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<a href="ProcessData_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: Florian Zeller $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Lukas Mueller, Markus Mueller $</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> <span class="comment">//</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="comment"></span><span class="comment">//</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="comment">// PEAK DETECTION OF FOURIER TRANSFORME MS INSTRUMENT DATA</span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="comment">//</span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="comment">// written by Markus Mueller, markus.mueller@imsb.biol.ethz.ch</span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="comment">// and Lukas Mueller, Lukas.Mueller@imsb.biol.ethz.ch</span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="comment">// October 2005</span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="comment">//</span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="comment">// Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch</span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="comment">// December 2010</span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="comment">//</span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="comment">// Group of Prof. Ruedi Aebersold, IMSB, ETH Hoenggerberg, Zurich</span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="comment">//</span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="comment">//</span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</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">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_PROCESSDATA_H</span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_PROCESSDATA_H</span></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="preprocessor">#include <map></span></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#include <string></span></div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor">#include <list></span></div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> {</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div>
<div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html"> 63</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a></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> </div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="comment">// declaration of the private members:</span></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> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#af18558f60329d153e5f439e6b6cbc6fa"> 71</a></span>  <span class="keyword">typedef</span> std::multimap<int, MSPeak> <a class="code" href="classOpenMS_1_1ProcessData.html#af18558f60329d153e5f439e6b6cbc6fa">elution_peak</a>;</div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#ab69ab1a8bcf64e4e36a57672502f93dc"> 72</a></span>  <span class="keyword">typedef</span> std::vector<elution_peak> <a class="code" href="classOpenMS_1_1ProcessData.html#ab69ab1a8bcf64e4e36a57672502f93dc">MZ_series</a>;</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a79e6b2973636a97ad0228a737ddcbed6"> 73</a></span>  <span class="keyword">typedef</span> std::vector<elution_peak>::iterator <a class="code" href="classOpenMS_1_1ProcessData.html#a79e6b2973636a97ad0228a737ddcbed6">MZ_series_ITERATOR</a>;</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a10ee7dd9ccf6967fedce8a20656bd5bb"> 74</a></span>  <span class="keyword">typedef</span> std::multimap<double, MZ_series> <a class="code" href="classOpenMS_1_1ProcessData.html#a10ee7dd9ccf6967fedce8a20656bd5bb">main_data_structure</a>;</div>
<div class="line"><a name="l00075"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070"> 75</a></span>  <span class="keyword">typedef</span> main_data_structure::iterator <a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a>;</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="comment">// declaration of the public members:</span></div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="comment">// map that tracts all observed masses in keys</span></div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </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="comment">// clustering of ms peak along time axis:</span></div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> <span class="comment">// bool TIME_CLUSTERING_BY_RETENTION_TIME;</span></div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="comment">// max_distance from next elution peak member in scan numbers:</span></div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a3553563b4e9f10de51af73aab0bb7ae5"> 89</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1ProcessData.html#a3553563b4e9f10de51af73aab0bb7ae5">max_inter_scan_distance</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"> 91</span>  <span class="comment">// cluster data structure:</span></div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a7016fa595c5406be9e3ced4ad1bce3c5"> 92</a></span>  <a class="code" href="classOpenMS_1_1LCMSCData.html">LCMSCData</a> * <a class="code" href="classOpenMS_1_1ProcessData.html#a7016fa595c5406be9e3ced4ad1bce3c5">data_</a>;</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="comment">// and stores as contents vectors of type</span></div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a7c7714105bef941ae216ae393ef432d7"> 95</a></span>  <a class="code" href="classOpenMS_1_1ProcessData.html#a10ee7dd9ccf6967fedce8a20656bd5bb">main_data_structure</a> <a class="code" href="classOpenMS_1_1ProcessData.html#a7c7714105bef941ae216ae393ef432d7">pMZ_LIST</a>;</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="comment">// tracks the number of observed mz cluster</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="comment">// elements:</span></div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a82e427ba10c56dc1c49702e3f6d713dd"> 99</a></span>  std::map<double, int> <a class="code" href="classOpenMS_1_1ProcessData.html#a82e427ba10c56dc1c49702e3f6d713dd">MZ_CLUSTER</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a32976d9206a75664928ba47acd712e85"> 100</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1ProcessData.html#a32976d9206a75664928ba47acd712e85">LC_elution_peak_counter</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="comment">// data processing classes:</span></div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a38fab6bbdb8c344b8ef8770640d0cba8"> 105</a></span>  <a class="code" href="classOpenMS_1_1BackgroundControl.html">BackgroundControl</a> * <a class="code" href="classOpenMS_1_1ProcessData.html#a38fab6bbdb8c344b8ef8770640d0cba8">backgroundController</a>;</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> </div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="comment">/*</span></div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> <span class="comment"> // minimal intensity level:</span></div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> <span class="comment"> static float INTENSITY_THRESHOLD;</span></div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> <span class="comment"></span></div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> <span class="comment"> // m/z tolerance value:</span></div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="comment"> static double MZ_TOLERANCE;</span></div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="comment"></span></div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> <span class="comment"> // max_distance from next elution peak member in min.:</span></div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="comment"> static double max_inter_scan_retention_time_distance;</span></div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="comment"></span></div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> <span class="comment"> // define minimal number of members in LC elution peaks cluster</span></div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span> <span class="comment"> static int min_nb_cluster_members;</span></div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> <span class="comment"></span></div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="comment"> static std::map<int, float> scan_TR_index;</span></div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span> <span class="comment"></span></div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> <span class="comment"> // to track detected monoistopic mass for debugging:</span></div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> <span class="comment"> static bool MonoIsoDebugging;</span></div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> <span class="comment"> static double DebugMonoIsoMassMin;</span></div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="comment"> static double DebugMonoIsoMassMax;</span></div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> <span class="comment"> static double MS1_intensity_apex_percentil_cutoff;</span></div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> <span class="comment"> static double MS1_TR_RESOLUTION;</span></div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="comment"> // if data are in centroid form or not:</span></div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="comment"> static bool CENTROID_DATA_MODUS;</span></div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="comment">// class destructor</span></div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  ~<a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a>();</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">// class constructor</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a>();</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="comment">// class copy constructor</span></div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> &);</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> </div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="comment">// inputs raw /centroided data into the object:</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordtype">void</span> add_scan_raw_data(<span class="keywordtype">int</span>, <span class="keywordtype">float</span>, <a class="code" href="classOpenMS_1_1CentroidData.html">CentroidData</a> *);</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="comment">// inputs raw data into the object:</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keywordtype">void</span> add_scan_raw_data(std::vector<MSPeak>);</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> </div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="comment">// overload operators:</span></div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> &);</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> & operator<=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> &);</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> & operator>=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> &);</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> & operator<(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> &);</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> & operator>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> &);</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>  <span class="comment">// insert an already observed mz into the data structure, checks</span></div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="comment">// if it belongs to an existing LC elution peak or starts a new one:</span></div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="keywordtype">void</span> insert_observed_mz(<a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a>, <a class="code" href="classOpenMS_1_1MSPeak.html">MSPeak</a> *);</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="comment">// insert a newly observed mz into the data structure</span></div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordtype">void</span> insert_new_observed_mz(<a class="code" href="classOpenMS_1_1MSPeak.html">MSPeak</a> *);</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> </div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> </div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="comment">// converts DeconvPeak list to ms_peak vector</span></div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordtype">void</span> convert_ms_peaks(<span class="keywordtype">int</span>, <span class="keywordtype">double</span>, std::list<DeconvPeak> &, std::vector<MSPeak> &);</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span> </div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="comment">// check if the ms peak is in the selected mz, z, int range</span></div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordtype">bool</span> filterDeisotopicMSPeak(<a class="code" href="classOpenMS_1_1MSPeak.html">MSPeak</a> *);</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="comment">// function which check if a data structure iterator is similar</span></div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="comment">// to a peak and should be considered</span></div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="comment">// returns 1 if ok</span></div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="comment">// returns 0 if not</span></div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="comment">// returns -1 if scan range exceeded</span></div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="keywordtype">int</span> compareIteratorToPeak(<a class="code" href="classOpenMS_1_1MSPeak.html">MSPeak</a> *, <a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a>);</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="comment">// checks if a mz value has already been seen,</span></div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="comment">// also look for very close ones and cluster them</span></div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a> check_MZ_occurence(<a class="code" href="classOpenMS_1_1MSPeak.html">MSPeak</a> *);</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="l00185"></a><span class="lineno"> 185</span>  <span class="comment">// process a series of MS peaks</span></div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="comment">// set the signal to noise level:</span></div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="keywordtype">void</span> processMSPeaks(std::multimap<int, MSPeak> *);</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> </div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="comment">// get the full summed up intensity</span></div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="keywordtype">double</span> getPeakIntensitySum(<span class="keywordtype">double</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">// check if a peak with this scan number belong to this elution cluster:</span></div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keywordtype">bool</span> check_elution_peak_belong(<a class="code" href="classOpenMS_1_1ProcessData.html#a79e6b2973636a97ad0228a737ddcbed6">MZ_series_ITERATOR</a>, <a class="code" href="classOpenMS_1_1MSPeak.html">MSPeak</a> *);</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="comment">// returns the distance to this elution peak:</span></div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="keywordtype">int</span> getElutionPeakDistance(<a class="code" href="classOpenMS_1_1ProcessData.html#a79e6b2973636a97ad0228a737ddcbed6">MZ_series_ITERATOR</a>, <span class="keywordtype">int</span>);</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span> </div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="comment">// runs through the whole data structure and puts the elution_peaks into</span></div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="comment">// a proper LC_elution peak object</span></div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keywordtype">void</span> extract_elution_peaks();</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">// check if this elution peak is accepted as a really LC-elution peak:</span></div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="keywordtype">bool</span> check_elution_peak(<a class="code" href="classOpenMS_1_1ProcessData.html#a79e6b2973636a97ad0228a737ddcbed6">MZ_series_ITERATOR</a>);</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>  <span class="comment">// convert the MZ_series elution peak element into a LC_elution_peak object</span></div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="keywordtype">void</span> convert_to_LC_elution_peak(<a class="code" href="classOpenMS_1_1ProcessData.html#a79e6b2973636a97ad0228a737ddcbed6">MZ_series_ITERATOR</a>, <span class="keywordtype">double</span>);</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span> </div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="comment">// find a retention time by the scan number:</span></div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordtype">double</span> find_retention_time(<span class="keywordtype">double</span>);</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>  <span class="comment">// find closest match mz mass in the main structure</span></div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a> find_closest_mz_match(<span class="keywordtype">double</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>  <span class="comment">// go back to the MS1 level and</span></div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="comment">// find the correct precursor mass by mz and z:</span></div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keywordtype">void</span> adjustCorrectToMS1Precursor(<span class="keywordtype">double</span> *, <span class="keywordtype">int</span>, <span class="keywordtype">int</span>, <span class="keywordtype">int</span>);</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span> </div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span> </div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="comment">// access methods to the object variables:</span></div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> </div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="comment">// get an observed MZ mass, otherwise end of list iterator</span></div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  <a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a> get_MZ(<span class="keywordtype">double</span>);</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <span class="comment">// get an observed MZ mass, otherwise end of list iterator</span></div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a> get_MZ_lower_bound(<span class="keywordtype">double</span>);</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="comment">// get end of MZ list:</span></div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a> get_MZ_LIST_end();</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <span class="comment">// get start of MZ list:</span></div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a> get_MZ_LIST_start();</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="comment">// erase element in MZ list:</span></div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <span class="keywordtype">void</span> erase_MZ_LIST_element(<a class="code" href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">main_iterator</a>);</div>
<div class="line"><a name="l00234"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#ab559d8971bc725f9a6dd1fa320a8adfb"> 234</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1ProcessData.html#ab559d8971bc725f9a6dd1fa320a8adfb">getNbMSTraces</a>(){ <span class="keywordflow">return</span> (<span class="keywordtype">int</span>) pMZ_LIST.size(); }</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> </div>
<div class="line"><a name="l00237"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#abd169e874a63c1497de353040f73d46d"> 237</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1ProcessData.html#abd169e874a63c1497de353040f73d46d">getMinimalIntensityLevel</a>(){<span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1SuperHirnParameters.html#a1c9ef970722f45c71eedac9f9630d267">SuperHirnParameters::instance</a>()-><a class="code" href="classOpenMS_1_1SuperHirnParameters.html#a452ed82e48ddd8b4937eb7b175fe48d1">getIntensityThreshold</a>(); }</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span> </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> </div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="comment">// access the MZ_CLUSTER:</span></div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="comment">// find element numbers:</span></div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  std::map<double, int>::iterator get_nb_MZ_cluster_elements(<span class="keywordtype">double</span>);</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="comment">// erase an element:</span></div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <span class="keywordtype">void</span> erase_MZ_cluster_element(std::map<double, int>::iterator);</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="comment">// insert an element:</span></div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <span class="keywordtype">void</span> insert_MZ_cluster_element(<span class="keywordtype">double</span>, <span class="keywordtype">int</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>  <span class="comment">// add the scan vs TR index to the data structure:</span></div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="comment">// void add_scan_TR_index(std::map<int, float> IN){scan_TR_index = IN;};</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>  <span class="comment">// get the processed data:</span></div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#ac77817e1b393d38b27090bcd6ed536d9"> 253</a></span>  <a class="code" href="classOpenMS_1_1LCMSCData.html">LCMSCData</a> * <a class="code" href="classOpenMS_1_1ProcessData.html#ac77817e1b393d38b27090bcd6ed536d9">getProcessedData</a>(){<span class="keywordflow">return</span> data_; }</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span> </div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  <span class="comment">// increase the LC_elution_profile counter:</span></div>
<div class="line"><a name="l00256"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a391833c98b8674d0eacf826d658e2a45"> 256</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ProcessData.html#a391833c98b8674d0eacf826d658e2a45">increase_LC_elution_peak_counter</a>(){LC_elution_peak_counter++; }</div>
<div class="line"><a name="l00257"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a189d2aeef9d582f3ce0ae97cc57f686e"> 257</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1ProcessData.html#a189d2aeef9d582f3ce0ae97cc57f686e">get_LC_elution_peak_counter</a>(){<span class="keywordflow">return</span> LC_elution_peak_counter; }</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="comment">// get the maximal scan distance between two same monoisotopic masses</span></div>
<div class="line"><a name="l00260"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a304e0857de6eaad1a7a5c301866f42d8"> 260</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1ProcessData.html#a304e0857de6eaad1a7a5c301866f42d8">getMaxScanDistance</a>(){ <span class="keywordflow">return</span> max_inter_scan_distance; }</div>
<div class="line"><a name="l00261"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProcessData.html#a70c1d8bfb156a0354f54cbc00b26d0cc"> 261</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ProcessData.html#a70c1d8bfb156a0354f54cbc00b26d0cc">setMaxScanDistance</a>(<span class="keywordtype">int</span> in){ max_inter_scan_distance = in; }</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> </div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span> </div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="comment">// build up an index scan vs retention time:</span></div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="comment">// static void insert_into_scan_TR_index(int IN, float TR){scan_TR_index.insert(std::pair<int, float>(IN,TR));};</span></div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span> </div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  };</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span> </div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span> } <span class="comment">// ns</span></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="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_PROCESSDATA_H</span></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html">OpenMS::ProcessData</a></div><div class="ttdef"><b>Definition:</b> ProcessData.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1BackgroundControl_html"><div class="ttname"><a href="classOpenMS_1_1BackgroundControl.html">OpenMS::BackgroundControl</a></div><div class="ttdef"><b>Definition:</b> BackgroundControl.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_ab559d8971bc725f9a6dd1fa320a8adfb"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#ab559d8971bc725f9a6dd1fa320a8adfb">OpenMS::ProcessData::getNbMSTraces</a></div><div class="ttdeci">int getNbMSTraces()</div><div class="ttdef"><b>Definition:</b> ProcessData.h:234</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a70c1d8bfb156a0354f54cbc00b26d0cc"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a70c1d8bfb156a0354f54cbc00b26d0cc">OpenMS::ProcessData::setMaxScanDistance</a></div><div class="ttdeci">void setMaxScanDistance(int in)</div><div class="ttdef"><b>Definition:</b> ProcessData.h:261</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_abd169e874a63c1497de353040f73d46d"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#abd169e874a63c1497de353040f73d46d">OpenMS::ProcessData::getMinimalIntensityLevel</a></div><div class="ttdeci">double getMinimalIntensityLevel()</div><div class="ttdef"><b>Definition:</b> ProcessData.h:237</div></div>
<div class="ttc" id="classOpenMS_1_1CentroidData_html"><div class="ttname"><a href="classOpenMS_1_1CentroidData.html">OpenMS::CentroidData</a></div><div class="ttdef"><b>Definition:</b> CentroidData.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a7c7714105bef941ae216ae393ef432d7"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a7c7714105bef941ae216ae393ef432d7">OpenMS::ProcessData::pMZ_LIST</a></div><div class="ttdeci">main_data_structure pMZ_LIST</div><div class="ttdef"><b>Definition:</b> ProcessData.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a82e427ba10c56dc1c49702e3f6d713dd"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a82e427ba10c56dc1c49702e3f6d713dd">OpenMS::ProcessData::MZ_CLUSTER</a></div><div class="ttdeci">std::map< double, int > MZ_CLUSTER</div><div class="ttdef"><b>Definition:</b> ProcessData.h:99</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_abc5bd1250c0801f7bbd4a9d5b2aed070"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#abc5bd1250c0801f7bbd4a9d5b2aed070">OpenMS::ProcessData::main_iterator</a></div><div class="ttdeci">main_data_structure::iterator main_iterator</div><div class="ttdef"><b>Definition:</b> ProcessData.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a32976d9206a75664928ba47acd712e85"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a32976d9206a75664928ba47acd712e85">OpenMS::ProcessData::LC_elution_peak_counter</a></div><div class="ttdeci">unsigned int LC_elution_peak_counter</div><div class="ttdef"><b>Definition:</b> ProcessData.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a189d2aeef9d582f3ce0ae97cc57f686e"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a189d2aeef9d582f3ce0ae97cc57f686e">OpenMS::ProcessData::get_LC_elution_peak_counter</a></div><div class="ttdeci">unsigned int get_LC_elution_peak_counter()</div><div class="ttdef"><b>Definition:</b> ProcessData.h:257</div></div>
<div class="ttc" id="classOpenMS_1_1MSPeak_html"><div class="ttname"><a href="classOpenMS_1_1MSPeak.html">OpenMS::MSPeak</a></div><div class="ttdef"><b>Definition:</b> MSPeak.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a38fab6bbdb8c344b8ef8770640d0cba8"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a38fab6bbdb8c344b8ef8770640d0cba8">OpenMS::ProcessData::backgroundController</a></div><div class="ttdeci">BackgroundControl * backgroundController</div><div class="ttdef"><b>Definition:</b> ProcessData.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1SuperHirnParameters_html_a452ed82e48ddd8b4937eb7b175fe48d1"><div class="ttname"><a href="classOpenMS_1_1SuperHirnParameters.html#a452ed82e48ddd8b4937eb7b175fe48d1">OpenMS::SuperHirnParameters::getIntensityThreshold</a></div><div class="ttdeci">float getIntensityThreshold()</div><div class="ttdef"><b>Definition:</b> SuperHirnParameters.h:283</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_af18558f60329d153e5f439e6b6cbc6fa"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#af18558f60329d153e5f439e6b6cbc6fa">OpenMS::ProcessData::elution_peak</a></div><div class="ttdeci">std::multimap< int, MSPeak > elution_peak</div><div class="ttdef"><b>Definition:</b> ProcessData.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a10ee7dd9ccf6967fedce8a20656bd5bb"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a10ee7dd9ccf6967fedce8a20656bd5bb">OpenMS::ProcessData::main_data_structure</a></div><div class="ttdeci">std::multimap< double, MZ_series > main_data_structure</div><div class="ttdef"><b>Definition:</b> ProcessData.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a79e6b2973636a97ad0228a737ddcbed6"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a79e6b2973636a97ad0228a737ddcbed6">OpenMS::ProcessData::MZ_series_ITERATOR</a></div><div class="ttdeci">std::vector< elution_peak >::iterator MZ_series_ITERATOR</div><div class="ttdef"><b>Definition:</b> ProcessData.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_ab69ab1a8bcf64e4e36a57672502f93dc"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#ab69ab1a8bcf64e4e36a57672502f93dc">OpenMS::ProcessData::MZ_series</a></div><div class="ttdeci">std::vector< elution_peak > MZ_series</div><div class="ttdef"><b>Definition:</b> ProcessData.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_ac77817e1b393d38b27090bcd6ed536d9"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#ac77817e1b393d38b27090bcd6ed536d9">OpenMS::ProcessData::getProcessedData</a></div><div class="ttdeci">LCMSCData * getProcessedData()</div><div class="ttdef"><b>Definition:</b> ProcessData.h:253</div></div>
<div class="ttc" id="classOpenMS_1_1SuperHirnParameters_html_a1c9ef970722f45c71eedac9f9630d267"><div class="ttname"><a href="classOpenMS_1_1SuperHirnParameters.html#a1c9ef970722f45c71eedac9f9630d267">OpenMS::SuperHirnParameters::instance</a></div><div class="ttdeci">static SuperHirnParameters * instance()</div><div class="ttdef"><b>Definition:</b> SuperHirnParameters.h:222</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a391833c98b8674d0eacf826d658e2a45"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a391833c98b8674d0eacf826d658e2a45">OpenMS::ProcessData::increase_LC_elution_peak_counter</a></div><div class="ttdeci">void increase_LC_elution_peak_counter()</div><div class="ttdef"><b>Definition:</b> ProcessData.h:256</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a7016fa595c5406be9e3ced4ad1bce3c5"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a7016fa595c5406be9e3ced4ad1bce3c5">OpenMS::ProcessData::data_</a></div><div class="ttdeci">LCMSCData * data_</div><div class="ttdef"><b>Definition:</b> ProcessData.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1LCMSCData_html"><div class="ttname"><a href="classOpenMS_1_1LCMSCData.html">OpenMS::LCMSCData</a></div><div class="ttdef"><b>Definition:</b> LCMSCData.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a304e0857de6eaad1a7a5c301866f42d8"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a304e0857de6eaad1a7a5c301866f42d8">OpenMS::ProcessData::getMaxScanDistance</a></div><div class="ttdeci">int getMaxScanDistance()</div><div class="ttdef"><b>Definition:</b> ProcessData.h:260</div></div>
<div class="ttc" id="classOpenMS_1_1ProcessData_html_a3553563b4e9f10de51af73aab0bb7ae5"><div class="ttname"><a href="classOpenMS_1_1ProcessData.html#a3553563b4e9f10de51af73aab0bb7ae5">OpenMS::ProcessData::max_inter_scan_distance</a></div><div class="ttdeci">int max_inter_scan_distance</div><div class="ttdef"><b>Definition:</b> ProcessData.h:89</div></div>
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