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<div class="title">MS2ConsensusSpectrum.h</div> </div>
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<a href="MS2ConsensusSpectrum_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_MS2CONSENSUSSPECTRUM_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_MS2CONSENSUSSPECTRUM_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 <<a class="code" href="Types_8h.html">OpenMS/CONCEPT/Types.h</a>></span></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#include <string></span></div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor">#include <map></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"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html"> 62</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</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> </div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="comment">// declaration of the private members:</span></div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="keyword">private</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>  <span class="comment">// stores the MS2 fragments:</span></div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a33e7be7728eeed501e939ea1c9f81150"> 72</a></span>  std::multimap<double, MS2Fragment> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a33e7be7728eeed501e939ea1c9f81150">MS2FragmentPeaks</a>;</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </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">protected</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="comment">// declaration of the public members:</span></div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a512f8f4761ecd410b2cedd0178b55d9d"> 81</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a512f8f4761ecd410b2cedd0178b55d9d">startTR</a>;</div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a2d55eedd3dc6d8b96b39c9ab2cbb8e80"> 82</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a2d55eedd3dc6d8b96b39c9ab2cbb8e80">endTR</a>;</div>
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a14f94e529dff0b8bfba8e16fbe9755d6"> 83</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a14f94e529dff0b8bfba8e16fbe9755d6">z</a>;</div>
<div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ae01995af0b5069adad5d98980424329e"> 84</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ae01995af0b5069adad5d98980424329e">apexScan</a>;</div>
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#acae6faa978ec29ffb9254b97c25f4d0b"> 85</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#acae6faa978ec29ffb9254b97c25f4d0b">startScan</a>;</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a157246a51ac3c84b8b19745cccc75102"> 86</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a157246a51ac3c84b8b19745cccc75102">endScan</a>;</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> </div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> <span class="keyword">public</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"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ac5b7a45b97e2838a2f716fec5b5debe0"> 91</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ac5b7a45b97e2838a2f716fec5b5debe0">precursorMZ</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#af6d5ab3629ea17ec17a1733f29f8a0d9"> 92</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#af6d5ab3629ea17ec17a1733f29f8a0d9">TR</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> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="comment">// mass to charge tolerance for MS2 trace level:</span></div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a784ba0e8fd18aa821a12b7491c6f3584"> 96</a></span>  <span class="keyword">static</span> <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a784ba0e8fd18aa821a12b7491c6f3584">MS2_MZ_TOLERANCE</a>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="comment">// class destructor</span></div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  ~<a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a>();</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="comment">// class constructor</span></div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a>();</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a>(<a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> *);</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a>(<span class="keywordtype">double</span> iPrecursorMZ, <span class="keywordtype">double</span> iTR, <span class="keywordtype">int</span> iChrg, <span class="keywordtype">int</span> iApexScan);</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>  <span class="comment">// class copy constructor</span></div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> &);</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="comment">// class copy constructor</span></div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> *);</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> </div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="comment">// overload operators:</span></div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> &);</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keywordtype">bool</span> operator==(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> &);</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> & operator<=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> &);</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> & operator>=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> &);</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> & operator<(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> &);</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> & operator>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html">MS2ConsensusSpectrum</a> &);</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="comment">// copmute the similarity of the elution shape of the</span></div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="comment">// MS2 fragment to this MS2 consensus spectrum</span></div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordtype">double</span> getLCElutionPeakSimilarity(<a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> *);</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="comment">// add a MS2 fragment:</span></div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordtype">void</span> addMS2Fragment(<a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> *);</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="comment">// compute MS2 parameters</span></div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordtype">void</span> computeMS2SpectrumParameters();</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">//*** PK removed, never used</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">// process the stored fragments:</span></div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span> <span class="comment">// void processConsenusSpectraFragments();</span></div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">// remove outlier fragments based on their:</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="comment">// MS2Fragment::OutlierAttribute = ...</span></div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="comment">// 1: retention time</span></div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="comment">// 2: precursor mass</span></div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="comment">// etc.</span></div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> <span class="comment">// void removeOutlierFragments();</span></div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span> </div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="comment">// remove H2O loss region of the MS2 spectra</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="comment">// void removeWaterLossRegion( );</span></div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> </div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="comment">// show MS2 spectrum info:</span></div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="keywordtype">void</span> show_info();</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </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>  <span class="comment">// find a corresponding MS2 fragment</span></div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> * findMS2Fragment(<span class="keywordtype">double</span>);</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</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> </div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="comment">// start here all the get / set</span></div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="comment">// function to access the</span></div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="comment">// variables of the class</span></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="comment">// precursor mass:</span></div>
<div class="line"><a name="l00165"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#af454969bce509d6ccbead8d122e3275f"> 165</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#af454969bce509d6ccbead8d122e3275f">getPrecursorMZ</a>(){<span class="keywordflow">return</span> precursorMZ; }</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="comment">// TR:</span></div>
<div class="line"><a name="l00168"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a1f42ac65106ca909c7f6ec30a4dcb914"> 168</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a1f42ac65106ca909c7f6ec30a4dcb914">getTR</a>(){<span class="keywordflow">return</span> TR; }</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="comment">// start TR</span></div>
<div class="line"><a name="l00170"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ad2059c92b90989921be291156cae6d66"> 170</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ad2059c92b90989921be291156cae6d66">getStartTR</a>(){<span class="keywordflow">return</span> startTR; }</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="comment">// end TR</span></div>
<div class="line"><a name="l00172"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ad275baa611d6c9bf0e1f1275e407a33d"> 172</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ad275baa611d6c9bf0e1f1275e407a33d">getEndTR</a>(){<span class="keywordflow">return</span> endTR; }</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"> 175</span>  <span class="comment">// set / get the charge state of the precursor MZ:</span></div>
<div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#aeced7cdac763485acf95d1c1e7783008"> 176</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#aeced7cdac763485acf95d1c1e7783008">setPrecursorChrg</a>(<span class="keywordtype">int</span> IN){ z = IN; }</div>
<div class="line"><a name="l00177"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#af43904345cdb9728ab0699dfae81d9b1"> 177</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#af43904345cdb9728ab0699dfae81d9b1">getPrecursorChrg</a>(){ <span class="keywordflow">return</span> z; }</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="comment">// apex scan:</span></div>
<div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a4f4c019219138d6bcc2cc5bbd576a772"> 179</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a4f4c019219138d6bcc2cc5bbd576a772">getApexScan</a>(){<span class="keywordflow">return</span> apexScan; }</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="comment">// start scan</span></div>
<div class="line"><a name="l00181"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a40ff9a78a344d0b49f95fca034205a99"> 181</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a40ff9a78a344d0b49f95fca034205a99">getStartScan</a>(){<span class="keywordflow">return</span> startScan; }</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="comment">// end scan</span></div>
<div class="line"><a name="l00183"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a637c645784fce9d2fbde29e4162f7f75"> 183</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a637c645784fce9d2fbde29e4162f7f75">getEndScan</a>(){<span class="keywordflow">return</span> endScan; }</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="comment">// get the number of consensus fragments:</span></div>
<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ae5f5a57818352666ccc5509bb2c3c2c6"> 185</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#ae5f5a57818352666ccc5509bb2c3c2c6">getNbMS2Fragments</a>(){<span class="keywordflow">return</span> (<span class="keywordtype">int</span>) MS2FragmentPeaks.size(); }</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> </div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="comment">// get the MS2 fragments list iterator:</span></div>
<div class="line"><a name="l00188"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#aa9e8451956d10d5e0260a4d7e80c8387"> 188</a></span>  std::multimap<double, MS2Fragment>::iterator <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#aa9e8451956d10d5e0260a4d7e80c8387">getMS2FragmentPeakStart</a>(){<span class="keywordflow">return</span> MS2FragmentPeaks.begin(); }</div>
<div class="line"><a name="l00189"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a47ab62d2d6c75909b3b855f2b03f4670"> 189</a></span>  std::multimap<double, MS2Fragment>::iterator <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a47ab62d2d6c75909b3b855f2b03f4670">getMS2FragmentPeakEnd</a>(){<span class="keywordflow">return</span> MS2FragmentPeaks.end(); }</div>
<div class="line"><a name="l00190"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a8c391abd15ec1bbaec945632a20d9d5e"> 190</a></span>  std::multimap<double, MS2Fragment> * <a class="code" href="classOpenMS_1_1MS2ConsensusSpectrum.html#a8c391abd15ec1bbaec945632a20d9d5e">getMS2FragmentMap</a>(){<span class="keywordflow">return</span> &MS2FragmentPeaks; }</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> </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">// ns</span></div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> <span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MS2CONSENSUSSPECTRUM_H</span></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a33e7be7728eeed501e939ea1c9f81150"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a33e7be7728eeed501e939ea1c9f81150">OpenMS::MS2ConsensusSpectrum::MS2FragmentPeaks</a></div><div class="ttdeci">std::multimap< double, MS2Fragment > MS2FragmentPeaks</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:72</div></div>
<div class="ttc" id="Types_8h_html"><div class="ttname"><a href="Types_8h.html">Types.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a8c391abd15ec1bbaec945632a20d9d5e"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a8c391abd15ec1bbaec945632a20d9d5e">OpenMS::MS2ConsensusSpectrum::getMS2FragmentMap</a></div><div class="ttdeci">std::multimap< double, MS2Fragment > * getMS2FragmentMap()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:190</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a637c645784fce9d2fbde29e4162f7f75"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a637c645784fce9d2fbde29e4162f7f75">OpenMS::MS2ConsensusSpectrum::getEndScan</a></div><div class="ttdeci">int getEndScan()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:183</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a4f4c019219138d6bcc2cc5bbd576a772"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a4f4c019219138d6bcc2cc5bbd576a772">OpenMS::MS2ConsensusSpectrum::getApexScan</a></div><div class="ttdeci">int getApexScan()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:179</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a2d55eedd3dc6d8b96b39c9ab2cbb8e80"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a2d55eedd3dc6d8b96b39c9ab2cbb8e80">OpenMS::MS2ConsensusSpectrum::endTR</a></div><div class="ttdeci">double endTR</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:82</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_af43904345cdb9728ab0699dfae81d9b1"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#af43904345cdb9728ab0699dfae81d9b1">OpenMS::MS2ConsensusSpectrum::getPrecursorChrg</a></div><div class="ttdeci">int getPrecursorChrg()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:177</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a40ff9a78a344d0b49f95fca034205a99"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a40ff9a78a344d0b49f95fca034205a99">OpenMS::MS2ConsensusSpectrum::getStartScan</a></div><div class="ttdeci">int getStartScan()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:181</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_acae6faa978ec29ffb9254b97c25f4d0b"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#acae6faa978ec29ffb9254b97c25f4d0b">OpenMS::MS2ConsensusSpectrum::startScan</a></div><div class="ttdeci">int startScan</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:85</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_ad275baa611d6c9bf0e1f1275e407a33d"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#ad275baa611d6c9bf0e1f1275e407a33d">OpenMS::MS2ConsensusSpectrum::getEndTR</a></div><div class="ttdeci">double getEndTR()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:172</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a157246a51ac3c84b8b19745cccc75102"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a157246a51ac3c84b8b19745cccc75102">OpenMS::MS2ConsensusSpectrum::endScan</a></div><div class="ttdeci">int endScan</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_aa9e8451956d10d5e0260a4d7e80c8387"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#aa9e8451956d10d5e0260a4d7e80c8387">OpenMS::MS2ConsensusSpectrum::getMS2FragmentPeakStart</a></div><div class="ttdeci">std::multimap< double, MS2Fragment >::iterator getMS2FragmentPeakStart()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:188</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a1f42ac65106ca909c7f6ec30a4dcb914"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a1f42ac65106ca909c7f6ec30a4dcb914">OpenMS::MS2ConsensusSpectrum::getTR</a></div><div class="ttdeci">double getTR()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:168</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_aeced7cdac763485acf95d1c1e7783008"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#aeced7cdac763485acf95d1c1e7783008">OpenMS::MS2ConsensusSpectrum::setPrecursorChrg</a></div><div class="ttdeci">void setPrecursorChrg(int IN)</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:176</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a784ba0e8fd18aa821a12b7491c6f3584"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a784ba0e8fd18aa821a12b7491c6f3584">OpenMS::MS2ConsensusSpectrum::MS2_MZ_TOLERANCE</a></div><div class="ttdeci">static double MS2_MZ_TOLERANCE</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:96</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_af6d5ab3629ea17ec17a1733f29f8a0d9"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#af6d5ab3629ea17ec17a1733f29f8a0d9">OpenMS::MS2ConsensusSpectrum::TR</a></div><div class="ttdeci">double TR</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_af454969bce509d6ccbead8d122e3275f"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#af454969bce509d6ccbead8d122e3275f">OpenMS::MS2ConsensusSpectrum::getPrecursorMZ</a></div><div class="ttdeci">double getPrecursorMZ()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:165</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a14f94e529dff0b8bfba8e16fbe9755d6"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a14f94e529dff0b8bfba8e16fbe9755d6">OpenMS::MS2ConsensusSpectrum::z</a></div><div class="ttdeci">int z</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:83</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_ac5b7a45b97e2838a2f716fec5b5debe0"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#ac5b7a45b97e2838a2f716fec5b5debe0">OpenMS::MS2ConsensusSpectrum::precursorMZ</a></div><div class="ttdeci">double precursorMZ</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:91</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_ae5f5a57818352666ccc5509bb2c3c2c6"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#ae5f5a57818352666ccc5509bb2c3c2c6">OpenMS::MS2ConsensusSpectrum::getNbMS2Fragments</a></div><div class="ttdeci">int getNbMS2Fragments()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:185</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html">OpenMS::MS2ConsensusSpectrum</a></div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a47ab62d2d6c75909b3b855f2b03f4670"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a47ab62d2d6c75909b3b855f2b03f4670">OpenMS::MS2ConsensusSpectrum::getMS2FragmentPeakEnd</a></div><div class="ttdeci">std::multimap< double, MS2Fragment >::iterator getMS2FragmentPeakEnd()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:189</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_ae01995af0b5069adad5d98980424329e"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#ae01995af0b5069adad5d98980424329e">OpenMS::MS2ConsensusSpectrum::apexScan</a></div><div class="ttdeci">int apexScan</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_a512f8f4761ecd410b2cedd0178b55d9d"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#a512f8f4761ecd410b2cedd0178b55d9d">OpenMS::MS2ConsensusSpectrum::startTR</a></div><div class="ttdeci">double startTR</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:81</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html">OpenMS::MS2Fragment</a></div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1MS2ConsensusSpectrum_html_ad2059c92b90989921be291156cae6d66"><div class="ttname"><a href="classOpenMS_1_1MS2ConsensusSpectrum.html#ad2059c92b90989921be291156cae6d66">OpenMS::MS2ConsensusSpectrum::getStartTR</a></div><div class="ttdeci">double getStartTR()</div><div class="ttdef"><b>Definition:</b> MS2ConsensusSpectrum.h:170</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:17 using doxygen 1.8.5</font></TD>
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