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<a href="FTPeakDetectController_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">// written by Lukas N Mueller, 30.3.05</span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="comment">// Lukas.Mueller@imsb.biol.ethz.ch</span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="comment">// Group of Prof. Ruedi Aebersold, IMSB, ETH Hoenggerberg, Zurich</span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="comment">//</span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="comment">// Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch</span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="comment">// December 2010</span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="comment">//</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">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_FTPEAKDETECTCONTROLLER_H</span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_FTPEAKDETECTCONTROLLER_H</span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <boost/shared_ptr.hpp></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> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> {</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html"> 53</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  {</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="comment">// declaration of the private members:</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">private</span>:</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="comment">// declaration of the public members:</span></div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="comment">// LCMS runs</span></div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="comment">//LCMS* THIS_LCMS;</span></div>
<div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#ac56216d2eaee0b17526ab30bde705633"> 66</a></span>  <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a> * <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#ac56216d2eaee0b17526ab30bde705633">lcms_</a>;</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="comment">// std::vector<SHFeature> fakeFeatureList_;</span></div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#a3cc8e9d731d513f6035aa939aa930dc3"> 68</a></span>  std::vector<LCMS> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a3cc8e9d731d513f6035aa939aa930dc3">lcmsRuns_</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>  <span class="comment">// paths:</span></div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#a80f8b25ae517b0c4d1be5c33efbd09f7"> 71</a></span>  std::string <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a80f8b25ae517b0c4d1be5c33efbd09f7">targetMzXML</a>;</div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#a6df0d0f2a6a38e07978a50c228779254"> 72</a></span>  std::string <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a6df0d0f2a6a38e07978a50c228779254">SOURCE_DIR</a>;</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#a56c465b2241921e9feffb9b90a95f990"> 73</a></span>  std::string <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a56c465b2241921e9feffb9b90a95f990">OUTPUT_DIR</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> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#a515f849141329d6b8dfe895a70b16b7e"> 77</a></span>  <span class="keyword">typedef</span> std::pair<double, boost::shared_ptr<RawData> > <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a515f849141329d6b8dfe895a70b16b7e">Map</a>;</div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#a209cbb01adefd4b632c5619302ef9c01"> 78</a></span>  <span class="keyword">typedef</span> std::vector<Map> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a209cbb01adefd4b632c5619302ef9c01">Vec</a>;</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="comment">// static bool CREATE_FEATURE_ELUTION_PROFILES;</span></div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> <span class="comment">// static bool LCelutionPeakDebugging;</span></div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> <span class="comment">// static double LCelutionPeakMassMin;</span></div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <span class="comment">// static double LCelutionPeakMassMax;</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">// static MS2Feature* SearchedM2Feature;</span></div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="comment">// static bool FEATURE_FAKE_INSERTION_BASED_ON_MS2_FEATURE;</span></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="comment">// class destructor</span></div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  ~<a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a>();</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="comment">// class constructor</span></div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a>();</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="comment">// class copy constructor</span></div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> &);</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="comment">// function for batch processing of mzXML data</span></div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="comment">// parses LC-MS from runs from a directory or file of raw mzXML data:</span></div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="keywordtype">void</span> parseMzXMLData();</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// mzXML parsing functions for a single MzXML file:</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="comment">// start the scan parsing of a mzXML file:</span></div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordtype">void</span> startScanParsing(<a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a209cbb01adefd4b632c5619302ef9c01">Vec</a> datavec);</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">// **** for the MS1 level post processing:</span></div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="comment">// process MS1 level data</span></div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordtype">void</span> process_MS1_level_data_structure(<a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> *);</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="comment">// adds an elution peak to the LC/MS run:</span></div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordtype">void</span> add_raw_peak_to_LC_MS_run(<a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> *);</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="comment">// function to add the elution profile to the feature:</span></div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">void</span> addLCelutionProfile(<a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> *, <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> *);</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="comment">// reads already paths of existing LC-MS runs in xml format into the</span></div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="comment">// memory</span></div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="comment">// for now, open file system for every check, but otherwise could eb done</span></div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="comment">// in the constructor</span></div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordtype">bool</span> checkIfFeatureExtractionExists(std::string);</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="comment">// **** for the MS2 level post processing:</span></div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="comment">// process MS2 level data</span></div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordtype">void</span> process_MS2_level_data_structure(<a class="code" href="classOpenMS_1_1ProcessData.html">ProcessData</a> *);</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="comment">// processes the tracted signals on teh MS2 level</span></div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordtype">void</span> extract_MS2_elution_features();</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="comment">// combine the MS2 feature trace data to the MS1 features:</span></div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordtype">void</span> associateMS2FeatureToMS1Feature(<a class="code" href="classOpenMS_1_1MS2Feature.html">MS2Feature</a> *);</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="comment">// add an observed MS2 feature to the MS1 feature</span></div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="comment">// if an observation is already there, then</span></div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="comment">// construct a merged MS2 feature</span></div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordtype">void</span> addMS2FeatureToMS1Feature(<a class="code" href="classOpenMS_1_1MS2Feature.html">MS2Feature</a> *, <a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> *);</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">// construct here fake ms1 features based on a observed MS2 feature</span></div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="comment">// which however could not be matched to a exiting ms1 feature</span></div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordtype">void</span> constructMS1FeatureFromMS2Feature(<a class="code" href="classOpenMS_1_1MS2Feature.html">MS2Feature</a> *);</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span> </div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">// write a parsed LC/MS into directory:</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordtype">void</span> write_out_parsed_LC_MS(<a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a> *);</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="comment">// add fake MS/MS information for the MS1 feature:</span></div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordtype">void</span> addFakeMSMSToFeature(<a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</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">// overload operators:</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> &);</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> & operator<=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> &);</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> & operator>=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> &);</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> & operator<(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> &);</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> & operator>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html">FTPeakDetectController</a> &);</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="comment">// start here all the get / set</span></div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="comment">// function to access the</span></div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="comment">// variables of the class</span></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="comment">// target file:</span></div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordtype">void</span> set_target_file(std::string IN);</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  std::string get_target_file();</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> <span class="comment">// get the vector of LC/MS runs:</span></div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> <span class="comment">//std::vector<LCMS> getParsedData();</span></div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="comment">//bool getParsedDataEmpty();</span></div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> <span class="comment">//std::vector<LCMS>::iterator get_parsed_DATA_START();</span></div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> <span class="comment">//std::vector<LCMS>::iterator get_parsed_DATA_END();</span></div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a> * getLCMS();</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> </div>
<div class="line"><a name="l00170"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#a499a6fd28e5d5ee4428696c29bfa4cf2"> 170</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a499a6fd28e5d5ee4428696c29bfa4cf2">FTPeakDetectController::set_target_file</a>(std::string IN)</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>  <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a80f8b25ae517b0c4d1be5c33efbd09f7">targetMzXML</a> = IN;</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  }</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> </div>
<div class="line"><a name="l00175"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#adc5d7482761d2b21015d29b1790aab39"> 175</a></span>  <span class="keyword">inline</span> std::string <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#adc5d7482761d2b21015d29b1790aab39">FTPeakDetectController::get_target_file</a>()</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>  <span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a80f8b25ae517b0c4d1be5c33efbd09f7">targetMzXML</a>;</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  }</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">/*</span></div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> <span class="comment"> // get the vector of LC/MS runs:</span></div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> <span class="comment"> inline std::vector<LCMS> FTPeakDetectController::getParsedData()</span></div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span> <span class="comment"> {</span></div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span> <span class="comment"> return lcmsRuns_;</span></div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span> <span class="comment"> }</span></div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> <span class="comment"></span></div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> <span class="comment"> inline bool FTPeakDetectController::getParsedDataEmpty()</span></div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> <span class="comment"> {</span></div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span> <span class="comment"> return LC_MS_RUNS.empty();</span></div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span> <span class="comment"> }</span></div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> <span class="comment"></span></div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span> <span class="comment"> inline std::vector<LCMS>::iterator FTPeakDetectController::get_parsed_DATA_START()</span></div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span> <span class="comment"> {</span></div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span> <span class="comment"> return LC_MS_RUNS.begin();</span></div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span> <span class="comment"> }</span></div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> <span class="comment"></span></div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> <span class="comment"> inline std::vector<LCMS>::iterator FTPeakDetectController::get_parsed_DATA_END()</span></div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span> <span class="comment"> {</span></div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span> <span class="comment"> return LC_MS_RUNS.end();</span></div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span> <span class="comment"> }</span></div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div>
<div class="line"><a name="l00203"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FTPeakDetectController.html#a659c64c10abc90aa1e93c8262ceb8e77"> 203</a></span>  <span class="keyword">inline</span> <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a> * <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#a659c64c10abc90aa1e93c8262ceb8e77">FTPeakDetectController::getLCMS</a>()</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  {</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1FTPeakDetectController.html#ac56216d2eaee0b17526ab30bde705633">lcms_</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> </div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span> } <span class="comment">// ns</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="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_FTPEAKDETECTCONTROLLER_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_1FTPeakDetectController_html_a3cc8e9d731d513f6035aa939aa930dc3"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#a3cc8e9d731d513f6035aa939aa930dc3">OpenMS::FTPeakDetectController::lcmsRuns_</a></div><div class="ttdeci">std::vector< LCMS > lcmsRuns_</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html_a209cbb01adefd4b632c5619302ef9c01"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#a209cbb01adefd4b632c5619302ef9c01">OpenMS::FTPeakDetectController::Vec</a></div><div class="ttdeci">std::vector< Map > Vec</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html_a659c64c10abc90aa1e93c8262ceb8e77"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#a659c64c10abc90aa1e93c8262ceb8e77">OpenMS::FTPeakDetectController::getLCMS</a></div><div class="ttdeci">LCMS * getLCMS()</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:203</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html_a6df0d0f2a6a38e07978a50c228779254"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#a6df0d0f2a6a38e07978a50c228779254">OpenMS::FTPeakDetectController::SOURCE_DIR</a></div><div class="ttdeci">std::string SOURCE_DIR</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html_a56c465b2241921e9feffb9b90a95f990"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#a56c465b2241921e9feffb9b90a95f990">OpenMS::FTPeakDetectController::OUTPUT_DIR</a></div><div class="ttdeci">std::string OUTPUT_DIR</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html">OpenMS::FTPeakDetectController</a></div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html"><div class="ttname"><a href="classOpenMS_1_1LCMS.html">OpenMS::LCMS</a></div><div class="ttdef"><b>Definition:</b> LCMS.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html_ac56216d2eaee0b17526ab30bde705633"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#ac56216d2eaee0b17526ab30bde705633">OpenMS::FTPeakDetectController::lcms_</a></div><div class="ttdeci">LCMS * lcms_</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Feature_html"><div class="ttname"><a href="classOpenMS_1_1MS2Feature.html">OpenMS::MS2Feature</a></div><div class="ttdef"><b>Definition:</b> MS2Feature.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html_a499a6fd28e5d5ee4428696c29bfa4cf2"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#a499a6fd28e5d5ee4428696c29bfa4cf2">OpenMS::FTPeakDetectController::set_target_file</a></div><div class="ttdeci">void set_target_file(std::string IN)</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:170</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html_a515f849141329d6b8dfe895a70b16b7e"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#a515f849141329d6b8dfe895a70b16b7e">OpenMS::FTPeakDetectController::Map</a></div><div class="ttdeci">std::pair< double, boost::shared_ptr< RawData > > Map</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html_adc5d7482761d2b21015d29b1790aab39"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#adc5d7482761d2b21015d29b1790aab39">OpenMS::FTPeakDetectController::get_target_file</a></div><div class="ttdeci">std::string get_target_file()</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:175</div></div>
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html">OpenMS::LCElutionPeak</a></div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1SHFeature_html"><div class="ttname"><a href="classOpenMS_1_1SHFeature.html">OpenMS::SHFeature</a></div><div class="ttdef"><b>Definition:</b> SHFeature.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1FTPeakDetectController_html_a80f8b25ae517b0c4d1be5c33efbd09f7"><div class="ttname"><a href="classOpenMS_1_1FTPeakDetectController.html#a80f8b25ae517b0c4d1be5c33efbd09f7">OpenMS::FTPeakDetectController::targetMzXML</a></div><div class="ttdeci">std::string targetMzXML</div><div class="ttdef"><b>Definition:</b> FTPeakDetectController.h:71</div></div>
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