  }</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span> </div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  }</div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span> </div>
<div class="line"><a name="l00461"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html#acee142f4f394a06534b33c828b42f7ec"> 461</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html#acee142f4f394a06534b33c828b42f7ec">outsideExtractionWindow_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ReactionMonitoringTransition.html">ReactionMonitoringTransition</a>& transition, <span class="keywordtype">double</span> current_rt,</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  <span class="keyword">const</span> <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="l00463"></a><span class="lineno"> 463</span>  {</div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="keywordflow">if</span> (rt_extraction_window < 0)</div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  {</div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</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> </div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  <span class="comment">// Get the expected retention time, apply the RT-transformation</span></div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  <span class="comment">// (which describes the normalization) and then take the difference.</span></div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  <span class="comment">// Note that we inverted the transformation in the beginning because</span></div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  <span class="comment">// we want to transform from normalized to real RTs here and not the</span></div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  <span class="comment">// other way round.</span></div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <span class="keywordtype">double</span> expected_rt = PeptideRTMap_[transition.<a class="code" href="classOpenMS_1_1ReactionMonitoringTransition.html#a8d50acc4d8e15a1bb76c3d321679f300">getPeptideRef</a>()];</div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  <span class="keywordtype">double</span> de_normalized_experimental_rt = trafo.<a class="code" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">apply</a>(expected_rt);</div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  <span class="keywordflow">if</span> (current_rt < de_normalized_experimental_rt - rt_extraction_window || current_rt > de_normalized_experimental_rt + rt_extraction_window)</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>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  }</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  }</div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</span> </div>
<div class="line"><a name="l00483"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramExtractor.html#ae505eef01d0c7c8b342bac83fcd81f23"> 483</a></span>  std::map<OpenMS::String, double> <a class="code" href="classOpenMS_1_1ChromatogramExtractor.html#ae505eef01d0c7c8b342bac83fcd81f23">PeptideRTMap_</a>;</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> </div>
<div class="line"><a name="l00487"></a><span class="lineno"> 487</span> }</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> <span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramExtractor_html_aebc0d6b93b7fbc4d7a7b1230d55489a0"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html#aebc0d6b93b7fbc4d7a7b1230d55489a0">OpenMS::ChromatogramExtractor::ChromatogramExtractor</a></div><div class="ttdeci">ChromatogramExtractor()</div><div class="ttdoc">Constructor. </div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:68</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_1ChromatogramExtractor_html_ae505eef01d0c7c8b342bac83fcd81f23"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html#ae505eef01d0c7c8b342bac83fcd81f23">OpenMS::ChromatogramExtractor::PeptideRTMap_</a></div><div class="ttdeci">std::map< OpenMS::String, double > PeptideRTMap_</div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:483</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html">OpenMS::DataProcessing</a></div><div class="ttdoc">Descripton of the applied preprocessing steps. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_a3c61b885b58c7b8ed6c09913229342d3"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#a3c61b885b58c7b8ed6c09913229342d3">OpenMS::Precursor::setIsolationWindowUpperOffset</a></div><div class="ttdeci">void setIsolationWindowUpperOffset(DoubleReal bound)</div><div class="ttdoc">sets the upper offset from the target m/z </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_1ChromatogramExtractor_html_acee142f4f394a06534b33c828b42f7ec"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html#acee142f4f394a06534b33c828b42f7ec">OpenMS::ChromatogramExtractor::outsideExtractionWindow_</a></div><div class="ttdeci">bool outsideExtractionWindow_(const ReactionMonitoringTransition &transition, double current_rt, const TransformationDescription &trafo, double rt_extraction_window)</div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:461</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramExtractor_html_a476e590e0e0491b81412da274dd84eb8"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html#a476e590e0e0491b81412da274dd84eb8">OpenMS::ChromatogramExtractor::extract_value_tophat</a></div><div class="ttdeci">void extract_value_tophat(const SpectrumT &input, const double &mz, Size &peak_idx, double &integrated_intensity, const double &extract_window, const bool ppm)</div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:187</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html"><div class="ttname"><a href="classOpenMS_1_1Precursor.html">OpenMS::Precursor</a></div><div class="ttdoc">Precursor meta information. </div><div class="ttdef"><b>Definition:</b> Precursor.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Product_html"><div class="ttname"><a href="classOpenMS_1_1Product.html">OpenMS::Product</a></div><div class="ttdoc">Product meta information. </div><div class="ttdef"><b>Definition:</b> Product.h:49</div></div>
<div class="ttc" id="namespaceOpenMS_html_a013338b7bdbb5c3b4c78666656070e23"><div class="ttname"><a href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">OpenMS::PeakType</a></div><div class="ttdeci">Peak2D PeakType</div><div class="ttdef"><b>Definition:</b> MassTrace.h:49</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_a046066b9d4e7b06a0ce6b883346689f6"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#a046066b9d4e7b06a0ce6b883346689f6">OpenMS::Precursor::setIsolationWindowLowerOffset</a></div><div class="ttdeci">void setIsolationWindowLowerOffset(DoubleReal bound)</div><div class="ttdoc">sets the lower offset from the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1Product_html_a94893c6a36a1281bfd8ff45c0199bd35"><div class="ttname"><a href="classOpenMS_1_1Product.html#a94893c6a36a1281bfd8ff45c0199bd35">OpenMS::Product::setMZ</a></div><div class="ttdeci">void setMZ(DoubleReal mz)</div><div class="ttdoc">sets the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html">OpenMS::SpectrumSettings</a></div><div class="ttdoc">Representation of 1D spectrum settings. </div><div class="ttdef"><b>Definition:</b> SpectrumSettings.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_ab9c4ce5d172a75d6de2c6f5f1847c9ab"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">OpenMS::Peak1D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType mz)</div><div class="ttdoc">Mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_abc7d814820a48da344e780a775dfc5ac"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#abc7d814820a48da344e780a775dfc5ac">OpenMS::TargetedExperiment::sortTransitionsByProductMZ</a></div><div class="ttdeci">void sortTransitionsByProductMZ()</div><div class="ttdoc">Lexicographically sorts the transitions by their product m/z. </div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide_html_a04646756cfb9003cfa0fdbe7bafef165"><div class="ttname"><a href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a04646756cfb9003cfa0fdbe7bafef165">OpenMS::TargetedExperimentHelper::Peptide::rts</a></div><div class="ttdeci">std::vector< RetentionTime > rts</div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:333</div></div>
<div class="ttc" id="classOpenMS_1_1ReactionMonitoringTransition_html_a8d50acc4d8e15a1bb76c3d321679f300"><div class="ttname"><a href="classOpenMS_1_1ReactionMonitoringTransition.html#a8d50acc4d8e15a1bb76c3d321679f300">OpenMS::ReactionMonitoringTransition::getPeptideRef</a></div><div class="ttdeci">const String & getPeptideRef() const </div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_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="classOpenMS_1_1ChromatogramExtractor_html_ab8e5068d0d5799146b80ea6282ff0a6c"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html#ab8e5068d0d5799146b80ea6282ff0a6c">OpenMS::ChromatogramExtractor::extractChromatograms</a></div><div class="ttdeci">void extractChromatograms(const ExperimentT &input, ExperimentT &output, OpenMS::TargetedExperiment &transition_exp, double extract_window, bool ppm, TransformationDescription trafo, double rt_extraction_window, String filter)</div><div class="ttdoc">Extract chromatograms defined by the TargetedExperiment from the input map and write them to the outp...</div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide_html_a76010eef1edc0406cc2375c25d2a433d"><div class="ttname"><a href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a76010eef1edc0406cc2375c25d2a433d">OpenMS::TargetedExperimentHelper::Peptide::id</a></div><div class="ttdeci">String id</div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:334</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_af3100e829c8edc47e845f2c73c0de0c2"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#af3100e829c8edc47e845f2c73c0de0c2">OpenMS::TargetedExperiment::getTransitions</a></div><div class="ttdeci">const std::vector< ReactionMonitoringTransition > & getTransitions() const </div><div class="ttdoc">returns the transition list </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="TargetedExperiment_8h_html"><div class="ttname"><a href="TargetedExperiment_8h.html">TargetedExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ReactionMonitoringTransition_html_aeaba1d2d17aad5f9a659c1b66ac77989"><div class="ttname"><a href="classOpenMS_1_1ReactionMonitoringTransition.html#aeaba1d2d17aad5f9a659c1b66ac77989">OpenMS::ReactionMonitoringTransition::getPrecursorMZ</a></div><div class="ttdeci">DoubleReal getPrecursorMZ() const </div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramExtractor_html_a1409f6f0d2531350d7b9e7b0dd4601fc"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html#a1409f6f0d2531350d7b9e7b0dd4601fc">OpenMS::ChromatogramExtractor::~ChromatogramExtractor</a></div><div class="ttdeci">~ChromatogramExtractor()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramExtractor_html"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html">OpenMS::ChromatogramExtractor</a></div><div class="ttdoc">The ChromatogramExtractor extracts chromatograms from a mzML file. </div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">OpenMS::ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide_html_a3d81a52752fe56b49914dbe273521b5d"><div class="ttname"><a href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a3d81a52752fe56b49914dbe273521b5d">OpenMS::TargetedExperimentHelper::Peptide::sequence</a></div><div class="ttdeci">String sequence</div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:337</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramExtractor_html_acc6dd6bb5820778b452b8adf9334421e"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html#acc6dd6bb5820778b452b8adf9334421e">OpenMS::ChromatogramExtractor::prepareSpectra_</a></div><div class="ttdeci">void prepareSpectra_(SpectrumSettingsT &settings, std::vector< ChromatogramT > &chromatograms, OpenMS::TargetedExperiment &transition_exp)</div><div class="ttdoc">This populates the chromatograms vector with empty chromatograms (but sets their meta-information) ...</div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:401</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_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="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="classOpenMS_1_1ReactionMonitoringTransition_html_ad368341c22d3447e324134c47adff081"><div class="ttname"><a href="classOpenMS_1_1ReactionMonitoringTransition.html#ad368341c22d3447e324134c47adff081">OpenMS::ReactionMonitoringTransition::getNativeID</a></div><div class="ttdeci">const String & getNativeID() const </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_1ChromatogramExtractor_html_a8ae1f016ab62bf4c23427e15495e0784"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html#a8ae1f016ab62bf4c23427e15495e0784">OpenMS::ChromatogramExtractor::extract_value_bartlett</a></div><div class="ttdeci">void extract_value_bartlett(const SpectrumT &input, const double &mz, Size &peak_idx, double &integrated_intensity, const double &extract_window, const bool ppm)</div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:254</div></div>
<div class="ttc" id="classOpenMS_1_1ReactionMonitoringTransition_html_ac6730e2e483fad81620fb1adfde156e8"><div class="ttname"><a href="classOpenMS_1_1ReactionMonitoringTransition.html#ac6730e2e483fad81620fb1adfde156e8">OpenMS::ReactionMonitoringTransition::getProductMZ</a></div><div class="ttdeci">DoubleReal getProductMZ() const </div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramExtractor_html_a6935de84f69c85bfdf90e5119f705c07"><div class="ttname"><a href="classOpenMS_1_1ChromatogramExtractor.html#a6935de84f69c85bfdf90e5119f705c07">OpenMS::ChromatogramExtractor::extract_value_tophat</a></div><div class="ttdeci">void extract_value_tophat(const std::vector< double >::const_iterator &mz_start, std::vector< double >::const_iterator &mz_it, const std::vector< double >::const_iterator &mz_end, std::vector< double >::const_iterator &int_it, const double &mz, double &integrated_intensity, double &extract_window, bool ppm)</div><div class="ttdef"><b>Definition:</b> ChromatogramExtractor.h:324</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="classOpenMS_1_1TargetedExperiment_html_a81362aa067155119d3122af3555227f9"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a81362aa067155119d3122af3555227f9">OpenMS::TargetedExperiment::getPeptides</a></div><div class="ttdeci">const std::vector< Peptide > & getPeptides() const </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="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_1TargetedExperimentHelper_1_1Peptide_html"><div class="ttname"><a href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">OpenMS::TargetedExperimentHelper::Peptide</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:211</div></div>
<div class="ttc" id="classOpenMS_1_1ReactionMonitoringTransition_html"><div class="ttname"><a href="classOpenMS_1_1ReactionMonitoringTransition.html">OpenMS::ReactionMonitoringTransition</a></div><div class="ttdoc">This class stores a SRM/MRM transition. </div><div class="ttdef"><b>Definition:</b> ReactionMonitoringTransition.h:53</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 11:19:11 using doxygen 1.8.5</font></TD>
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